<link>https://www.uppmax.uu.se/changelog</link> <description /> <item> <title>[apps] freesurfer/7.4.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferWiki">freesurfer </a>(A software package for the analysis and visualization of structural and functional neuroimaging data from cross-sectional or longitudinal studies.) version 7.4.1 installed on all systems as module freesurfer/7.4.1.</p> <p></p> Thu, 22 Feb 2024 12:52:00 GMT https://www.uppmax.uu.se/changelog 2024-02-22T12:52:00Z [bio] modkit/0.2.5-rc2 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/nanoporetech/modkit">modkit </a>(bioinformatics tool for working with modified bases from Oxford Nanopore) version 0.2.5-rc2 installed on all systems as module modkit/0.2.5-rc2.</p> <p></p> Tue, 20 Feb 2024 08:40:00 GMT https://www.uppmax.uu.se/changelog 2024-02-20T08:40:00Z [bio] CHEUI/20230518-c1c9ab6 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/comprna/CHEUI">CHEUI </a>((Methylation (CH3) Estimation Using Ionic current) is an RNA modification detection software for Oxford Nanopore direct RNA sequencing data. CHEUI can be used to detect m6A and m5C in individual reads at single-nucleotide resolution from any sample (e.g. single condition), or detect differential m6A or m5C between any two conditions.) version 20230518-c1c9ab6 installed on all systems as module CHEUI/20230518-c1c9ab6.<br /> &nbsp;</p> <p></p> Tue, 20 Feb 2024 08:38:00 GMT https://www.uppmax.uu.se/changelog 2024-02-20T08:38:00Z [bio] HiCExplorer/3.7.3 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://hicexplorer.readthedocs.io/en/latest/index.html">HiCExplorer </a>(Set of programs to process, analyze and visualize Hi-C and cHi-C data) version 3.7.3 installed on all systems as module HiCExplorer/3.7.3.<br /> &nbsp;</p> <p></p> Wed, 07 Feb 2024 18:01:00 GMT https://www.uppmax.uu.se/changelog 2024-02-07T18:01:00Z [bio] HATK/2.0beta installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/WansonChoi/HATK">HATK </a>(HLA Analysis Tool-Kit) is a collection of tools and modules to perform HLA fine-mapping analysis, which is to identify which HLA allele or amino acid position of the HLA gene is driving the disease. HLA fine-mapping analysis is an indispensable analysis in studies of autoimmune diseases.) version 2.0beta installed on all systems as module HATK/2.0beta.<br /> &nbsp;</p> <p></p> Wed, 07 Feb 2024 15:55:00 GMT https://www.uppmax.uu.se/changelog 2024-02-07T15:55:00Z [bio] LDAK/5.2 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://dougspeed.com/">LDAK </a>(LDAK is a software package for analysing association study data. In total, it has over 30 different functions (see Main Arguments for a full list). ) version 5.2 installed on all systems as module LDAK/5.2.<br /> &nbsp;</p> <p></p> Wed, 07 Feb 2024 15:53:00 GMT https://www.uppmax.uu.se/changelog 2024-02-07T15:53:00Z [bio] Trycycler/0.5.4 installed on all systems https://www.uppmax.uu.se/changelog <p>Trycycler (Trycycler is a tool for generating consensus long-read assemblies for bacterial genomes.) version 0.5.4 installed on all systems as module Trycycler/0.5.4.</p> Fri, 12 Jan 2024 09:26:00 GMT https://www.uppmax.uu.se/changelog 2024-01-12T09:26:00Z [bio] Polypolish/5.0 installed on all systems https://www.uppmax.uu.se/changelog <p>Polypolish (Polypolish is a tool for polishing genome assemblies with short reads.) version 5.0 installed on all systems as module Polypolish/5.0.</p> Fri, 12 Jan 2024 08:43:00 GMT https://www.uppmax.uu.se/changelog 2024-01-12T08:43:00Z [bio] HUMAnN/3.8 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/biobakery/humann3">HUMAnN </a>((the HMP Unified Metabolic Analysis Network) is a method for efficiently and accurately profiling the abundance of microbial metabolic pathways and other molecular functions from metagenomic or metatranscriptomic sequencing data.) version 3.8 installed on all systems as module HUMAnN/3.8.<br /> &nbsp;</p> <p></p> Mon, 04 Dec 2023 10:08:00 GMT https://www.uppmax.uu.se/changelog 2023-12-04T10:08:00Z [bio] MetaPhlAn4/4.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://huttenhower.sph.harvard.edu/metaphlan/">MetaPhlAn4</a> (is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea and Eukaryotes) from metagenomic shotgun sequencing data (i.e. not 16S) with species-level.) version 4.0 installed on all systems as module MetaPhlAn4/4.0.<br /> &nbsp;</p> <p></p> Mon, 04 Dec 2023 10:07:00 GMT https://www.uppmax.uu.se/changelog 2023-12-04T10:07:00Z [apps] Gurobi/10.0.2 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.gurobi.com/downloads/gurobi-software">Gurobi </a>(The fastest and most powerful mathematical programming solver available for your LP, QP and MIP (MILP, MIQP, and MIQCP) problems.) version 10.0.2 installed on all systems as module Gurobi/10.0.2.</p> Tue, 03 Oct 2023 15:18:00 GMT https://www.uppmax.uu.se/changelog 2023-10-03T15:18:00Z [bio] DATES/4010 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/MoorjaniLab">DATES </a>((Distribution of Ancestry Tracts of Evolutionary Signals) is a method to estimate the time of admixture in ancient DNA samples described in Chintalapati et al. 2022 biorxiv) version 4010 installed on all systems as module DATES/4010.<br /> &nbsp;</p> Tue, 03 Oct 2023 15:02:00 GMT https://www.uppmax.uu.se/changelog 2023-10-03T15:02:00Z [bio] plink2/2.00-alpha-5-20230923 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.cog-genomics.org/plink/2.0/">plink2 </a>(association analysis toolset) version 2.00-alpha-5-20230923 installed on all systems as module plink2/2.00-alpha-5-20230923.<br /> &nbsp;</p> <p></p> Mon, 02 Oct 2023 13:28:00 GMT https://www.uppmax.uu.se/changelog 2023-10-02T13:28:00Z [bio] pbmm2/1.13.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/PacificBiosciences/pbmm2">pbmm2</a> (pbmm2 is a SMRT C++ wrapper for minimap2's C API. Its purpose is to support native PacBio in- and output, provide sets of recommended parameters, generate sorted output on-the-fly, and postprocess alignments.) version 1.13.0 installed on all systems as module pbmm2/1.13.0.</p> <p></p> Sun, 24 Sep 2023 14:09:00 GMT https://www.uppmax.uu.se/changelog 2023-09-24T14:09:00Z [apps] Matlab R2023a installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://se.mathworks.com/">MATLAB </a>(a proprietary multi-paradigm programming language and numeric computing environment&nbsp;) version R2023a installed on all systems as module matlab/R2023a.</p> Fri, 15 Sep 2023 14:09:00 GMT https://www.uppmax.uu.se/changelog 2023-09-15T14:09:00Z [bio] paml/4.10.7 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://abacus.gene.ucl.ac.uk/software/paml.html">paml</a> (PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood.) version 4.10.7 installed on all systems as module paml/4.10.7.<br /> &nbsp;</p> <p></p> Fri, 25 Aug 2023 14:28:00 GMT https://www.uppmax.uu.se/changelog 2023-08-25T14:28:00Z [bio] phyx/1.3 installed on all systems https://www.uppmax.uu.se/changelog <p>phyx (phyx performs phylogenetics analyses on trees and sequences) version 1.3 installed on all systems as module phyx/1.3.&nbsp;https://github.com/FePhyFoFum/phyx<br /> &nbsp;</p> Wed, 16 Aug 2023 09:19:00 GMT https://www.uppmax.uu.se/changelog 2023-08-16T09:19:00Z [comp] python/3.11.4 and python3/3.11.4 installed on all systems https://www.uppmax.uu.se/changelog <p>The Python programming language version 3.11.4 plus a handful of widely used packages.</p> Mon, 07 Aug 2023 14:48:00 GMT https://www.uppmax.uu.se/changelog 2023-08-07T14:48:00Z [bio] HyPhy/2.5.51-mpi installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://www.hyphy.org">HyPhy </a>(Open-source software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning.) version 2.5.51-mpi installed on all systems as module HyPhy/2.5.51-mpi.<br /> &nbsp;</p> Tue, 27 Jun 2023 15:15:00 GMT https://www.uppmax.uu.se/changelog 2023-06-27T15:15:00Z [bio] HyPhy/2.5.51 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://www.hyphy.org">HyPhy </a>(Open-source software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning.) version 2.5.51 installed on all systems as module HyPhy/2.5.51.<br /> &nbsp;</p> Tue, 27 Jun 2023 15:14:00 GMT https://www.uppmax.uu.se/changelog 2023-06-27T15:14:00Z [bio] InterProScan/5.62-94.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://www.ebi.ac.uk/interpro">InterProScan </a>(InterPro provides functional analysis of proteins by classifying them into families and predicting domains and important sites.) version 5.62-94.0 installed on all systems as module InterProScan/5.62-94.0.<br /> &nbsp;</p> Tue, 27 Jun 2023 11:07:00 GMT https://www.uppmax.uu.se/changelog 2023-06-27T11:07:00Z [bio] Multi-CSAR/20180316-8fd582c installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/ablab-nthu/Multi-CSAR">Multi-CSAR</a> (a scaffolding tool that can order and orient the contigs of a target draft genome based on multiple complete and/or incomplete reference genomes of related organisms) version 20180316-8fd582c installed on all systems as module Multi-CSAR/20180316-8fd582c.</p> Wed, 21 Jun 2023 14:18:00 GMT https://www.uppmax.uu.se/changelog 2023-06-21T14:18:00Z [bio] Juicer/2.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/aidenlab/juicer">Juicer </a>(Juicer is a platform for analyzing kilobase resolution Hi-C data.) version 2.0 installed on all systems as module Juicer/2.0.<br /> &nbsp;</p> Tue, 30 May 2023 11:47:00 GMT https://www.uppmax.uu.se/changelog 2023-05-30T11:47:00Z [apps] python_GIS_packages/3.10.8 installed on all systems https://www.uppmax.uu.se/changelog <p>python_GIS_packages (Python package for GIS installation) version 3.10.8 installed on all systems as module python_GIS_packages/3.10.8.</p> Tue, 30 May 2023 11:32:00 GMT https://www.uppmax.uu.se/changelog 2023-05-30T11:32:00Z [apps] Mathematica 13.2 installed on Rackham and Snowy https://www.uppmax.uu.se/changelog <p>Mathematica: high-powered computation with thousands of Wolfram Language functions, natural language input, real-world data, mobile support.&nbsp;https://www.wolfram.com/mathematica/</p> Mon, 08 May 2023 06:42:00 GMT https://www.uppmax.uu.se/changelog 2023-05-08T06:42:00Z [bio] VarDictJava/1.8.3 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/AstraZeneca-NGS/VarDictJava">VarDictJava</a> (a variant discovery program written in Java and Perl, a Java port of VarDict variant caller) version 1.8.3 installed on all systems as module VarDictJava/1.8.3.<br /> &nbsp;</p> Thu, 04 May 2023 13:45:00 GMT https://www.uppmax.uu.se/changelog 2023-05-04T13:45:00Z [apps] WPS/4.3.1 installed on Rackham and Snowy https://www.uppmax.uu.se/changelog <p><a href="http://www.wrf-model.org">WPS</a> (WRF Preprocessing System (WPS) for WRF. The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale numerical weather prediction system designed to serve both operational forecasting and atmospheric research needs.) version 4.3.1 installed on all Rackham and Snowy as module WPS/4.3.1.<br /> &nbsp;</p> <p></p> Tue, 11 Apr 2023 09:32:00 GMT https://www.uppmax.uu.se/changelog 2023-04-11T09:32:00Z [apps] WRF/4.3.0-dm-gcc installed on Rackham and Snowy https://www.uppmax.uu.se/changelog <p><a href="https://www.mmm.ucar.edu/weather-research-and-forecasting-model">WRF</a> (The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale numerical weather prediction system designed to serve both operational forecasting and atmospheric research needs.) version 4.3.0-dm-gcc installed on Rackham and Snowy&nbsp;as module WRF/4.3.0-dm-gcc.<br /> &nbsp;</p> <p></p> Tue, 11 Apr 2023 09:30:00 GMT https://www.uppmax.uu.se/changelog 2023-04-11T09:30:00Z [bio] snakemake/7.25.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/snakemake/snakemake">snakemake</a> (The Snakemake workflow management system is a tool to create reproducible and scalable data analyses) version 7.25.0 installed on all systems as module snakemake/7.25.0.<br /> &nbsp;</p> Tue, 11 Apr 2023 09:28:00 GMT https://www.uppmax.uu.se/changelog 2023-04-11T09:28:00Z [bio] IRMA/1.0.3 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://wonder.cdc.gov/amd/flu/irma/">IRMA</a> (Iterative Refinement Meta-Assembler. IRMA was designed for the robust assembly, variant calling, and phasing of highly variable RNA viruses.) version 1.0.3 installed on all systems as module IRMA/1.0.3.<br /> &nbsp;</p> Tue, 11 Apr 2023 09:25:00 GMT https://www.uppmax.uu.se/changelog 2023-04-11T09:25:00Z [bio] XP-CLR/1.1.2 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/hardingnj/xpclr">XP-CLR</a> (Code to compute xp-clr values as per Chen, Patterson &amp; Reich 2010) version 1.1.2 installed on all systems as module XP-CLR/1.1.2.</p> <p></p> Sat, 11 Mar 2023 11:45:00 GMT https://www.uppmax.uu.se/changelog 2023-03-11T11:45:00Z [bio] dentist/4.0.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/a-ludi/dentist">dentist </a>(Long sequencing reads allow increasing contiguity and completeness of fragmented, short-read based genome assemblies by closing assembly gaps, ideally at high accuracy.) version 4.0.0 installed on all systems as module dentist/4.0.0.</p> <p></p> Sat, 11 Mar 2023 11:12:00 GMT https://www.uppmax.uu.se/changelog 2023-03-11T11:12:00Z [apps] Moses/4.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www2.statmt.org/moses/">Moses</a> is a statistical machine translation system that allows you to automatically train translation models for any language pair.</p> Mon, 06 Mar 2023 10:10:00 GMT https://www.uppmax.uu.se/changelog 2023-03-06T10:10:00Z [bio] MEMEsuite/5.5.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://meme-suite.org">MEMEsuite </a>(Motif-based sequence analysis tools) version 5.5.1 installed on all systems as module MEMEsuite/5.5.1.</p> Thu, 02 Mar 2023 15:07:00 GMT https://www.uppmax.uu.se/changelog 2023-03-02T15:07:00Z [bio] PCAngsd/1.11 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/Rosemeis/pcangsd">PCAngsd </a>(framework for analyzing low depth NGS data in heterogeneous populations using PCA) version 1.11 installed on all systems as module PCAngsd/1.11.</p> Thu, 02 Mar 2023 15:04:00 GMT https://www.uppmax.uu.se/changelog 2023-03-02T15:04:00Z [bio] Cytoscape/3.9.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://cytoscape.org/index.html">Cytoscape </a>(A software platform for visualizing complex networks and integrating these with any type of attribute data.) version 3.9.1 installed on all systems as module Cytoscape/3.9.1.<br /> &nbsp;</p> Thu, 02 Mar 2023 14:59:00 GMT https://www.uppmax.uu.se/changelog 2023-03-02T14:59:00Z [apps] VSCodium/latest installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://vscodium.com/">VSCodium</a> is a community-driven, freely-licensed binary distribution of Microsofts editor VS Code.</p> Mon, 27 Feb 2023 08:10:00 GMT https://www.uppmax.uu.se/changelog 2023-02-27T08:10:00Z [bio] SLiM/4.0.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://messerlab.org/slim/">SLiM </a>(An evolutionary simulation framework that combines a powerful engine for population genetic simulations with the capability of modeling arbitrarily complex evolutionary scenarios.) version 4.0.1 installed on all systems as module SLiM/4.0.1.<br /> &nbsp;</p> Fri, 17 Feb 2023 10:21:00 GMT https://www.uppmax.uu.se/changelog 2023-02-17T10:21:00Z [bio] gcta/1.94.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://cnsgenomics.com/software/gcta/">gcta </a>(analyses to better understand the genetic architecture of complex traits) version 1.94.1 installed on all systems as module gcta/1.94.1.<br /> &nbsp;</p> <p></p> Fri, 03 Feb 2023 12:20:00 GMT https://www.uppmax.uu.se/changelog 2023-02-03T12:20:00Z [comp] julia/1.6.7_LTS installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://julialang.org">julia </a>(Julia is a high-level, high-performance dynamic language for technical computing.) version 1.6.7_LTS installed on all systems as module julia/1.6.7_LTS.<br /> &nbsp;</p> Mon, 30 Jan 2023 12:58:00 GMT https://www.uppmax.uu.se/changelog 2023-01-30T12:58:00Z [comp] julia/1.8.5 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://julialang.org">julia </a>(Julia is a high-level, high-performance dynamic language for technical computing) version 1.8.5 installed on all systems as module julia/1.8.5.<br /> &nbsp;</p> Mon, 30 Jan 2023 12:54:00 GMT https://www.uppmax.uu.se/changelog 2023-01-30T12:54:00Z [bio] plink2/2.00-alpha-3.7-20221024 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.cog-genomics.org/plink/2.0/">plink2 </a>(association analysis toolset) version 2.00-alpha-3.7-20221024 installed on all systems as module plink2/2.00-alpha-3.7-20221024.<br /> &nbsp;</p> <p></p> Tue, 24 Jan 2023 08:56:00 GMT https://www.uppmax.uu.se/changelog 2023-01-24T08:56:00Z [libs] PROJ/9.1.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://proj.org">PROJ </a>(Cartographic Projections and Coordinate Transformations Library) version 9.1.1 installed on all systems as module PROJ/9.1.1.<br /> &nbsp;</p> <p></p> Tue, 10 Jan 2023 13:56:00 GMT https://www.uppmax.uu.se/changelog 2023-01-10T13:56:00Z [libs] libtiff/4.5.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.libtiff.org">libtiff </a>(This software provides support for the Tag Image File Format (TIFF), a widely used format for storing image data.) version 4.5.0 installed on all systems as module libtiff/4.5.0.<br /> &nbsp;</p> <p></p> Tue, 10 Jan 2023 12:34:00 GMT https://www.uppmax.uu.se/changelog 2023-01-10T12:34:00Z [bio] delly/1.1.6 installed on all systems https://www.uppmax.uu.se/changelog <p>&nbsp;<a href="https://github.com/dellytools/delly">delly</a> (an integrated structural variant (SV) prediction method that can<br /> &nbsp; discover, genotype and visualize deletions, tandem duplications, inversions<br /> &nbsp; and translocations at single-nucleotide resolution in short-read and<br /> &nbsp; long-read massively parallel sequencing data) version 1.1.6 installed on<br /> &nbsp; all systems as module delly/1.1.6.</p> Tue, 13 Dec 2022 09:33:00 GMT https://www.uppmax.uu.se/changelog 2022-12-13T09:33:00Z [bio] MMseqs2/14-7e284 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/soedinglab/mmseqs2">MMseqs2</a> (ultra fast and sensitive sequence search and clustering suite) version 14-7e284 installed on all systems as module MMseqs2/14-7e284.<br /> &nbsp;</p> Fri, 04 Nov 2022 07:14:00 GMT https://www.uppmax.uu.se/changelog 2022-11-04T07:14:00Z [bio] htseq/2.0.2 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://htseq.readthedocs.io">HTSeq</a> (Analysing high-throughput sequencing data with Python) version 2.0.2 installed on all systems as module htseq/2.0.2.</p> Thu, 03 Nov 2022 10:54:00 GMT https://www.uppmax.uu.se/changelog 2022-11-03T10:54:00Z [bio] spaln/2.4.13c installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/ogotoh/spaln">spaln</a> (stand-alone program that maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence in a single job) version 2.4.13c installed on all systems as module spaln/2.4.13c.<br /> &nbsp;</p> Thu, 27 Oct 2022 09:50:00 GMT https://www.uppmax.uu.se/changelog 2022-10-27T09:50:00Z [bio] fastsimcoal/2.7.93 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://cmpg.unibe.ch/software/fastsimcoal2/">fastsimcoal</a> (fast sequential markov coalescent simulation of genomic data under complex evolutionary models) version 2.7.93 installed on all systems as module fastsimcoal/2.7.93.<br /> &nbsp;</p> Wed, 26 Oct 2022 12:50:00 GMT https://www.uppmax.uu.se/changelog 2022-10-26T12:50:00Z [bio] nf-core/2.6 installed on all systems https://www.uppmax.uu.se/changelog <p>nf-core (A companion tool is available for nf-core to help with common tasks.) version 2.6 installed on all systems as module nf-core/2.6.<br /> https://github.com/nf-core/tools</p> Tue, 25 Oct 2022 11:31:00 GMT https://www.uppmax.uu.se/changelog 2022-10-25T11:31:00Z [bio] Nextflow/22.10.0 installed on all systems https://www.uppmax.uu.se/changelog <p>Nextflow (A DSL for data-driven computational pipelines http://nextflow.io) version 22.10.0 installed on all systems as module Nextflow/22.10.0.<br /> https://github.com/nextflow-io/nextflow</p> Tue, 25 Oct 2022 10:45:00 GMT https://www.uppmax.uu.se/changelog 2022-10-25T10:45:00Z [bio] abricate/1.0.1-20200512-955d402 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/tseemann/abricate">abricate</a> (mass screening of contigs for antimicrobial and virulence genes) version 1.0.1-20200512-955d402 installed on all systems as module abricate/1.0.1-20200512-955d402.<br /> &nbsp;</p> Mon, 24 Oct 2022 14:47:00 GMT https://www.uppmax.uu.se/changelog 2022-10-24T14:47:00Z [bio] any2fasta/0.4.2 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/tseemann/any2fasta">any2fasta</a> (Convert various sequence formats to FASTA) version 0.4.2 installed on all systems as module any2fasta/0.4.2.<br /> &nbsp;</p> Thu, 20 Oct 2022 15:30:00 GMT https://www.uppmax.uu.se/changelog 2022-10-20T15:30:00Z [bio] datamash/1.8 installed on all systems https://www.uppmax.uu.se/changelog <p>datamash (Datamash is a grouping and summarizing tool on tabular data files) version 1.8 installed on all systems as module datamash/1.8.</p> Mon, 17 Oct 2022 13:52:00 GMT https://www.uppmax.uu.se/changelog 2022-10-17T13:52:00Z [bio] KrakenUniq/1.0.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/fbreitwieser/KrakenUniq">KrakenUniq</a> (confident and fast metagenomics classification using unique k-mer counts) version 1.0.1 installed on all systems as module KrakenUniq/1.0.1.<br /> &nbsp;</p> Wed, 12 Oct 2022 15:28:00 GMT https://www.uppmax.uu.se/changelog 2022-10-12T15:28:00Z [bio] pathPhynder/1.a-20221011-a407a97 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/douglasgscofield/pathPhynder">pathPhynder</a> (workflow for ancient DNA placement into reference phylogenies) version 1.a-20221011-a407a97 installed on all systems as module pathPhynder/1.a-20221011-a407a97.</p> Mon, 10 Oct 2022 11:41:00 GMT https://www.uppmax.uu.se/changelog 2022-10-10T11:41:00Z [data] fastq_screen_data/latest updated on all systems https://www.uppmax.uu.se/changelog <p><a href="https://stevenwingett.github.io/FastQ-Screen/#obtaining-reference-genomes">fastq_screen_data</a> (reference genomes for FastQ Screen, both standard and bisulfite) version 20220330 installed on all systems as module fastq_screen_data/latest. See 'module help fastq_screen_data/latest' for more information.</p> Tue, 04 Oct 2022 13:57:00 GMT https://www.uppmax.uu.se/changelog 2022-10-04T13:57:00Z [libs] gsl/2.7 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.gnu.org/software/gsl/">gsl</a> (numerical library for C and C++ programmers) version 2.7 installed on all systems as module gsl/2.7.</p> Tue, 04 Oct 2022 13:16:00 GMT https://www.uppmax.uu.se/changelog 2022-10-04T13:16:00Z [libs] GEOS/3.11.0-gcc10.3.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://libgeos.org/">GEOS</a> (GEOS (Geometry Engine - Open Source) is a C++ port of the JTS Topology Suite (JTS). It aims to contain the complete functionality of JTS in C++. This includes all the OpenGIS Simple Features for SQL spatial predicate functions and spatial operators, as well as specific JTS enhanced functions. GEOS provides spatial functionality to many other projects and products.) version 3.11.0-gcc10.3.0 installed on all systems as module GEOS/3.11.0-gcc10.3.0.</p> Tue, 04 Oct 2022 12:29:00 GMT https://www.uppmax.uu.se/changelog 2022-10-04T12:29:00Z [data] KrakenUniq_data/latest installed on all systems https://www.uppmax.uu.se/changelog <p>KrakenUniq_data (latest database build for KrakenUniq, plus prebuilt databases available externally) version latest installed on all systems as module KrakenUniq_data/latest.&nbsp; See 'module help KrakenUniq_data/latest' for more information.<br /> &nbsp;</p> Tue, 04 Oct 2022 11:29:00 GMT https://www.uppmax.uu.se/changelog 2022-10-04T11:29:00Z [bio] fastq_screen/0.15.2 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://stevenwingett.github.io/FastQ-Screen/">fastq_screen</a> (contamination screening for NGS data sets) version 0.15.2 installed on all systems as module fastq_screen/0.15.2.<br /> &nbsp;</p> Tue, 04 Oct 2022 08:41:00 GMT https://www.uppmax.uu.se/changelog 2022-10-04T08:41:00Z [apps] VMD/1.9.3 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.ks.uiuc.edu/Research/vmd/">VMD</a> (molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting) version 1.9.3 installed on all systems as module VMD/1.9.3.<br /> &nbsp;</p> <p></p> Fri, 30 Sep 2022 15:14:00 GMT https://www.uppmax.uu.se/changelog 2022-09-30T15:14:00Z [apps] VMD/1.9.4-alpha-57 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.ks.uiuc.edu/Research/vmd/">VMD</a> (molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting) version 1.9.4-alpha-57 installed on all systems as module VMD/1.9.4-alpha-57.<br /> &nbsp;</p> <p></p> Fri, 30 Sep 2022 15:12:00 GMT https://www.uppmax.uu.se/changelog 2022-09-30T15:12:00Z [bio] KrakenUniq/1.0.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/fbreitwieser/KrakenUniq">KrakenUniq</a> (confident and fast metagenomics classification using unique k-mer counts) version 1.0.0 installed on all systems as module KrakenUniq/1.0.0.<br /> &nbsp;</p> Fri, 30 Sep 2022 09:06:00 GMT https://www.uppmax.uu.se/changelog 2022-09-30T09:06:00Z [bio] minimap2/2.24-r1122 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/lh3/minimap2">minimap2</a> (versatile pairwise aligner for genomic and spliced nucleotide sequences) version 2.24-r1122 installed on all systems as module minimap2/2.24-r1122.<br /> &nbsp;</p> Wed, 28 Sep 2022 06:02:00 GMT https://www.uppmax.uu.se/changelog 2022-09-28T06:02:00Z [bio] vcfstats/0.4.2 installed on all systems https://www.uppmax.uu.se/changelog <p>[bio] vcfstats/0.4.2&nbsp;installed on all systems</p> Tue, 27 Sep 2022 13:35:00 GMT https://www.uppmax.uu.se/changelog 2022-09-27T13:35:00Z [bio] GeneMark/4.69-es installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://exon.gatech.edu/GeneMark">GeneMark</a> (Gene prediction in eurkaryotes) version 4.69-es installed on all systems as module GeneMark/4.69-es.<br /> &nbsp;</p> Tue, 27 Sep 2022 08:06:00 GMT https://www.uppmax.uu.se/changelog 2022-09-27T08:06:00Z [bio] phast/1.6 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://compgen.cshl.edu/phast/index.php">phast </a>(Phylogenetic Analysis with Space/Time models (PHAST) is a freely available software package consisting of a collection of command-line programs and supporting libraries for comparative and evolutionary genomics.) version 1.6 installed on all systems as module phast/1.6.<br /> &nbsp;</p> <p></p> Wed, 21 Sep 2022 13:02:00 GMT https://www.uppmax.uu.se/changelog 2022-09-21T13:02:00Z [bio] satsuma2/37c5f38-20200304 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/bioinfologics/satsuma2">satsuma2 </a>(optimised version of Satsuma, a tool to reliably align large and complex DNA sequences providing maximum sensitivity (to find all there is to find), specificity (to only find real homology) and speed (to accomodate the billions of base pairs in vertebrate genomes).) version 37c5f38-20200304 installed on all systems as module satsuma2/37c5f38-20200304.<br /> &nbsp;</p> <p></p> Wed, 21 Sep 2022 13:01:00 GMT https://www.uppmax.uu.se/changelog 2022-09-21T13:01:00Z [libs] zlib/1.2.12 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://zlib.net/">zlib</a> (a free, general-purpose, legally unencumbered -- that is, not covered by any patents -- lossless data-compression library for use on virtually any computer hardware and operating system) version 1.2.12 installed on all systems as module zlib/1.2.12.<br /> &nbsp;</p> Tue, 20 Sep 2022 17:06:00 GMT https://www.uppmax.uu.se/changelog 2022-09-20T17:06:00Z [libs] bzip2/1.0.8 installed on all system https://www.uppmax.uu.se/changelog <p><a href="https://sourceware.org/bzip2">bzip2</a> version 1.0.8 installed on all systems as module bzip2/1.0.8.<br /> &nbsp;</p> Tue, 20 Sep 2022 13:10:00 GMT https://www.uppmax.uu.se/changelog 2022-09-20T13:10:00Z [apps] RStudio/2022.07.1-554 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://rstudio.com">RStudio</a> (Integrated development environment for the R language) version 2022.07.1-554 installed on all systems as module RStudio/2022.07.1-554.<br /> &nbsp;</p> Tue, 20 Sep 2022 10:42:00 GMT https://www.uppmax.uu.se/changelog 2022-09-20T10:42:00Z [apps] xz/5.2.6 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://tukaani.org/xz">xz</a> (general-purpose data compression software with a high compression ratio) version 5.2.6 installed on all systems as module xz/5.2.6.<br /> &nbsp;</p> Tue, 20 Sep 2022 10:12:00 GMT https://www.uppmax.uu.se/changelog 2022-09-20T10:12:00Z [bio] grenedalf/0.2.0-beta installed on all systems https://www.uppmax.uu.se/changelog <p>grenedalf is a collection of commands for working with population genetic data, in particular from pool sequencing. Its main focus are stat<br /> istical analyses such as Tajima's D and Fst, following the approaches of PoPoolation and PoPoolation2)</p> <p>version 0.2.0-beta installed on all systems as<br /> module grenedalf/0.2.0-beta<br /> &nbsp;</p> Tue, 20 Sep 2022 06:17:00 GMT https://www.uppmax.uu.se/changelog 2022-09-20T06:17:00Z [libs] libcurl/7.85.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://curl.se/">libcurl</a> (a free and easy-to-use client-side URL transfer library supporting many formats) version 7.85.0 installed on all systems as module libcurl/7.85.0.<br /> &nbsp;</p> Mon, 19 Sep 2022 16:37:00 GMT https://www.uppmax.uu.se/changelog 2022-09-19T16:37:00Z [apps] texlive/2022-09-18 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.tug.org/texlive/">texlive</a> (full TeX document production system) version 2022-09-18 installed on all systems as module texlive/2022-09-18.<br /> &nbsp;</p> Mon, 19 Sep 2022 15:14:00 GMT https://www.uppmax.uu.se/changelog 2022-09-19T15:14:00Z [libs] zstd/1.5.2 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/facebook/zstd">zstd</a> (a fast lossless compression algorithm, targeting real-time compression scenarios at zlib-level and better compression ratios) version 1.5.2 installed on all systems as module zstd/1.5.2.</p> Mon, 19 Sep 2022 13:05:00 GMT https://www.uppmax.uu.se/changelog 2022-09-19T13:05:00Z [bio] octopus/17a597d-20220708 https://www.uppmax.uu.se/changelog <p><a href="https://github.com/luntergroup/octopus">octopus</a> (Mapping-based variant caller that implements several calling models within a unified haplotype-aware framework) version 17a597d-20220708 installed on all systems as module octopus/17a597d-20220708.<br /> &nbsp;</p> Fri, 16 Sep 2022 09:10:00 GMT https://www.uppmax.uu.se/changelog 2022-09-16T09:10:00Z [bio] MAGeCK2/20211209-435eacd https://www.uppmax.uu.se/changelog <p><a href="https://github.com/davidliwei/mageck2">MAGeCK2 </a>(Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout) version 20211209-435eacd installed on all systems as module MAGeCK2/20211209-435eacd.<br /> &nbsp;</p> Tue, 06 Sep 2022 10:44:00 GMT https://www.uppmax.uu.se/changelog 2022-09-06T10:44:00Z [bio] MAPGD/0.4.40 installed on all systems https://www.uppmax.uu.se/changelog <p>MAPGD (MAPGD is a series of related programs that estimate allele frequency, heterozygosity, Hardy-Weinberg disequilibrium, linkage disequilibrium and identity-by-descent (IBD) coefficients from population genomic data using a statistically rigor<br /> ous maximum likelihood approach.)</p> <p><a href="https://github.com/LynchLab/MAPGD">https://github.com/LynchLab/MAPGD</a><br /> &nbsp;</p> Mon, 05 Sep 2022 09:05:00 GMT https://www.uppmax.uu.se/changelog 2022-09-05T09:05:00Z [build] bubblewrap/0.6.2 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/containers/bubblewrap">bubblewrap</a> (Unprivileged sandboxing) version 0.6.2 installed on all systems as module bubblewrap/0.6.2. Note that this is not installed setuid, which may be insufficient for some tools.<br /> &nbsp;</p> Wed, 10 Aug 2022 11:33:00 GMT https://www.uppmax.uu.se/changelog 2022-08-10T11:33:00Z [bio] ORFfinder/0.4.3 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.ncbi.nlm.nih.gov/orffinder">ORFfinder</a> (ORF finder searches for open reading frames (ORFs) in a DNA sequence) version 0.4.3 installed on all systems as module ORFfinder/0.4.3.<br /> &nbsp;</p> Tue, 14 Jun 2022 09:21:00 GMT https://www.uppmax.uu.se/changelog 2022-06-14T09:21:00Z [bio] fastsimcoal/2.7.9 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://cmpg.unibe.ch/software/fastsimcoal2/">fastsimcoal</a> (fast sequential markov coalescent simulation of genomic data under complex evolutionary models) version 2.7.9 installed on all systems as module fastsimcoal/2.7.9.<br /> &nbsp;</p> Tue, 31 May 2022 08:56:00 GMT https://www.uppmax.uu.se/changelog 2022-05-31T08:56:00Z [bio] Arlequin/3.5.2.2 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://cmpg.unibe.ch/software/arlequin35/">Arlequin</a> (An Integrated Software for Population Genetics Data Analysis) version 3.5.2.2 installed on all systems as module Arlequin/3.5.2.2. This module includes the latest <strong>arlsumstat</strong> executable.<br /> &nbsp;</p> Tue, 31 May 2022 08:54:00 GMT https://www.uppmax.uu.se/changelog 2022-05-31T08:54:00Z [bio] ABCtoolbox/20131120 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://cmpg.unibe.ch/software/ABCtoolbox/">ABCtoolbox</a> (Performs Approximate Bayesian Computation (ABC) estimations using various recently published algorithms including MCMC without likelihood and Population Monte Carlo) version 20131120 installed on all systems as module ABCtoolbox/20131120.<br /> &nbsp;</p> Tue, 31 May 2022 08:35:00 GMT https://www.uppmax.uu.se/changelog 2022-05-31T08:35:00Z [comp] julia/1.7.2 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://julialang.org">julia </a>(high-level, high-performance dynamic language for technical computing.) versionstems as module julia/1.7.2.</p> <p></p> Tue, 31 May 2022 07:20:00 GMT https://www.uppmax.uu.se/changelog 2022-05-31T07:20:00Z [bio] spaln/2.4.9 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/ogotoh/spaln">spaln</a> (stand-alone program that maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence in a single job) version 2.4.9 installed on all systems as module spaln/2.4.9.<br /> &nbsp;</p> Wed, 11 May 2022 08:03:00 GMT https://www.uppmax.uu.se/changelog 2022-05-11T08:03:00Z [libs] slurm-drmaa/1.1.3-slurm21.08.8 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/natefoo/slurm-drmaa">slurm-drmaa</a> (DRMAA for Slurm Workload Manager (Slurm) is an implementation of Open Grid Forum Distributed Resource Management Application API (DRMAA) version 1 for submission and control of jobs to Slurm. Using DRMAA, grid applications builders, portal developers and ISVs can use the same high-level API to link their software with different cluster/resource management systems. Built against SLURM 21.08.8) version 1.1.3-slurm21.08.8 installed on all systems as module slurm-drmaa/1.1.3-slurm21.08.8.<br /> &nbsp;</p> Tue, 10 May 2022 07:59:00 GMT https://www.uppmax.uu.se/changelog 2022-05-10T07:59:00Z [bio] KrakenUniq/0.6 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/fbreitwieser/KrakenUniq">KrakenUniq</a> (confident and fast metagenomics classification using unique k-mer counts) version 0.6 installed on all systems as module KrakenUniq/0.6.<br /> &nbsp;</p> Mon, 09 May 2022 12:57:00 GMT https://www.uppmax.uu.se/changelog 2022-05-09T12:57:00Z [bio] bwa-mem2/2.2.1-20211213-edc703f installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/bwa-mem2/bwa-mem2">bwa-mem2</a> (the next version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case, dataset and the running machine.) version 2.2.1-20211213-edc703f installed on all systems as module bwa-mem2/2.2.1-20211213-edc703f.</p> Thu, 05 May 2022 08:13:00 GMT https://www.uppmax.uu.se/changelog 2022-05-05T08:13:00Z [bio] cutadapt/4.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://cutadapt.readthedocs.io/en/stable/index.html">cutadapt</a> (finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads) version 4.0 installed on all systems as module cutadapt/4.0.<br /> &nbsp;</p> Tue, 03 May 2022 21:42:00 GMT https://www.uppmax.uu.se/changelog 2022-05-03T21:42:00Z [bio] SQuIRE/885bf4d-20190301 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/wyang17/SQuIRE">SQuIRE</a> (Software for Quantifying Interspersed Repeat Expression) version 885bf4d-20190301 installed on all systems as module SQuIRE/885bf4d-20190301.<br /> &nbsp;</p> <p></p> Wed, 27 Apr 2022 08:21:00 GMT https://www.uppmax.uu.se/changelog 2022-04-27T08:21:00Z [bio] BioBloomTools/2.3.3-20210218-151b0c0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/bcgsc/biobloom">BioBloomTools</a> (Create Bloom filters for a given reference and then use it to categorize sequences) version 2.3.3-20210218-151b0c0 installed on all systems as module BioBloomTools/2.3.3-20210218-151b0c0.<br /> &nbsp;</p> Tue, 12 Apr 2022 09:08:00 GMT https://www.uppmax.uu.se/changelog 2022-04-12T09:08:00Z [comp] LLVM/13.0.1 installed on all systems https://www.uppmax.uu.se/changelog <p>LLVM (The LLVM package contains a collection of modular and reusable compiler and toolchain technologies.) version 13.0.1 installed on all systems as module LLVM/13.0.1.</p> Wed, 06 Apr 2022 06:24:00 GMT https://www.uppmax.uu.se/changelog 2022-04-06T06:24:00Z [bio] pblat-cluster/1.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://icebert.github.io/pblat-cluster/">pblat-cluster</a> (blat with cluster parallel hybrid computing support) version 1.1 installed on all systems as module pblat-cluster/1.1.<br /> &nbsp;</p> Tue, 05 Apr 2022 20:45:00 GMT https://www.uppmax.uu.se/changelog 2022-04-05T20:45:00Z [bio] pblat/2.5 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://icebert.github.io/pblat/">pblat</a> (parallelized blat with multi-threads support) version 2.5 installed on all systems as module pblat/2.5.<br /> &nbsp;</p> Tue, 05 Apr 2022 20:09:00 GMT https://www.uppmax.uu.se/changelog 2022-04-05T20:09:00Z [comp] binutils/2.38 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.gnu.org/software/binutils/">binutils</a> (a collection of binary tools, built with plugin support) version 2.38 installed on all systems but miarka as module binutils/2.38.<br /> &nbsp;</p> Tue, 05 Apr 2022 16:32:00 GMT https://www.uppmax.uu.se/changelog 2022-04-05T16:32:00Z [comp] gdb/11.2 installed on all systems https://www.uppmax.uu.se/changelog <p>gdb version 11.2 installed on all systems as module gdb/11.2.</p> Mon, 04 Apr 2022 15:09:00 GMT https://www.uppmax.uu.se/changelog 2022-04-04T15:09:00Z [bio] BlobToolKit/3.1.0 installed on all systems https://www.uppmax.uu.se/changelog <p>BlobToolKit (A new implementation of BlobTools with support for interactive data exploration via the BlobToolKit viewer) version 3.1.0 installed on all systems as module BlobToolKit/3.1.0.</p> Mon, 04 Apr 2022 15:09:00 GMT https://www.uppmax.uu.se/changelog 2022-04-04T15:09:00Z [bio] Kraken/1.1.1-20210927-375654f installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/DerrickWood/kraken">Kraken</a> (taxonomic sequence classification system) version 1.1.1-20210927-375654f installed on all systems as module Kraken/1.1.1-20210927-375654f.</p> <p>Note that Kraken is superseded by Kraken2, and the latest Kraken2 module, for example Kraken2/2.1.2-20211210-4f648f5, should be used in preference to this.</p> Mon, 04 Apr 2022 11:28:00 GMT https://www.uppmax.uu.se/changelog 2022-04-04T11:28:00Z [bio] metaMATE/20220327-3cdacd7 installed on all systems https://www.uppmax.uu.se/changelog <div>metaMATE version 20220327-3cdacd7 installed on all systems as module metaMATE/20220327-3cdacd7.</div> <div>https://github.com/tjcreedy/metamate</div> Mon, 04 Apr 2022 10:19:00 GMT https://www.uppmax.uu.se/changelog 2022-04-04T10:19:00Z [bio] CROP/1.33 installed on all systems https://www.uppmax.uu.se/changelog <div>CROP version 1.33 installed on all systems as module CROP/1.33.</div> <div>https://github.com/tingchenlab/CROP</div> Mon, 04 Apr 2022 10:18:00 GMT https://www.uppmax.uu.se/changelog 2022-04-04T10:18:00Z [libs] libicu/5.2-4 installed on all systems https://www.uppmax.uu.se/changelog <p>The <a href="https://icu.unicode.org/">libicu</a>&nbsp;library on EL8 has been updated to v60&nbsp;with no legacy libraries for v50. The libicu/5.2-4 module contains the contents of libicu.x86_64 and libicu-devel.x86_64 from CentOS7 for use by executables running on an EL8 system. Executables using these libraries should have their RPATH information updated to point to subdirectories within this module, and the module itself can also be used as a development dependency.</p> Thu, 31 Mar 2022 10:56:00 GMT https://www.uppmax.uu.se/changelog 2022-03-31T10:56:00Z [libs] readline/6.2-11 installed on all systems https://www.uppmax.uu.se/changelog <p>The <a href="https://tiswww.case.edu/php/chet/readline/rltop.html">readline</a> library on EL8 has been updated to v7 with no legacy libraries for v6. The readline/6.2-11 module contains the contents of readline.x86_64 and readline-devel.x86_64 from CentOS7 for use by executables running on an EL8 system. Executables using these libraries should have their RPATH information updated to point to subdirectories within this module, and the module itself can also be used as a development dependency.</p> Thu, 31 Mar 2022 10:16:00 GMT https://www.uppmax.uu.se/changelog 2022-03-31T10:16:00Z [apps] python_ML_packages/3.9.5-cpu installed on all systems https://www.uppmax.uu.se/changelog <div>python_ML_packages (Python package installation) version 3.9.5-cpu installed on all systems as module python_ML_packages/3.9.5-cpu.</div> Thu, 31 Mar 2022 07:29:00 GMT https://www.uppmax.uu.se/changelog 2022-03-31T07:29:00Z [apps] python_ML_packages/3.9.5-gpu installed on all systems https://www.uppmax.uu.se/changelog <p>python_ML_packages (Python package installation) version 3.9.5-gpu installed on all systems as module python_ML_packages/3.9.5-gpu.</p> Thu, 31 Mar 2022 07:28:00 GMT https://www.uppmax.uu.se/changelog 2022-03-31T07:28:00Z [bio] ATLAS_aDNA/0.9.9 installed on all systems https://www.uppmax.uu.se/changelog <p>ATLAS_aDNA (ATLAS stands for Analysis Tools for Low-coverage and Ancient Samples. These tools cover all programs necessary to obtain variant calls, estimates of heterozygosity and more from a BAM file.) version 0.9.9 installed on all systems as module ATLAS_aDNA/0.9.9.</p> Thu, 31 Mar 2022 07:27:00 GMT https://www.uppmax.uu.se/changelog 2022-03-31T07:27:00Z [bio] fastq_demux/20200918-1e2c079 installed on all systems https://www.uppmax.uu.se/changelog <p>fastq_demux (A simple program to demultiplex Illumina FASTQ files based on barcodes in the FASTQ headers) version 20200918-1e2c079 installed on all systems as module fastq_demux/20200918-1e2c079.</p> Thu, 31 Mar 2022 07:26:00 GMT https://www.uppmax.uu.se/changelog 2022-03-31T07:26:00Z [apps] PsN/5.3.0 installed on all systems https://www.uppmax.uu.se/changelog <p>PsN (Perl-speaks-NONMEM \(PsN\) is a collection of Perl modules and programs aiding in the development of non-linear mixed effect models using NONMEM) version 5.3.0 installed on all systems as module PsN/5.3.0.</p> Thu, 31 Mar 2022 07:25:00 GMT https://www.uppmax.uu.se/changelog 2022-03-31T07:25:00Z [bio] metaMATE/20220327-3cdacd7 installed on all systems https://www.uppmax.uu.se/changelog <p>metaMATE version 20220327-3cdacd7 installed on all systems as module metaMATE/20220327-3cdacd7.</p> Thu, 31 Mar 2022 07:23:00 GMT https://www.uppmax.uu.se/changelog 2022-03-31T07:23:00Z [libs] SDSL/2.1.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/simongog/sdsl-lite">SDSL</a> (a powerful and flexible C++11 library implementing succinct data structures) version 2.1.1 installed on all systems as module SDSL/2.1.1.<br /> &nbsp;</p> Wed, 30 Mar 2022 15:24:00 GMT https://www.uppmax.uu.se/changelog 2022-03-30T15:24:00Z [libs] sparsehash/2.0.4 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/sparsehash/sparsehash">Sparsehash</a> version 2.0.4 installed on all systems as module sparsehash/2.0.4.<br /> &nbsp;</p> Wed, 30 Mar 2022 13:30:00 GMT https://www.uppmax.uu.se/changelog 2022-03-30T13:30:00Z [bio] muscle/5.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/rcedgar/muscle">MUSCLE</a> (Multiple sequence alignment with top benchmark scores scalable to thousands of sequences. Generates replicate alignments, enabling assessment of downstream analyses such as trees and predicted structures) version 5.1 installed on all systems as module muscle/5.1.<br /> &nbsp;</p> Tue, 29 Mar 2022 13:33:00 GMT https://www.uppmax.uu.se/changelog 2022-03-29T13:33:00Z [bio] tRNAscan-SE/2.0.9 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://lowelab.ucsc.edu/tRNAscan-SE/">tRNAscan-SE</a> (Improved Detection and Functional Classification of Transfer RNA Genes) version 2.0.9 installed on all systems as module tRNAscan-SE/2.0.9.<br /> &nbsp;</p> Mon, 28 Mar 2022 09:33:00 GMT https://www.uppmax.uu.se/changelog 2022-03-28T09:33:00Z [bio] infernal/1.1.4 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://eddylab.org/infernal/">infernal</a> (&quot;INFERence of RNA ALignment&quot; --&nbsp;is for searching DNA sequence databases for RNA structure and sequence similarities) version 1.1.4 installed on all systems as module infernal/1.1.4.<br /> &nbsp;</p> Mon, 28 Mar 2022 08:47:00 GMT https://www.uppmax.uu.se/changelog 2022-03-28T08:47:00Z [apps] gromacs/4.5.7.th.dp (double precision) is installed on Rackham https://www.uppmax.uu.se/changelog Mon, 21 Mar 2022 12:20:00 GMT https://www.uppmax.uu.se/changelog 2022-03-21T12:20:00Z [bio] VESPA/1.0.1 installed on all systems https://www.uppmax.uu.se/changelog <p>VESPA (The VESPA (Very large-scale Evolution and Selective Pressure analyses) toolkit is a collection of commands designed to simplify molecular evolutionary analyses.) version 1.0.1 installed on all systems as module VESPA/1.0.1.</p> <p>https://vespa-evol.readthedocs.io/en/latest/</p> Mon, 21 Mar 2022 08:15:00 GMT https://www.uppmax.uu.se/changelog 2022-03-21T08:15:00Z [apps] CPLEXOptimizationStudio/20.10 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.ibm.com/se-en/analytics/cplex-optimizer">CPLEX Optimization Studio</a>&nbsp;version 20.10 is installed on all systems as module CPLEXOptimizationStudio/20.10. CPLEX Optimizer provides flexible, high-performance mathematical programming solvers for linear programming, mixed integer programming, quadratic programming and quadratically constrained programming problems. These solvers include a distributed parallel algorithm for mixed integer programming to leverage multiple computers to solve difficult problems.</p> Fri, 18 Mar 2022 16:02:00 GMT https://www.uppmax.uu.se/changelog 2022-03-18T16:02:00Z [apps] CPLEXOptimizationStudio/12.9.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.ibm.com/se-en/analytics/cplex-optimizer">CPLEX Optimization Studio</a>&nbsp;version 12.9.0 installed on all systems as module CPLEXOptimizationStudio/12.9.0. CPLEX Optimizer provides flexible, high-performance mathematical programming solvers for linear programming, mixed integer programming, quadratic programming and quadratically constrained programming problems. These solvers include a distributed parallel algorithm for mixed integer programming to leverage multiple computers to solve difficult problems.<br /> &nbsp;</p> Fri, 18 Mar 2022 15:54:00 GMT https://www.uppmax.uu.se/changelog 2022-03-18T15:54:00Z [bio] CAMMiQ/20211015-6142150 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/algo-cancer/CAMMiQ">CAMMiQ</a> (CAMMiQ is a software tool for microbial identification and quantification.) version 20211015-6142150 installed on all systems as module CAMMiQ/20211015-6142150.<br /> &nbsp;</p> Fri, 18 Mar 2022 15:32:00 GMT https://www.uppmax.uu.se/changelog 2022-03-18T15:32:00Z [bio] fastp/0.23.2 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/OpenGene/fastp">fastp</a> version 0.23.2 installed on all systems as module fastp/0.23.2.&nbsp; fastp is a&nbsp;tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance.</p> Tue, 15 Mar 2022 16:32:00 GMT https://www.uppmax.uu.se/changelog 2022-03-15T16:32:00Z [data] Pfam/35.0 installed on all systems https://www.uppmax.uu.se/changelog <p>The data module Pfam/35.0, containing protein families that are part of the <a href="http://pfam.xfam.org/">35.0 release of Pfam</a>, is now available. The earlier releases Pfam/2011, Pfam/28.0 and Pfam/31.0 are also now available as data modules.</p> Tue, 15 Mar 2022 12:58:00 GMT https://www.uppmax.uu.se/changelog 2022-03-15T12:58:00Z [apps] RStudio/2022.02.0-443 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://rstudio.com">RStudio</a> (Integrated development environment for the R language) version 2022.02.0-443 installed on all systems as module RStudio/2022.02.0-443.<br /> &nbsp;</p> Mon, 14 Mar 2022 11:05:00 GMT https://www.uppmax.uu.se/changelog 2022-03-14T11:05:00Z [bio] BclConverter/3.9.3 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://support-docs.illumina.com/SW/BCL_Convert/Content/SW/FrontPages/BCL_Convert.htm">BclConverter</a> (converts per cycle binary data output by Illumina sequencers containing basecall files and quality scores to per read FASTQ files) version 3.9.3 installed on all systems as module BclConverter/3.9.3.<br /> &nbsp;</p> Wed, 09 Mar 2022 11:32:00 GMT https://www.uppmax.uu.se/changelog 2022-03-09T11:32:00Z [libs] reinstalled SuperLU/5.2.1 with shared and static libraries https://www.uppmax.uu.se/changelog <p><a href="https://github.com/xiaoyeli/superlu">SuperLU</a> (a set of subroutines to solve a sparse linear system A*X=B) version 5.2.1 is now installed with both shared and static libraries as module SuperLU/5.2.1.</p> Tue, 08 Mar 2022 13:32:00 GMT https://www.uppmax.uu.se/changelog 2022-03-08T13:32:00Z [apps] PsN/5.3.0 installed on all systems https://www.uppmax.uu.se/changelog <p>PsN (Perl-speaks-NONMEM \(PsN\) is a collection of Perl modules and programs aiding in the development of non-linear mixed effect models using NONMEM) version 5.3.0 installed on all systems as module PsN/5.3.0.</p> Mon, 07 Mar 2022 15:54:00 GMT https://www.uppmax.uu.se/changelog 2022-03-07T15:54:00Z [bio] atlas/0.9.9 installed on all systems https://www.uppmax.uu.se/changelog <p>atlas (ATLAS stands for Analysis Tools for Low-coverage and Ancient Samples. These tools cover all programs necessary to obtain variant calls, estimates of heterozygosity and more from a BAM file.) version 0.9.9 installed on all systems as module atlas/0.9.9.</p> Mon, 07 Mar 2022 06:19:00 GMT https://www.uppmax.uu.se/changelog 2022-03-07T06:19:00Z [bio] fastq_demux/20200918-1e2c079 installed on all systems https://www.uppmax.uu.se/changelog <p>fastq_demux (A simple program to demultiplex Illumina FASTQ files based on barcodes in the FASTQ headers) version 20200918-1e2c079 installed on all systems as module fastq_demux/20200918-1e2c079.</p> Mon, 07 Mar 2022 06:19:00 GMT https://www.uppmax.uu.se/changelog 2022-03-07T06:19:00Z [bio] GAAS/1.2.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/NBISweden/GAAS">GAAS</a> (Suite of tools related to Genome Assembly Annotation Service tasks) version 1.2.0 installed on all systems as module GAAS/1.2.0.<br /> &nbsp;</p> Fri, 25 Feb 2022 15:50:00 GMT https://www.uppmax.uu.se/changelog 2022-02-25T15:50:00Z [bio] metaSNV/2.0.1 installed on all systems https://www.uppmax.uu.se/changelog <p>metaSNV (a metagenomic SNV calling pipeline.) version 2.0.1 installed on all systems as module metaSNV/2.0.1.</p> Thu, 24 Feb 2022 11:48:00 GMT https://www.uppmax.uu.se/changelog 2022-02-24T11:48:00Z [bio] metaSNV/1.0.3 installed on all systems https://www.uppmax.uu.se/changelog <p>metaSNV (a metagenomic SNV calling pipeline.) version 1.0.3 installed on all systems as module metaSNV/1.0.3.</p> Thu, 24 Feb 2022 11:47:00 GMT https://www.uppmax.uu.se/changelog 2022-02-24T11:47:00Z [apps] pandoc/2.17.1.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://pandoc.org/">pandoc</a> (Pandoc is a Haskell library for converting from one markup format to another, and a command-line tool that uses this library.) version 2.17.1.1 installed on all systems as module pandoc/2.17.1.1.<br /> &nbsp;</p> Thu, 24 Feb 2022 10:08:00 GMT https://www.uppmax.uu.se/changelog 2022-02-24T10:08:00Z [bio] RevBayes/1.1.1-mpi installed on all systems https://www.uppmax.uu.se/changelog <p>RevBayes (Bayesian phylogenetic inference using probabilistic graphical models and an interactive language.) version 1.1.1-mpi installed on all systems as module RevBayes/1.1.1-mpi.</p> Mon, 21 Feb 2022 16:43:00 GMT https://www.uppmax.uu.se/changelog 2022-02-21T16:43:00Z [bio] RevBayes/1.1.1 installed on all systems https://www.uppmax.uu.se/changelog <p>RevBayes (Bayesian phylogenetic inference using probabilistic graphical models and an interactive language.) version 1.1.1 installed on all systems as module RevBayes/1.1.1.</p> Mon, 21 Feb 2022 16:42:00 GMT https://www.uppmax.uu.se/changelog 2022-02-21T16:42:00Z [libs] boost/1.78.0-gcc11.2.0_mpi4.1.2 installed on all systems https://www.uppmax.uu.se/changelog <p>boost (free peer-reviewed portable C++ source libraries) version 1.78.0-gcc11.2.0_mpi4.1.2 installed on all systems as module boost/1.78.0-gcc11.2.0-mpi4.1.2.</p> Mon, 21 Feb 2022 16:41:00 GMT https://www.uppmax.uu.se/changelog 2022-02-21T16:41:00Z [libs] boost/1.78.0_gcc11.2.0 installed on all systems https://www.uppmax.uu.se/changelog <p>boost (free peer-reviewed portable C++ source libraries) version 1.78.0_gcc11.2.0 installed on all systems as module boost/1.78.0_gcc11.2.0.</p> Mon, 21 Feb 2022 16:41:00 GMT https://www.uppmax.uu.se/changelog 2022-02-21T16:41:00Z [comp] Intel OneAPI installed on all systems https://www.uppmax.uu.se/changelog <p>The package Intel OneAPI with subpackages are installed on all systems</p> Mon, 21 Feb 2022 12:49:00 GMT https://www.uppmax.uu.se/changelog 2022-02-21T12:49:00Z [build] cmake/3.22.2 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://cmake.org/">CMake</a> (open-source, cross-platform family of tools designed to build, test and package software) version 3.22.2 installed on all systems as module cmake/3.22.2.<br /> &nbsp;</p> Fri, 18 Feb 2022 11:21:00 GMT https://www.uppmax.uu.se/changelog 2022-02-18T11:21:00Z [apps] gromacs/2021.5.th installed on Rackham and Snowy https://www.uppmax.uu.se/changelog <p>[apps] gromacs/2021.5.th installed on Rackham and Snowy</p> Fri, 18 Feb 2022 09:26:00 GMT https://www.uppmax.uu.se/changelog 2022-02-18T09:26:00Z [bio] Kraken2/2.1.2-20211210-4f648f5 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/DerrickWood/kraken2">Kraken2</a> (a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds) version 2.1.2-20211210-4f648f5 installed on all systems as module Kraken2/2.1.2-20211210-4f648f5. This version is identical to version 2.1.2, but with a couple of small changes to account for changes in the methods of accessing some remote databases.<br /> &nbsp;</p> Sun, 13 Feb 2022 14:14:00 GMT https://www.uppmax.uu.se/changelog 2022-02-13T14:14:00Z [bio] diamond/2.0.14 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/bbuchfink/diamond">DIAMOND</a>&nbsp;(sequence aligner for protein and translated DNA searches, designed for high performance analysis of big sequence data) version 2.0.14 installed on all systems as module diamond/2.0.14.<br /> &nbsp;</p> Fri, 11 Feb 2022 14:45:00 GMT https://www.uppmax.uu.se/changelog 2022-02-11T14:45:00Z [data] ncbi_taxonomy/latest installed on all systems https://www.uppmax.uu.se/changelog <p>The <a href="https://www.uppmax.uu.se/resources/databases/ncbi-taxonomy-databases/">NCBI taxonomy databases</a> are now available through the newly installed&nbsp;data module ncbi_taxonomy/latestX. This module defines the environment variable NCBI_TAXONOMY_ROOT, which contains the location of the local UPPMAX mirror of the NCBI taxonomy databases located at /sw/data/ncbi_taxonomy/latest. See&nbsp;<a href="https://www.ncbi.nlm.nih.gov/guide/taxonomy/">https://www.ncbi.nlm.nih.gov/guide/taxonomy/</a> for more on the internal contents of the databases.</p> Fri, 11 Feb 2022 13:50:00 GMT https://www.uppmax.uu.se/changelog 2022-02-11T13:50:00Z [apps] Amber version 20 installed on Rackham and Snowy (GPU) https://www.uppmax.uu.se/changelog <p>[apps] <a href="https://ambermd.org/GetAmber.php">Amber</a>,&nbsp;a suite of biomolecular simulation programs,&nbsp;version 20 is installed on Rackham and Snowy (GPU)&nbsp;as module Amber/20 for Rackham and Amber/20-GPU for Snowy GPU with CUDA support.&nbsp;</p> Thu, 10 Feb 2022 15:05:00 GMT https://www.uppmax.uu.se/changelog 2022-02-10T15:05:00Z [bio] FusionCatcher/1.33 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/ndaniel/fusioncatcher">FusionCatcher</a> (Finder of somatic fusion-genes in RNA-seq data) version 1.33 installed on all systems as module FusionCatcher/1.33.<br /> &nbsp;</p> Thu, 10 Feb 2022 13:58:00 GMT https://www.uppmax.uu.se/changelog 2022-02-10T13:58:00Z [apps] ORCA 5.0.2 installed on Rackham and Snowy https://www.uppmax.uu.se/changelog <p><a href="https://orcaforum.kofo.mpg.de">ORCA</a>&nbsp;version 5.0.2 is installed on Rackham and Snowy as module ORCA/5.0.2. ORCA&nbsp;is a quantum-chemical software package consisting of methods in the fields of density functional theory as well as correlated wave-function based methods.</p> Thu, 10 Feb 2022 09:04:00 GMT https://www.uppmax.uu.se/changelog 2022-02-10T09:04:00Z [bio] MultiQC/1.12 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://multiqc.info">MultiQC</a> (Aggregate results from bioinformatics analyses across many samples into a single report) version 1.12 installed on all systems as module MultiQC/1.12.<br /> &nbsp;</p> Wed, 09 Feb 2022 08:55:00 GMT https://www.uppmax.uu.se/changelog 2022-02-09T08:55:00Z [bio] ngsLD/1.1.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/fgvieira/ngsLD">ngsLD</a> (Calculation of pairwise Linkage Disequilibrium (LD) under a probabilistic framework) version 1.1.1 installed on all systems as module ngsLD/1.1.1.<br /> &nbsp;</p> Tue, 01 Feb 2022 09:24:00 GMT https://www.uppmax.uu.se/changelog 2022-02-01T09:24:00Z [libs] slurm-drmaa/1.1.3-slurm19.05.8 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/natefoo/slurm-drma">slurm-drmaa</a> (DRMAA for Slurm Workload Manager (Slurm) is an implementation of Open Grid Forum Distributed Resource Management Application API (DRMAA) version 1 for submission and control of jobs to Slurm. Using DRMAA, grid applications builders, portal developers and ISVs can use the same high-level API to link their software with different cluster/resource management systems. Built against SLURM 19.05.8) version 1.1.3-slurm19.05.8 installed on all systems as module slurm-drmaa/1.1.3-slurm19.05.8. Version slurm-drmaa/1.1.3-slurm21.08.2 is installed on miarka.</p> Mon, 31 Jan 2022 15:08:00 GMT https://www.uppmax.uu.se/changelog 2022-01-31T15:08:00Z [bio] PEPPER-Margin-DeepVariant/r0.4 installed on all systems https://www.uppmax.uu.se/changelog <p>PEPPER-Margin-DeepVariant (PEPPER is a genome inference module based on recurrent neural networks that enables long-read variant calling and nanopore assembly polishing in the PEPPER-Margin-DeepVariant pipeline.) version r0.4 installed on all systems as module PEPPER-Margin-DeepVariant/r0.4.</p> Mon, 31 Jan 2022 09:07:00 GMT https://www.uppmax.uu.se/changelog 2022-01-31T09:07:00Z [bio] HUMAnN/3.0.0.a.4 installed on all systems https://www.uppmax.uu.se/changelog <p>UMAnN (\(the HMP Unified Metabolic Analysis Network\) is a method for efficiently and accurately profiling the abundance of microbial metabolic pathways and other molecular functions from metagenomic or metatranscriptomic sequencing data.) version 3.0.0.a.4 installed on all systems as module HUMAnN/3.0.0.a.4.</p> Mon, 31 Jan 2022 09:06:00 GMT https://www.uppmax.uu.se/changelog 2022-01-31T09:06:00Z [bio] Nextflow/21.10.6 installed on all systems https://www.uppmax.uu.se/changelog <p>Nextflow (A DSL for data-driven computational pipelines http://nextflow.io) version 21.10.6 installed on all systems as module Nextflow/21.10.6.</p> Mon, 31 Jan 2022 09:06:00 GMT https://www.uppmax.uu.se/changelog 2022-01-31T09:06:00Z [bio] PEPPER-Margin-DeepVariant/r0.7 installed on all systems https://www.uppmax.uu.se/changelog <p>PEPPER-Margin-DeepVariant (PEPPER is a genome inference module based on recurrent neural networks that enables long-read variant calling and nanopore assembly polishing in the PEPPER-Margin-DeepVariant pipeline.) version r0.7 installed on all systems as module PEPPER-Margin-DeepVariant/r0.7.</p> Mon, 31 Jan 2022 09:05:00 GMT https://www.uppmax.uu.se/changelog 2022-01-31T09:05:00Z [bio] DeepVariant/1.3.0 installed on all systems https://www.uppmax.uu.se/changelog <p>DeepVariant (DeepVariant is a deep learning-based variant caller that takes aligned reads (in BAM or CRAM format), produces pileup image tensors from them, classifies each tensor using a convolutional neural network, and finally reports the results in a standard VCF or gVCF file.) version 1.3.0 installed on all systems as module DeepVariant/1.3.0.</p> Mon, 31 Jan 2022 09:04:00 GMT https://www.uppmax.uu.se/changelog 2022-01-31T09:04:00Z [libs] PROJ/8.1.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://proj.org">PROJ</a> (Cartographic Projections and Coordinate Transformations Library) version 8.1.0 installed on all systems as module PROJ/8.1.0.<br /> &nbsp;</p> <p></p> Fri, 28 Jan 2022 15:51:00 GMT https://www.uppmax.uu.se/changelog 2022-01-28T15:51:00Z [bio] rMATS-turbo/4.1.2 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/Xinglab/rmats-turbo">rMATS-turbo</a> (computational tool to detect differential alternative splicing events from RNA-Seq data.) version 4.1.2 installed on all systems as module rMATS-turbo/4.1.2.<br /> &nbsp;</p> Fri, 28 Jan 2022 09:28:00 GMT https://www.uppmax.uu.se/changelog 2022-01-28T09:28:00Z [bio] SvABA/1.1.3-20201112-0f60e36 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/walaj/svaba">SvABA</a> (Structural variation and indel detection by local assembly) version 1.1.3-20201112-0f60e36 installed on all systems as module SvABA/1.1.3-20201112-0f60e36.<br /> &nbsp;</p> Thu, 27 Jan 2022 13:57:00 GMT https://www.uppmax.uu.se/changelog 2022-01-27T13:57:00Z [bio] SNP2HLA/1.0.3 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://software.broadinstitute.org/mpg/snp2hla/">SNP2HLA</a> (a tool to impute amino acid polymorphisms and single nucleotide polymorphisms in human luekocyte antigenes (HLA) within the major histocompatibility complex (MHC) region in chromosome 6) version 1.0.3 installed on all systems as module SNP2HLA/1.0.3.<br /> &nbsp;</p> Thu, 27 Jan 2022 12:52:00 GMT https://www.uppmax.uu.se/changelog 2022-01-27T12:52:00Z [bio] CNVnator/0.4.1-20200707-c73786d installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/abyzovlab/CNVnator">CNVnator</a> (a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads) version 0.4.1-20200707-c73786d installed on all systems as module CNVnator/0.4.1-20200707-c73786d.<br /> &nbsp;</p> Tue, 25 Jan 2022 15:28:00 GMT https://www.uppmax.uu.se/changelog 2022-01-25T15:28:00Z [bio] NextGenMap/0.5.5 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://cibiv.github.io/NextGenMap/">NextGenMap</a> (flexible highly sensitive short read mapping tool that handles much higher mismatch rates than comparable algorithms while still outperforming them in terms of runtime) version 0.5.5 installed on all systems as module NextGenMap/0.5.5. This is configured to be able to take advantage of GPU-containing nodes on snowy and bianca.<br /> &nbsp;</p> Mon, 24 Jan 2022 15:54:00 GMT https://www.uppmax.uu.se/changelog 2022-01-24T15:54:00Z [apps] MultiBUGS/2.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.multibugs.org/">MultiBUGS</a> (a software package for performing Bayesian inference. It builds on the existing algorithms and tools in OpenBUGS and WinBUGS, and so is applicable to the broad range of statistical models that can be fitted using BUGS-language software, but automatically parallelises the MCMC algorithm to dramatically speed up computation.) version 2.0 installed on all systems as module MultiBUGS/2.0.<br /> &nbsp;</p> Fri, 21 Jan 2022 16:16:00 GMT https://www.uppmax.uu.se/changelog 2022-01-21T16:16:00Z [bio] paml/4.9j installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://abacus.gene.ucl.ac.uk/software/paml.html">paml</a> (PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood.) version 4.9j installed on all systems as module paml/4.9j.<br /> &nbsp;</p> <p></p> Thu, 20 Jan 2022 08:48:00 GMT https://www.uppmax.uu.se/changelog 2022-01-20T08:48:00Z [apps] tesseract/4.1.3 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://tesseract-ocr.github.io">Tesseract</a> (Open-source optical character recognition (OCR) engine) version 4.1.3 installed on all systems as module tesseract/4.1.3.<br /> &nbsp;</p> Wed, 19 Jan 2022 14:44:00 GMT https://www.uppmax.uu.se/changelog 2022-01-19T14:44:00Z [bio] gmap-gsnap/2017-11-15 and gmap-gsnap/2021-12-17 nstalled on all systems https://www.uppmax.uu.se/changelog <p><a href="http://research-pub.gene.com/gmap/">gmap-gsnap</a> (Genomic Mapping and Alignment Program for mRNA and EST Sequences) versions 2017-11-15 2021-12-17 are installed on all systems as modules gmap-gsnap/2017-11-15 and gmap-gsnap/2021-12-17.<br /> &nbsp;</p> Tue, 18 Jan 2022 11:52:00 GMT https://www.uppmax.uu.se/changelog 2022-01-18T11:52:00Z [bio] TSEBRA/1.0.3-20211126-336c380 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/Gaius-Augustus/TSEBRA">TSEBRA</a> (a combiner tool that selects transcripts from gene predictions based on the support by extrisic evidence in form of introns and start/stop codons, developed to combine BRAKER1 and BRAKER2 predicitons to increase their accuracies) version 1.0.3-20211126-336c380 installed on all systems as module TSEBRA/1.0.3-20211126-336c380.<br /> &nbsp;</p> Mon, 17 Jan 2022 06:24:00 GMT https://www.uppmax.uu.se/changelog 2022-01-17T06:24:00Z [comp] git/2.34.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://git-scm.com/">git</a> (Source control management) version 2.34.1 installed on all systems as module git/2.34.1.<br /> &nbsp;</p> Mon, 10 Jan 2022 14:24:00 GMT https://www.uppmax.uu.se/changelog 2022-01-10T14:24:00Z [bio] RAxML-NG/1.1.0 and RAxML-NG/1.1.0-mpi installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/amkozlov/raxml-ng">RAxML-NG</a> (a phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion) version 1.1.0 installed on all systems as module RAxML-NG/1.1.0, statically linked with shared-memory threads support, and RAxML-NG/1.1.0-mpi, with parallelism support provided via OpenMPI.<br /> &nbsp;</p> Mon, 10 Jan 2022 14:15:00 GMT https://www.uppmax.uu.se/changelog 2022-01-10T14:15:00Z [apps] paraview/5.9.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.paraview.org/">paraview</a> (ParaView is an open-source, multi-platform data analysis and visualization application. ParaView users can quickly build visualizations to analyze their data using qualitative and quantitative techniques. ) version 5.9.1 installed on all systems as module paraview/5.9.1. Start tool with &quot;vgl_paraview&quot;.<br /> &nbsp;</p> <p></p> Wed, 22 Dec 2021 14:29:00 GMT https://www.uppmax.uu.se/changelog 2021-12-22T14:29:00Z [comp] julia/1.6.3 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://julialang.org">Julia </a>(a high-level, high-performance dynamic language for technical computing.) version 1.6.3 installed on all systems as module julia/1.6.3.<br /> &nbsp;</p> <p></p> Wed, 22 Dec 2021 11:10:00 GMT https://www.uppmax.uu.se/changelog 2021-12-22T11:10:00Z [comp] julia/1.0.5_LTS installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://julialang.org">julia</a> (Julia is a high-level, high-performance dynamic language for technical computing.) version 1.0.5_LTS installed on all systems as module julia/1.0.5_LTS.<br /> &nbsp;</p> <p></p> Wed, 22 Dec 2021 11:08:00 GMT https://www.uppmax.uu.se/changelog 2021-12-22T11:08:00Z [bio] Salmon/1.6.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://salmon.readthedocs.io/en/latest">Salmon</a> (a tool for wicked-fast transcript quantification from RNA-seq data) version 1.6.0 installed on all systems as module Salmon/1.6.0.<br /> &nbsp;</p> <p></p> Wed, 22 Dec 2021 10:25:00 GMT https://www.uppmax.uu.se/changelog 2021-12-22T10:25:00Z [bio] MetaCRAST/20200310-ed82df4 installed on all systems https://www.uppmax.uu.se/changelog <p>MetaCRAST (MetaCRAST (Metagenomic CRISPR Reference-Aided Search Tool) is a tool to detect CRISPR arrays in raw, unassembled metagenomes.) version 20200310-ed82df4 installed on all systems as module MetaCRAST/20200310-ed82df4.</p> Mon, 13 Dec 2021 13:11:00 GMT https://www.uppmax.uu.se/changelog 2021-12-13T13:11:00Z [bio] Guppy/5.0.16-gpu and Guppy/5.0.16-cpu nstalled on all systems https://www.uppmax.uu.se/changelog <p><a href="https://nanoporetech.com/nanopore-sequencing-data-analysis">Guppy</a> (Oxford Nanopore neural-net basecaller, <strong>GPU-enabled</strong>) version 5.0.16 installed on the Bianca and Snowy&nbsp;systems as module Guppy/5.0.16-gpu.</p> <p><a href="https://nanoporetech.com/nanopore-sequencing-data-analysis">Guppy</a>&nbsp;(Oxford Nanopore neural-net basecaller, <strong>CPU only</strong>) version 5.0.16&nbsp;installed on all systems as module Guppy/5.0.16-cpu.</p> Fri, 10 Dec 2021 12:53:00 GMT https://www.uppmax.uu.se/changelog 2021-12-10T12:53:00Z [bio] bismark/0.23.1 installed on all systems https://www.uppmax.uu.se/changelog <p>bismark (Bismark is a program to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step.) version 0.23.1 installed on all systems as module bismark/0.23.1</p> Wed, 08 Dec 2021 08:00:00 GMT https://www.uppmax.uu.se/changelog 2021-12-08T08:00:00Z [apps] RSPt/2021-10-04 installed on Rackham and Snowy https://www.uppmax.uu.se/changelog <p><a href="https://www.physics.uu.se/research/materials-theory/ongoing-research/code-development/rspt-main/">RSPt</a> is a code for electronic structure calculations based on the Full-Potential Linear Muffin-Tin Orbital (FP-LMTO) method.&nbsp;Version dated 2021-10-04 installed on all systems as module RSPt/2021-10-04.</p> Fri, 03 Dec 2021 12:40:00 GMT https://www.uppmax.uu.se/changelog 2021-12-03T12:40:00Z [bio] Chromium-cellranger/6.1.2 installed on all systems https://www.uppmax.uu.se/changelog <p>Chromium-cellranger (Cell line analysis system) version 6.1.2 installed on all systems as module cellranger/6.1.2.</p> Fri, 03 Dec 2021 12:31:00 GMT https://www.uppmax.uu.se/changelog 2021-12-03T12:31:00Z [bio] fastqtk/0.27 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/ndaniel/fastqtk">fastqtk</a> (fast and lightweight tool for interleaving/deinterleaving/counting/trimming FASTQ files) version 0.27 installed on all systems as module fastqtk/0.27.<br /> &nbsp;</p> Fri, 03 Dec 2021 10:17:00 GMT https://www.uppmax.uu.se/changelog 2021-12-03T10:17:00Z [apps] vim/8.2.3701 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.vim.org">vim</a> (VIM, the editor) version 8.2.3701 installed on all systems as module vim/8.2.3701.<br /> &nbsp;</p> Tue, 30 Nov 2021 09:07:00 GMT https://www.uppmax.uu.se/changelog 2021-11-30T09:07:00Z [apps] QuantumESPRESSO/6.8 installed on Rackham and Snowy https://www.uppmax.uu.se/changelog <p><a href="http://www.quantum-espresso.org" title="QuantumESPRESSO">QuantumESPRESSO</a>&nbsp;is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.&nbsp;Versions 6.8 installed on Rackham and Snowy as module QuantumESPRESSO/6.8 and QuantumESPRESSO/6.7MaX-Release, respectively.</p> Mon, 29 Nov 2021 16:07:00 GMT https://www.uppmax.uu.se/changelog 2021-11-29T16:07:00Z [bio] trimmomatic/0.39 installed on all systems https://www.uppmax.uu.se/changelog <p>trimmomatic (Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.) version 0.39 installed on all systems as module trimmomatic/0.39.</p> Wed, 17 Nov 2021 15:13:00 GMT https://www.uppmax.uu.se/changelog 2021-11-17T15:13:00Z [bio] fastp/0.23.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/OpenGene/fastp">fastp</a> (fast all-in-one preprocessing for FastQ files) version 0.23.1 installed on all systems as module fastp/0.23.1.<br /> &nbsp;</p> Sun, 14 Nov 2021 15:23:00 GMT https://www.uppmax.uu.se/changelog 2021-11-14T15:23:00Z [comp] nasm/2.15.05 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.nasm.us/">nasm</a> (Netwide Assembler (NASM), an asssembler for the x86 CPU architecture portable to nearly every modern platform, and with code generation for many platforms old and new) version 2.15.05 installed on all systems as module nasm/2.15.05.<br /> &nbsp;</p> Sun, 14 Nov 2021 15:05:00 GMT https://www.uppmax.uu.se/changelog 2021-11-14T15:05:00Z [bio] Conterminator/20200601-570993b installed on all systems https://www.uppmax.uu.se/changelog <p>Conterminator (Conterminator is an efficient method for detecting incorrectly labeled sequences across kingdoms by an exhaustive all-against-all sequence comparison.) version 20200601-570993b installed on all systems as module Conterminator/20200601-570993b.</p> Fri, 12 Nov 2021 09:17:00 GMT https://www.uppmax.uu.se/changelog 2021-11-12T09:17:00Z [apps] R_packages/4.1.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.uppmax.uu.se/support-sv//r_packages-module-guide">R_packages</a> (Omnibus package containing installations of as many R packages from CRAN, BioConductor and other user-requested sources as can be reasonably installed) version 4.1.1 installed on all systems as module R_packages/4.1.1.</p> Thu, 11 Nov 2021 15:00:00 GMT https://www.uppmax.uu.se/changelog 2021-11-11T15:00:00Z [apps] Cromwell/71 installed on all systems https://www.uppmax.uu.se/changelog <p>Cromwell (Cromwell is an open-source Workflow Management System for bioinformatics) version 71 installed on all systems as module Cromwell/71.</p> Wed, 10 Nov 2021 07:49:00 GMT https://www.uppmax.uu.se/changelog 2021-11-10T07:49:00Z [bio] vsearch/2.18.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/torognes/vsearch">vsearch</a> (Open-source alternative to USEARCH, supporting: supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, rereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting; FASTQ file analysis, filtering, conversion and merging of paired-end reads) version 2.18.0 installed on all systems as module vsearch/2.18.0.<br /> &nbsp;</p> Tue, 09 Nov 2021 15:25:00 GMT https://www.uppmax.uu.se/changelog 2021-11-09T15:25:00Z [bio] Bamsurgeon/1.3 installed on all systems https://www.uppmax.uu.se/changelog <p>Bamsurgeon (tools for adding mutations to .bam files, used for testing mutation callers) version 1.3 installed on all systems as module Bamsurgeon/1.3.</p> Tue, 09 Nov 2021 11:39:00 GMT https://www.uppmax.uu.se/changelog 2021-11-09T11:39:00Z pixy/1.2.5.beta1 installed on all systems https://www.uppmax.uu.se/changelog <p>pixy (pixy is a command-line tool for painlessly estimating average nucleotide diversity within (&pi;) and between (dxy) populations from a VCF) version 1.2.5.beta1 installed on all systems as module pixy/1.2.5.beta1.</p> Tue, 09 Nov 2021 08:29:00 GMT https://www.uppmax.uu.se/changelog 2021-11-09T08:29:00Z [bio] htslib/1.14 installed on all systems https://www.uppmax.uu.se/changelog <p>htslib (Tools for working with SAM/BAM/variant files) version 1.14 installed on all systems as module htslib/1.14.</p> Mon, 08 Nov 2021 15:53:00 GMT https://www.uppmax.uu.se/changelog 2021-11-08T15:53:00Z [bio] bcftools/1.14 installed on all systems https://www.uppmax.uu.se/changelog <p>bcftools (Tools for working with variant files) version 1.14 installed on all systems as module bcftools/1.14.</p> Mon, 08 Nov 2021 15:52:00 GMT https://www.uppmax.uu.se/changelog 2021-11-08T15:52:00Z [bio] NeuSomatic/0.2.1 installed on all systems https://www.uppmax.uu.se/changelog <p>NeuSomatic (NeuSomatic is based on deep convolutional neural networks for accurate somatic mutation detection.) version 0.2.1 installed on all systems as module NeuSomatic/0.2.1.</p> Mon, 08 Nov 2021 12:19:00 GMT https://www.uppmax.uu.se/changelog 2021-11-08T12:19:00Z [bio] samtools/1.14 installed on all systems https://www.uppmax.uu.se/changelog <p>samtools (Tools for working with SAM/BAM/variant files) version 1.14 installed on all systems as module samtools/1.14</p> Mon, 08 Nov 2021 12:14:00 GMT https://www.uppmax.uu.se/changelog 2021-11-08T12:14:00Z [bio] pysam/0.17.0-python3.9.5 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://pypi.python.org/pypi/pysam">pysam</a> (Pysam is a python module for reading and manipulating files in the SAM/BAM format) version 0.17.0-python3.9.5 installed on all systems as module pysam/0.17.0-python3.9.5.</p> Mon, 08 Nov 2021 11:51:00 GMT https://www.uppmax.uu.se/changelog 2021-11-08T11:51:00Z [bio] VIBRANT/1.2.1 installed on all systems https://www.uppmax.uu.se/changelog <p>VIBRANT (Virus Identification By iteRative ANnoTation) version 1.2.1 installed on all systems as module VIBRANT/1.2.1.</p> Mon, 08 Nov 2021 07:51:00 GMT https://www.uppmax.uu.se/changelog 2021-11-08T07:51:00Z [data] WPS-geog/4 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www2.mmm.ucar.edu/wrf/users/download/get_sources_wps_geog.html">WPS-geog</a> (WPS static geodata) version 4 installed on Rackham and Snowy as module WPS-geog/4.</p> <p></p> Thu, 28 Oct 2021 12:50:00 GMT https://www.uppmax.uu.se/changelog 2021-10-28T12:50:00Z [bio] canu/2.2 installed on all systems https://www.uppmax.uu.se/changelog <p>canu (a fork of the Celera Assembler\, designed for high-noise single-molecule sequencing \(such as the PacBio RS II/Sequel or Oxford Nanopore MinION\)) version 2.2 installed on all systems as module canu/2.2</p> Mon, 25 Oct 2021 14:04:00 GMT https://www.uppmax.uu.se/changelog 2021-10-25T14:04:00Z [bio] Flye/2.9 installed on all systems https://www.uppmax.uu.se/changelog <p>Flye (de novo assembler for single molecule sequencing reads\, such as those produced by PacBio and Oxford Nanopore Technologies) version 2.9 installed on all systems as module Flye/2.9.</p> Mon, 25 Oct 2021 14:03:00 GMT https://www.uppmax.uu.se/changelog 2021-10-25T14:03:00Z [bio] SMARTdenovo/20210224-8488de9 installed on all systems https://www.uppmax.uu.se/changelog <p>SMARTdenovo (SMARTdenovo is a de novo assembler for PacBio and Oxford Nanopore (ONT) data.) version 20210224-8488de9 installed on all systems as module SMARTdenovo/20210224-8488de9.</p> Mon, 25 Oct 2021 13:50:00 GMT https://www.uppmax.uu.se/changelog 2021-10-25T13:50:00Z [bio] NextDenovo/2.5.0 installed on all systems https://www.uppmax.uu.se/changelog <p>NextDenovo (NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT)) version 2.5.0 installed on all systems as module NextDenovo/2.5.0.</p> Mon, 25 Oct 2021 13:48:00 GMT https://www.uppmax.uu.se/changelog 2021-10-25T13:48:00Z [bio] star/2.7.9a installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/alexdobin/STAR">STAR</a> (Spliced Transcripts Alignment to a Reference) version 2.7.9a installed on all systems as module star/2.7.9a.<br /> &nbsp;</p> Wed, 20 Oct 2021 16:10:00 GMT https://www.uppmax.uu.se/changelog 2021-10-20T16:10:00Z [apps] rclone/1.56.2 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://rclone.org">rclone</a> (a command line program to manage files on cloud storage, supporting over 40 cloud storage products) version 1.56.2 installed on all systems as module rclone/1.56.2.</p> Tue, 19 Oct 2021 10:29:00 GMT https://www.uppmax.uu.se/changelog 2021-10-19T10:29:00Z [bio] NextDenovo/2.4.0 installed on all systems https://www.uppmax.uu.se/changelog <p>NextDenovo (NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT)) version 2.4.0 installed on all systems as module NextDenovo/2.4.0</p> Fri, 15 Oct 2021 04:59:00 GMT https://www.uppmax.uu.se/changelog 2021-10-15T04:59:00Z [bio] phaser/20210423-5d4926d installed on all systems https://www.uppmax.uu.se/changelog <p>phaser (phasing and Allele Specific Expression from RNA-seq) version 20210423-5d4926d installed on all systems as module phaser/20210423-5d4926d</p> Fri, 15 Oct 2021 04:54:00 GMT https://www.uppmax.uu.se/changelog 2021-10-15T04:54:00Z [bio] Racon/1.4.21 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/lbcb-sci/racon">Racon</a> (Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads) version 1.4.21 installed on all systems as module Racon/1.4.21.<br /> &nbsp;</p> Mon, 11 Oct 2021 15:17:00 GMT https://www.uppmax.uu.se/changelog 2021-10-11T15:17:00Z [bio] ucsc-utilities/v421 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://hgdownload.soe.ucsc.edu/admin/exe/">UCSC utilities</a> (Kent bioinformatics utilities) version v421 installed on all systems as module ucsc-utilities/v421.<br /> &nbsp;</p> Fri, 08 Oct 2021 15:43:00 GMT https://www.uppmax.uu.se/changelog 2021-10-08T15:43:00Z [bio] snakemake/6.9.1 installed on all systems https://www.uppmax.uu.se/changelog <p>snakemake (The Snakemake workflow management system is a tool to create reproducible and scalable data analyses) version 6.9.1 installed on all systems as module snakemake/6.9.1.</p> Mon, 04 Oct 2021 08:12:00 GMT https://www.uppmax.uu.se/changelog 2021-10-04T08:12:00Z [bio] NgsRelate/2.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/ANGSD/NgsRelate">NgsRelate</a> (Infers relatedness, inbreeding coefficients and many other summary statistics for pairs of individuals from low coverage Next Generation Sequencing (NGS) data by using genotype likelihoods instead of called genotypes. ) version 2.0 installed on all systems as module NgsRelate/2.0.<br /> &nbsp;</p> <p></p> Tue, 21 Sep 2021 15:25:00 GMT https://www.uppmax.uu.se/changelog 2021-09-21T15:25:00Z [bio] maker/3.01.04 installed on all systems https://www.uppmax.uu.se/changelog <p>maker (Portable and easily configurable genome annotation pipeline) version 3.01.04 installed on all systems as module maker/3.01.04</p> Tue, 21 Sep 2021 15:18:00 GMT https://www.uppmax.uu.se/changelog 2021-09-21T15:18:00Z [bio] nf-core-pipelines/latest installed on all systems https://www.uppmax.uu.se/changelog <p>nf-core-pipelines (pipelines that are currently available as part of nf-core) version latest installed on all systems as module nf-core-pipelines/latest</p> Tue, 21 Sep 2021 15:17:00 GMT https://www.uppmax.uu.se/changelog 2021-09-21T15:17:00Z [bio] alphafold/2.0.0 installed on all systems https://www.uppmax.uu.se/changelog <p>alphafold (This package provides an implementation of the inference pipeline of AlphaFold v2.0.) version 2.0.0 installed on all systems as module alphafold/2.0.0</p> Tue, 21 Sep 2021 15:16:00 GMT https://www.uppmax.uu.se/changelog 2021-09-21T15:16:00Z [bio] MACS/3.0.0a6 installed on all systems https://www.uppmax.uu.se/changelog <p>MACS (Model-based Analysis of ChIP-Seq) version 3.0.0a6 installed on all systems as module MACS/3.0.0a6.</p> Mon, 20 Sep 2021 06:33:00 GMT https://www.uppmax.uu.se/changelog 2021-09-20T06:33:00Z [bio] IMAP/1.0 installed on all systems https://www.uppmax.uu.se/changelog <p>IMAP (Chromosome-level genome assembler combining multiple de novo assemblies) version 1.0 installed on all systems as module IMAP/1.0.<br /> https://github.com/jkimlab/IMAP<br /> rackham, irma, bianca, snowy<br /> 1.0.0</p> Thu, 09 Sep 2021 08:22:00 GMT https://www.uppmax.uu.se/changelog 2021-09-09T08:22:00Z [bio] trinity/2.13.2 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/trinityrnaseq/trinityrnaseq/wiki">trinity</a> (assembles transcript sequences from Illumina RNA-Seq data) version 2.13.2 installed on all systems as module trinity/2.13.2.<br /> &nbsp;</p> Thu, 09 Sep 2021 07:32:00 GMT https://www.uppmax.uu.se/changelog 2021-09-09T07:32:00Z [apps] R/4.1.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.r-project.org">R</a> (free software environment for statistical computing and graphics) version 4.1.1 installed on all systems as module R/4.1.1. Its version of the omnibus R_packages module is not yet installed.</p> Mon, 06 Sep 2021 13:06:00 GMT https://www.uppmax.uu.se/changelog 2021-09-06T13:06:00Z [libs] cairo/1.17.4 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.cairographics.org/">cairo</a> (a 2D graphics library with support for multiple output devices) version 1.17.4 installed on all systems as module cairo/1.17.4.<br /> &nbsp;</p> Mon, 06 Sep 2021 09:52:00 GMT https://www.uppmax.uu.se/changelog 2021-09-06T09:52:00Z [apps] texlive/2021 installed on all systems https://www.uppmax.uu.se/changelog <p>A full installation of&nbsp;<a href="https://www.tug.org/texlive/">TeX Live</a> (a straightforward way to get up and running with the TeX document production system) version 2021 installed on all systems as module texlive/2021.</p> Tue, 31 Aug 2021 15:41:00 GMT https://www.uppmax.uu.se/changelog 2021-08-31T15:41:00Z [apps] SAIGE/0.44.6.5 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/weizhouUMICH/SAIGE">SAIGE</a> (an R package with Scalable and Accurate Implementation of Generalized mixed model (Chen, H. et al. 2016). It accounts for sample relatedness and is feasible for genetic association tests in large cohorts and biobanks (N &gt; 400,000).) version 0.44.6.5 installed on all systems as module SAIGE/0.44.6.5.<br /> &nbsp;</p> Fri, 27 Aug 2021 15:13:00 GMT https://www.uppmax.uu.se/changelog 2021-08-27T15:13:00Z [libs] ARPACK-NG/3.8.0 installed on all systems https://www.uppmax.uu.se/changelog <p>[libs] ARPACK-NG/3.8.0 installed on all systems<br /> ARPACK-NG (ARPACK-NG is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.) version 3.8.0 installed on all systems as module ARPACK-NG/3.8.0.<br /> https://github.com/opencollab/arpack-ng</p> <p></p> Wed, 18 Aug 2021 12:49:00 GMT https://www.uppmax.uu.se/changelog 2021-08-18T12:49:00Z [libs] SuperLU/5.2.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/xiaoyeli/superlu">SuperLU</a> (a set of subroutines to solve a sparse linear system A*X=B.) version 5.2.1 installed on all systems as module SuperLU/5.2.1.<br /> &nbsp;</p> Tue, 17 Aug 2021 10:07:00 GMT https://www.uppmax.uu.se/changelog 2021-08-17T10:07:00Z [bio] medaka/1.4.3 Installed on all systems https://www.uppmax.uu.se/changelog <p>[bio] medaka/1.4.3 Installed on all systems</p> Mon, 16 Aug 2021 07:45:00 GMT https://www.uppmax.uu.se/changelog 2021-08-16T07:45:00Z [libs] SymEngine/0.7.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/symengine/symengine">SymEngine</a> (standalone fast C++ symbolic manipulation library) version 0.7.0 installed on all systems as module SymEngine/0.7.0.</p> Thu, 12 Aug 2021 10:54:00 GMT https://www.uppmax.uu.se/changelog 2021-08-12T10:54:00Z [bio] nf-core/2.1 Installed on all systems https://www.uppmax.uu.se/changelog <p>[bio] nf-core/2.1 Installed on all systems</p> Tue, 10 Aug 2021 09:07:00 GMT https://www.uppmax.uu.se/changelog 2021-08-10T09:07:00Z [bio] InterProScan/5.52-86.0 Installed on all systems https://www.uppmax.uu.se/changelog <p>[bio] InterProScan/5.52-86.0 Installed on all systems</p> Mon, 09 Aug 2021 10:54:00 GMT https://www.uppmax.uu.se/changelog 2021-08-09T10:54:00Z [bio] Stacks/2.59 installed on all systems https://www.uppmax.uu.se/changelog <p>Stacks version 2.59 installed on all systems as module Stacks/2.59.</p> Fri, 06 Aug 2021 10:14:00 GMT https://www.uppmax.uu.se/changelog 2021-08-06T10:14:00Z [bio] TSEBRA/1.0.2-20210716-1f167ad installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/Gaius-Augustus/TSEBRA">TSEBRA</a> (a combiner tool that selects transcripts from gene predictions based on the support by extrisic evidence in form of introns and start/stop codons, developed to combine BRAKER1 and BRAKER2 predicitons to increase their accuracies) version 1.0.2-20210716-1f167ad installed on all systems as module TSEBRA/1.0.2-20210716-1f167ad.<br /> &nbsp;</p> Mon, 19 Jul 2021 09:01:00 GMT https://www.uppmax.uu.se/changelog 2021-07-19T09:01:00Z [bio] braker/2.1.6 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/Gaius-Augustus/BRAKER">braker</a> (pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes) version 2.1.6 installed on all systems as module braker/2.1.6.<br /> &nbsp;</p> Wed, 07 Jul 2021 19:41:00 GMT https://www.uppmax.uu.se/changelog 2021-07-07T19:41:00Z [bio] ProtHint/2.6.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/gatech-genemark/ProtHint">ProtHint</a> (pipeline for predicting and scoring hints \(in the form of introns\, start and stop codons\) in the genome of interest by mapping and spliced aligning predicted genes to a database of reference protein sequences) version 2.6.0 installed on all systems as module ProtHint/2.6.0.<br /> &nbsp;</p> Wed, 07 Jul 2021 19:08:00 GMT https://www.uppmax.uu.se/changelog 2021-07-07T19:08:00Z [bio] GeneMark/4.68-es installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://exon.gatech.edu/GeneMark">GeneMark</a> (Gene prediction in eurkaryotes) version 4.68-es installed on all systems as module GeneMark/4.68-es.<br /> &nbsp;</p> Wed, 07 Jul 2021 18:59:00 GMT https://www.uppmax.uu.se/changelog 2021-07-07T18:59:00Z [bio] PathPhynder Installed on all systems https://www.uppmax.uu.se/changelog <p>A workflow for ancient DNA placement into reference phylogenies.</p> Tue, 06 Jul 2021 12:57:00 GMT https://www.uppmax.uu.se/changelog 2021-07-06T12:57:00Z [bio] Phynder Installed on all systems https://www.uppmax.uu.se/changelog <p>Efficient likelihood calculations to place samples into a phylogenetic tree. In particular, phynder was originally designed for placing male ancient DNA samples into the Y chromosome phylogeny, when there are arbitrarily high rates of missing data. It has also been used for assigning ancient samples to whole mitochondrial genome phylogenies.</p> Tue, 06 Jul 2021 12:43:00 GMT https://www.uppmax.uu.se/changelog 2021-07-06T12:43:00Z [libs] plumed/2.7.1-gcc installed on Rackham https://www.uppmax.uu.se/changelog <p>plumed version 2.7.1-gcc installed on Rackham as module plumed/2.7.1-gcc.<br /> https://www.plumed.org</p> <p></p> Tue, 06 Jul 2021 12:26:00 GMT https://www.uppmax.uu.se/changelog 2021-07-06T12:26:00Z [apps] cp2k/8.1-gcc installed on Rackham https://www.uppmax.uu.se/changelog <p>cp2k (CP2K is a quantum chemistry and solid state physics software package that can perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems.) version 8.1-gcc installed on all systems as module cp2k/8.1-gcc.<br /> <a href="https://www.cp2k.org">https://www.cp2k.org/</a></p> Tue, 06 Jul 2021 08:22:00 GMT https://www.uppmax.uu.se/changelog 2021-07-06T08:22:00Z [bio] MultiQC/1.11 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://multiqc.info">MultiQC</a> (Aggregate results from bioinformatics analyses across many samples into a single report) version 1.11 installed on all systems as module MultiQC/1.11.<br /> &nbsp;</p> Mon, 05 Jul 2021 10:17:00 GMT https://www.uppmax.uu.se/changelog 2021-07-05T10:17:00Z [bio] IMPUTE5/1.1.5 installed on all systems https://www.uppmax.uu.se/changelog <p>IMPUTE5 (IMPUTE 5 is a genotype imputation method that can scale to reference panels with millions of samples.) version 1.1.5 installed on all systems as module IMPUTE5/1.1.5.<br /> https://jmarchini.org/software/&#35;impute-5</p> Tue, 22 Jun 2021 13:15:00 GMT https://www.uppmax.uu.se/changelog 2021-06-22T13:15:00Z [comp] julia/1.6.1 installed on all systems https://www.uppmax.uu.se/changelog <p>julia version 1.6.1 installed on all systems as module julia/1.6.1</p> Tue, 22 Jun 2021 09:38:00 GMT https://www.uppmax.uu.se/changelog 2021-06-22T09:38:00Z [bio] bonito/0.3.7-cpu installed on all systems https://www.uppmax.uu.se/changelog <p>bonito version 0.3.7-cpu installed on all systems as module bonito/0.3.7-cpu.<br /> https://github.com/nanoporetech/bonito/issues/70</p> Fri, 18 Jun 2021 13:22:00 GMT https://www.uppmax.uu.se/changelog 2021-06-18T13:22:00Z [comp] python/3.9.5 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://python.org/">Python</a> (programming language plus a handful of widely used packages) version 3.9.5 installed on all systems as module python/3.9.5. The module python3/3.9.5 is available that will not conflict with a python/2.y.z module. For a list of installed packages, including numpy and scipy, see the module help or run&nbsp;'pip3 list' when the module is loaded.</p> Thu, 03 Jun 2021 13:34:00 GMT https://www.uppmax.uu.se/changelog 2021-06-03T13:34:00Z [apps] emacs/27.2 installed on all systems https://www.uppmax.uu.se/changelog <p>[apps] emacs/27.2 installed on all systems</p> Thu, 03 Jun 2021 08:07:00 GMT https://www.uppmax.uu.se/changelog 2021-06-03T08:07:00Z [bio] pizzly/0.37.3 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/pmelsted/pizzly">pizzly</a> (Fast fusion detection using kallisto) version 0.37.3 installed on all systems as module pizzly/0.37.3.</p> Wed, 02 Jun 2021 12:04:00 GMT https://www.uppmax.uu.se/changelog 2021-06-02T12:04:00Z [bio] EDirect/15.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.ncbi.nlm.nih.gov/books/NBK179288/">EDirect</a> (EDirect provides access to the NCBI's suite of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a Unix terminal window) version 15.1 installed on all systems as module EDirect/15.1.<br /> &nbsp;</p> Mon, 31 May 2021 12:55:00 GMT https://www.uppmax.uu.se/changelog 2021-05-31T12:55:00Z [bio] gffread/0.12.6 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/gpertea/gffread">gffread</a> (GFF/GTF utility providing format conversions, filtering, FASTA sequence extraction and more) version 0.12.6 installed on all systems as module gffread/0.12.6.<br /> &nbsp;</p> Mon, 31 May 2021 12:18:00 GMT https://www.uppmax.uu.se/changelog 2021-05-31T12:18:00Z [libs] MPC/1.2.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://www.multiprecision.org/mpc/">MPC</a> (library for the arithmetic of complex numbers with arbitrarily high precision and correct rounding of the result) version 1.2.1 installed on all systems as module MPC/1.2.1.<br /> &nbsp;</p> Fri, 28 May 2021 12:51:00 GMT https://www.uppmax.uu.se/changelog 2021-05-28T12:51:00Z [bio] KAT/2.4.2 now based on python/3.7.2 https://www.uppmax.uu.se/changelog <p>The previous Kmer Analysis Toolkit module KAT/2.4.2, based on python/3.5.0, is moved to the name KAT/2.4.2_py3.5.0 and deprecated. The previous module KAT/2.4.2_py3.7.2 is renamed KAT/2.4.2, and KAT/2.4.2_py3.7.2 is an alias.</p> Fri, 28 May 2021 12:02:00 GMT https://www.uppmax.uu.se/changelog 2021-05-28T12:02:00Z [bio] annovar/2020.06.08 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://annovar.openbioinformatics.org/en/latest/">ANNOVAR</a> (an efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes) version 2020.06.08 installed on all systems as module annovar/2020.06.08.&nbsp; The databases have been organised into data modules and the latest are found in the data module annovar_data/2021.05.18.</p> Fri, 28 May 2021 11:58:00 GMT https://www.uppmax.uu.se/changelog 2021-05-28T11:58:00Z [bio] FALCON/2018.31.08-03.06 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/PacificBiosciences/FALCON_unzip/wiki/Binaries">FALCON</a> (PacBio diploid assembler) version 2018.31.08-03.06 installed on all systems as module FALCON/2018.31.08-03.06.</p> Tue, 18 May 2021 11:22:00 GMT https://www.uppmax.uu.se/changelog 2021-05-18T11:22:00Z [bio] trinotate/3.2.2 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/Trinotate/Trinotate.github.io/wiki">Trinotate</a> (comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms) version 3.2.2 installed on all systems as module trinotate/3.2.2.<br /> &nbsp;</p> Wed, 12 May 2021 15:11:00 GMT https://www.uppmax.uu.se/changelog 2021-05-12T15:11:00Z [libs] OpenBLAS 0.3.15 installed in several versions on all clusters https://www.uppmax.uu.se/changelog <p><a href="https://github.com/xianyi/OpenBLAS">OpenBLAS</a> (an optimized BLAS library based on GotoBLAS2 1.13 BSD version) version 0.3.15 is now installed in several module versions on all clusters.</p> <p>openblas/0.3.15 has standard multithreading support. openblas/0.3.15-openmp supports OpenMP multithreading.&nbsp; openblas/0.3.15-singlethread does not have multithreading support.</p> Tue, 11 May 2021 13:06:00 GMT https://www.uppmax.uu.se/changelog 2021-05-11T13:06:00Z [comp] bison/3.7.6 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.gnu.org/software/bison/">bison</a> (a general-purpose parser generator that converts an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables) version 3.7.6 installed on all systems as module bison/3.7.6.<br /> &nbsp;</p> Tue, 11 May 2021 09:01:00 GMT https://www.uppmax.uu.se/changelog 2021-05-11T09:01:00Z [comp] flex/2.6.4 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/westes/flex">flex</a> (The Fast Lexical Analyzer - scanner generator for lexing in C and C++) version 2.6.4 installed on all systems as module flex/2.6.4.<br /> &nbsp;</p> Tue, 11 May 2021 08:23:00 GMT https://www.uppmax.uu.se/changelog 2021-05-11T08:23:00Z [bio] CheckM/1.1.3 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://ecogenomics.github.io/CheckM/">CheckM</a> (Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes) version 1.1.3 installed on all systems as module CheckM/1.1.3.<br /> &nbsp;</p> Wed, 05 May 2021 12:24:00 GMT https://www.uppmax.uu.se/changelog 2021-05-05T12:24:00Z [bio] metaWRAP/1.3.2 installed on all systems https://www.uppmax.uu.se/changelog <p>metaWRAP (MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis) version 1.3.2 installed on all systems as module metaWRAP/1.3.2.</p> Tue, 04 May 2021 13:18:00 GMT https://www.uppmax.uu.se/changelog 2021-05-04T13:18:00Z [bio] SMC++/1.15.2 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/popgenmethods/smcpp">SMC++</a> (infers population history from whole-genome sequence data) version 1.15.2 installed on all systems as module SMC++/1.15.2.<br /> &nbsp;</p> Tue, 04 May 2021 10:31:00 GMT https://www.uppmax.uu.se/changelog 2021-05-04T10:31:00Z [bio] ArrowGrid/20191022-9759eb1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/skoren/ArrowGrid">ArrowGrid</a> (parallel wrapper around the Arrow consensus framework within the SMRT Analysis Software) version 20191022-9759eb1 installed on all systems as module ArrowGrid/20191022-9759eb1.&nbsp;This module has rough support for submitting multiple jobs through SLURM and we have attempted to give appropriate defaults to its SLURM parameters. See its documentation for specifying a CONFIG file.</p> Thu, 29 Apr 2021 15:55:00 GMT https://www.uppmax.uu.se/changelog 2021-04-29T15:55:00Z [bio] pbbam/1.6.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/PacificBiosciences/pbbam">pbbam</a> (software package provides components to create, query, &amp; edit PacBio BAM files and associated indices, including a core C++ library, bindings for additional languages, and command-line utilities) version 1.6.0 installed on all systems as module pbbam/1.6.0.<br /> &nbsp;</p> Thu, 29 Apr 2021 15:24:00 GMT https://www.uppmax.uu.se/changelog 2021-04-29T15:24:00Z [build] ninja/1.10.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://ninja-build.org/">ninja</a> (a small build system with a focus on speed) version 1.10.0 installed on all systems as module ninja/1.10.0.<br /> &nbsp;</p> Thu, 29 Apr 2021 15:06:00 GMT https://www.uppmax.uu.se/changelog 2021-04-29T15:06:00Z [build] meson/0.57.2 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://mesonbuild.com/">meson</a> (open source build system meant to be both extremely fast, and, even more importantly, as user friendly as possible) version 0.57.2 installed on all systems as module meson/0.57.2.<br /> &nbsp;</p> Thu, 29 Apr 2021 14:48:00 GMT https://www.uppmax.uu.se/changelog 2021-04-29T14:48:00Z [bio] snippy/4.6.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/tseemann/snippy">snippy </a>(finds SNPs between a haploid reference genome and your NGS sequence reads.) version 4.6.0 installed on all systems as module snippy/4.6.0.<br /> &nbsp;</p> <p></p> Thu, 29 Apr 2021 14:13:00 GMT https://www.uppmax.uu.se/changelog 2021-04-29T14:13:00Z [bio] HUMAnN/3.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/biobakery/humann3">HUMAnN </a>((the HMP Unified Metabolic Analysis Network) is a method for efficiently and accurately profiling the abundance of microbial metabolic pathways and other molecular functions from metagenomic or metatranscriptomic sequencing data.) version 3.0 installed on all systems as module HUMAnN/3.0.<br /> &nbsp;</p> <p></p> Thu, 29 Apr 2021 11:59:00 GMT https://www.uppmax.uu.se/changelog 2021-04-29T11:59:00Z [bio] KneadData/0.10.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/biobakery/kneaddata">KneadData</a> (is a tool designed to perform quality control on metagenomic and metatranscriptomic sequencing data, especially data from microbiome experiments.) version 0.10.0 installed on all systems as module KneadData/0.10.0.<br /> &nbsp;</p> <p></p> Thu, 29 Apr 2021 11:58:00 GMT https://www.uppmax.uu.se/changelog 2021-04-29T11:58:00Z [bio] PhyloPhlAn/3.0.2 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/biobakery/phylophlan/wiki">PhyloPhlAn</a> (is an integrated pipeline for large-scale phylogenetic profiling of genomes and metagenomes.) version 3.0.2 installed on all systems as module PhyloPhlAn/3.0.2.<br /> &nbsp;</p> <p></p> Thu, 29 Apr 2021 11:57:00 GMT https://www.uppmax.uu.se/changelog 2021-04-29T11:57:00Z [bio] MetaPhlAn3/3.0.8 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://huttenhower.sph.harvard.edu/metaphlan/">MetaPhlAn3 </a>(is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea and Eukaryotes) from metagenomic shotgun sequencing data (i.e. not 16S) with species-level.) version 3.0.8 installed on all systems as module MetaPhlAn3/3.0.8.<br /> &nbsp;</p> <p></p> Thu, 29 Apr 2021 11:55:00 GMT https://www.uppmax.uu.se/changelog 2021-04-29T11:55:00Z [bio] BioBakery/3.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/biobakery">BioBakery</a> (microbial community profiling) version 3.0 installed on all systems as module BioBakery/3.0.<br /> It is a metapackage&nbsp;including:&nbsp;HUMAnN/3.0,&nbsp;KneadData/0.10.0,&nbsp;MetaPhlAn3/3.0.8 and<br /> PhyloPhlAn/3.0.2</p> <p></p> <p></p> Thu, 29 Apr 2021 11:50:00 GMT https://www.uppmax.uu.se/changelog 2021-04-29T11:50:00Z [bio] MELT modules have been removed https://www.uppmax.uu.se/changelog <p>To use <a href="https://melt.igs.umaryland.edu/index.php">MELT</a> software (Mobile Element Locator Tool), each potential user must agree to its software license. As a result, we cannot provide MELT through the module system, and have removed the MELT/2.0.2 and MELT/2.2.2 modules.&nbsp; Each user that wishes to use MELT must agree to the MELT license and install the software for themselves.&nbsp; Note that if&nbsp;the software is installed for a research group, each user in the research group must agree to the MELT license as well.</p> Tue, 27 Apr 2021 09:51:00 GMT https://www.uppmax.uu.se/changelog 2021-04-27T09:51:00Z [bio] Salmon/1.4.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://salmon.readthedocs.io/en/latest">Salmon</a> (a tool for wicked-fast transcript quantification from RNA-seq data) version 1.4.0 installed on all systems as module Salmon/1.4.0.</p> Fri, 23 Apr 2021 14:15:00 GMT https://www.uppmax.uu.se/changelog 2021-04-23T14:15:00Z [bio] bonito/0.3.8 and bonito/0.3.8-cpu installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/nanoporetech/bonito">bonito</a> (a PyTorch Basecaller for Oxford Nanopore Reads) version 0.3.8 for GPUs installed on snowy and bianca as module bonito/0.3.8.&nbsp; Version 0.3.8 for CPUs only has been installed as module bonito/0.3.8-cpu on all systems.</p> <p>All training models have also been downloaded for both, see 'module help bonito/0.3.8' or 'module help bonito/0.3.8-cpu' for more information.<br /> &nbsp;</p> Fri, 23 Apr 2021 08:35:00 GMT https://www.uppmax.uu.se/changelog 2021-04-23T08:35:00Z [bio] unimap/0.1-r46-dirty installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/lh3/unimap">unimap</a> (fork of minimap2 optimized for assembly-to-reference alignment) version 0.1-r46-dirty installed on all systems as module unimap/0.1-r46-dirty.<br /> &nbsp;</p> Thu, 22 Apr 2021 15:11:00 GMT https://www.uppmax.uu.se/changelog 2021-04-22T15:11:00Z [bio] minimap2/2.18-r1015 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/lh3/minimap2">minimap2</a> (versatile pairwise aligner for genomic and spliced nucleotide sequences) version 2.18-r1015 installed on all systems as module minimap2/2.18-r1015. In addition to minimap2, this installation provides the sdust too, the paftools.js tool for manipulating paf-format alignments, and the minimap2.py python wrapper.</p> Thu, 22 Apr 2021 15:02:00 GMT https://www.uppmax.uu.se/changelog 2021-04-22T15:02:00Z [comp] k8/0.2.5 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/attractivechaos/k8">k8</a> (Javascript shell based on Google's V8 Javascript engine which adds the support of flexible byte arrays and file I/O) version 0.2.5 installed on all systems as module k8/0.2.5.&nbsp; k8 is designed for enabling Javascript as a general scripting language, rather than server-side operations.&nbsp;<br /> &nbsp;</p> Thu, 22 Apr 2021 14:13:00 GMT https://www.uppmax.uu.se/changelog 2021-04-22T14:13:00Z [libs] slurm-drmaa/1.1.2-slurm19.05.8 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/natefoo/slurm-drmaa">slurm-drmaa</a> (DRMAA for Slurm: Implementation of the DRMAA C bindings for Slurm) version 1.1.2-slurm19.05.8 installed on all systems as module slurm-drmaa/1.1.2-slurm19.05.8.</p> Wed, 21 Apr 2021 11:19:00 GMT https://www.uppmax.uu.se/changelog 2021-04-21T11:19:00Z [bio] NextPolish/1.3.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/Nextomics/NextPolish">NextPolish</a> (fix base errors (SNV/Indel) in the genome generated by noisy long reads, it can be used with short read data only or long read data only or a combination of both) version 1.3.1 installed on all systems as module NextPolish/1.3.1.<br /> &nbsp;</p> Wed, 21 Apr 2021 11:18:00 GMT https://www.uppmax.uu.se/changelog 2021-04-21T11:18:00Z [apps] jq/1.6 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://stedolan.github.io/jq/">jq</a> (a lightweight and flexible command-line JSON processor) version 1.6 installed on all systems as module jq/1.6.</p> Fri, 16 Apr 2021 13:39:00 GMT https://www.uppmax.uu.se/changelog 2021-04-16T13:39:00Z [apps] Tcl-Tk/8.6.11 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.tcl.tk/">Tcl-Tk</a> (Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more. Tk is a graphical user interface toolkit that takes developing desktop applications to a higher level than conventional approaches. Tk is the standard GUI for Tcl) version 8.6.11 installed on all systems as module Tcl-Tk/8.6.11.</p> Fri, 16 Apr 2021 13:38:00 GMT https://www.uppmax.uu.se/changelog 2021-04-16T13:38:00Z [apps] FFmpeg/4.4 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://ffmpeg.org">FFmpeg</a> (A complete, cross-platform solution to record, convert and stream audio and video) version 4.4 installed on all systems as module FFmpeg/4.4.</p> Fri, 16 Apr 2021 13:36:00 GMT https://www.uppmax.uu.se/changelog 2021-04-16T13:36:00Z [apps] COIN-OR-OptimizationSuite/1.8.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/coin-or/COIN-OR-OptimizationSuite">COIN-OR-OptimizationSuite</a> (a collection of interoperable open source solvers from the respository of open source software maintained by the COIN-OR Foundation) version 1.8.0 installed on all systems as module COIN-OR-OptimizationSuite/1.8.0.<br /> &nbsp;</p> Fri, 16 Apr 2021 13:35:00 GMT https://www.uppmax.uu.se/changelog 2021-04-16T13:35:00Z [apps] R_packages/4.0.4 installed on all systems https://www.uppmax.uu.se/changelog <p>An omnibus collection of R packages for R/4.0.4 has been installed on all systems as module <a href="https://www.uppmax.uu.se/support-sv//r_packages-module-guide">R_packages/4.0.4</a>.&nbsp;There are a total of 20663 CRAN and BioConductor packages installed, out of 20751 packages available.&nbsp;17354 CRAN packages are installed, out of 17428 available. 3309 BioConductor-specific packages are installed, out of 3323 available.</p> <p>Some packages may require the loading of other modules to function correctly. For example, the Rmpi package requires loading openmpi/3.1.5 after loading R_packages/4.0.4. For more information, see 'module help R_packages/4.0.4'.</p> Fri, 16 Apr 2021 13:17:00 GMT https://www.uppmax.uu.se/changelog 2021-04-16T13:17:00Z [comp] yasm/1.3.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://yasm.tortall.net/">Yasm</a> (Yasm is a complete rewrite of the NASM assembler under the 'new'&nbsp;BSD License) version 1.3.0 installed on all systems as module yasm/1.3.0.<br /> &nbsp;</p> Tue, 13 Apr 2021 14:30:00 GMT https://www.uppmax.uu.se/changelog 2021-04-13T14:30:00Z [libs] GEOS/3.9.1-gcc9.3.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://trac.osgeo.org/geos/">GEOS</a> (GEOS (Geometry Engine - Open Source) is a C++ port of the ​JTS Topology Suite (JTS). It aims to contain the complete functionality of JTS in C++. This includes all the ​OpenGIS Simple Features for SQL spatial predicate functions and spatial operators, as well as specific JTS enhanced functions. GEOS provides spatial functionality to many other projects and products.) version 3.9.1 compiled with gcc/9.3.0 is now installed on all systems as module GEOS/3.9.1-gcc9.3.0.<br /> &nbsp;</p> Tue, 13 Apr 2021 13:25:00 GMT https://www.uppmax.uu.se/changelog 2021-04-13T13:25:00Z [bio] BOLT-LMM/2.3.5 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://alkesgroup.broadinstitute.org/BOLT-LMM/BOLT-LMM_manual.html#x1-20001">BOLT-LMM </a>(software package currently consists of two main algorithms, the BOLT-LMM algorithm for mixed model association testing, and the BOLT-REML algorithm for variance components analysis (i.e., partitioning of SNP-heritability and estimation of genetic correlations). ) version 2.3.5 installed on all systems as module BOLT-LMM/2.3.5.<br /> &nbsp;</p> Tue, 13 Apr 2021 13:18:00 GMT https://www.uppmax.uu.se/changelog 2021-04-13T13:18:00Z [bio] HESS/0.5.4-beta installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://huwenboshi.github.io/hess/">HESS</a> (HESS (Heritability Estimation from Summary Statistics) is a software package for estimating and visualizing local SNP-heritability and genetic covariance (correlation) from GWAS summary association data.) version 0.5.4-beta installed on all systems as module HESS/0.5.4-beta.<br /> &nbsp;</p> Tue, 13 Apr 2021 10:30:00 GMT https://www.uppmax.uu.se/changelog 2021-04-13T10:30:00Z [apps] openbabel/3.1.1-gcc9.3.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/openbabel/openbabel">Open Babel</a>&nbsp;(chemical toolbox designed to speak the many languages of chemical data, compiled with gcc 9.3.0) version 3.1.1-gcc9.3.0 installed on all systems as module openbabel/3.1.1-gcc9.3.0.<br /> &nbsp;</p> Fri, 09 Apr 2021 16:00:00 GMT https://www.uppmax.uu.se/changelog 2021-04-09T16:00:00Z [apps] OpenBUGS/3.2.3 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://www.openbugs.net">OpenBUGS</a> (software package for performing Bayesian inference Using Gibbs Sampling) version 3.2.3 installed on all systems as module OpenBUGS/3.2.3.<br /> &nbsp;</p> Fri, 09 Apr 2021 14:50:00 GMT https://www.uppmax.uu.se/changelog 2021-04-09T14:50:00Z [bio] MetaPhlAn3/3.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://huttenhower.sph.harvard.edu/metaphlan/">MetaPhlAn3</a> (is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea and Eukaryotes) from metagenomic shotgun sequencing data (i.e. not 16S) with species-level.) version 3.0 installed on all systems as module MetaPhlAn3/3.0.</p> <p></p> Fri, 09 Apr 2021 14:19:00 GMT https://www.uppmax.uu.se/changelog 2021-04-09T14:19:00Z [bio] SLiM/3.6 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://messerlab.org/slim/">SLiM</a> (An evolutionary simulation framework that combines a powerful engine for population genetic simulations with the capability of modeling arbitrarily complex evolutionary scenarios.) version 3.6 installed on all systems as module SLiM/3.6.</p> <p></p> Thu, 08 Apr 2021 13:40:00 GMT https://www.uppmax.uu.se/changelog 2021-04-08T13:40:00Z [apps] ROOT/6.22.08 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://root.cern.ch/">ROOT</a> (modular scientific software toolkit. It provides all the functionalities needed to deal with big data processing, statistical analysis, visualisation and storage) version 6.22.08 installed on all systems as module ROOT/6.22.08.<br /> &nbsp;</p> Thu, 08 Apr 2021 13:36:00 GMT https://www.uppmax.uu.se/changelog 2021-04-08T13:36:00Z [apps] ImageMagick/7.0.11-3 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.imagemagick.org">ImageMagick</a> (create, edit, compose, or convert digital images) version 7.0.11-3 installed on all systems as module ImageMagick/7.0.11-3.<br /> &nbsp;</p> Tue, 06 Apr 2021 12:12:00 GMT https://www.uppmax.uu.se/changelog 2021-04-06T12:12:00Z [bio] MultiQC/1.10.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://multiqc.info">MultiQC</a> (Aggregate results from bioinformatics analyses across many samples into a single report) version 1.10.1 installed on all systems as module MultiQC/1.10.1.<br /> &nbsp;</p> Tue, 06 Apr 2021 07:49:00 GMT https://www.uppmax.uu.se/changelog 2021-04-06T07:49:00Z [apps] GhostPDL/9.53.3 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://ghostscript.com">GhostPDL</a> (interpreters for page description languages PS, PDF, XPS, PCL) version 9.53.3 installed on all systems as module GhostPDL/9.53.3.&nbsp; This includes the well-known Ghostscript interpreter, and also&nbsp;includes header files and the shared library libgs.so.</p> Fri, 26 Mar 2021 11:24:00 GMT https://www.uppmax.uu.se/changelog 2021-03-26T11:24:00Z [data] HaplotypeReferenceConsortium/r1.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://www.haplotype-reference-consortium.org/">HaplotypeReferenceConsortium</a> (The Haplotype Reference Consortium (HRC) will create a large reference panel of human haplotypes by combining together sequencing data from multiple cohorts) version r1.1 installed on all systems as module HaplotypeReferenceConsortium/r1.1.<br /> &nbsp;</p> Wed, 24 Mar 2021 12:28:00 GMT https://www.uppmax.uu.se/changelog 2021-03-24T12:28:00Z [bio] MaSuRCA/4.0.2 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/alekseyzimin/masurca">MaSuRCA </a>(The MaSuRCA (Maryland Super Read Cabog Assembler) genome assembly and analysis toolkit contains of MaSuRCA genome assembler, QuORUM error corrector for Illumina data, POLCA genome polishing software, Chromosome scaffolder, jellyfish mer counter, and MUMmer aligner.) version 4.0.2 installed on all systems as module MaSuRCA/4.0.2.</p> Tue, 23 Mar 2021 17:38:00 GMT https://www.uppmax.uu.se/changelog 2021-03-23T17:38:00Z [bio] Pilon/1.24 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/broadinstitute/pilon/wiki">Pilon </a>(Pilon is a software tool which can be used to: Automatically improve draft assemblies &amp; Find variation among strains, including large event detection) version 1.24 installed on all systems as module Pilon/1.24.<br /> &nbsp;</p> Tue, 23 Mar 2021 17:36:00 GMT https://www.uppmax.uu.se/changelog 2021-03-23T17:36:00Z [bio] NPStat/1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/lucaferretti/npstat">NPStat </a>(Population genetics tests and estimators for pooled NGS data) version 1 installed on all systems as module NPStat/1.<br /> &nbsp;</p> Mon, 22 Mar 2021 13:33:00 GMT https://www.uppmax.uu.se/changelog 2021-03-22T13:33:00Z [bio] MELT/2.2.2 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://melt.igs.umaryland.edu/index.php">MELT</a> (The Mobile Element Locator Tool (MELT) is a software package, written in Java, that discovers, annotates, and genotypes non-reference Mobile Element Insertions (MEIs) in Illumina DNA paired-end whole genome sequencing (WGS) data. ) version 2.2.2 installed on all systems as module MELT/2.2.2.<br /> &nbsp;</p> <p></p> Mon, 22 Mar 2021 08:44:00 GMT https://www.uppmax.uu.se/changelog 2021-03-22T08:44:00Z [bio] DANPOS/3.1.1 and 2.2.2 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://sites.google.com/site/danposdoc/">DANPOS</a> (A toolkit for Dynamic Analysis of Nucleosome and Protein Occupancy by Sequencing) version 3.1.1 installed on all systems as module DANPOS/3.1.1. Also, version 2.2.2 installed on all systems as module DANPOS/2.2.2.</p> <p></p> Fri, 19 Mar 2021 07:58:00 GMT https://www.uppmax.uu.se/changelog 2021-03-19T07:58:00Z [bio] bcftools/1.12, htslib/1.12, samtools/1.12 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://www.htslib.org">bcftools, htslib and samtools</a> (tools for working with SAM/BAM/CRAM format files and variant files) version 1.12 installed on all systems as module bcftools/1.12, htslib/1.12 and samtools/1.12.</p> Thu, 18 Mar 2021 11:39:00 GMT https://www.uppmax.uu.se/changelog 2021-03-18T11:39:00Z [bio] Roary/3.13.0 installed on all systems https://www.uppmax.uu.se/changelog <p>Roary (Roary is a high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome) version 3.13.0 installed on all systems as module Roary/3.13.0.<br /> http://sanger-pathogens.github.io/Roary/</p> Thu, 18 Mar 2021 08:48:00 GMT https://www.uppmax.uu.se/changelog 2021-03-18T08:48:00Z [bio] gmap-gsnap/2021-03-08 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://research-pub.gene.com/gmap/">gmap-gsnap</a> (Genomic Mapping and Alignment Program for mRNA and EST Sequences) version 2021-03-08 installed on all systems as module gmap-gsnap/2021-03-08.<br /> &nbsp;</p> Wed, 10 Mar 2021 13:53:00 GMT https://www.uppmax.uu.se/changelog 2021-03-10T13:53:00Z [libs] protobuf/3.15.5 and protobuf/3.15.5-gcc9.3.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/protocolbuffers/protobuf">Protocol Buffers</a> (a.k.a., protobuf) are Google's language-neutral, platform-neutral, extensible mechanism for serializing structured data.&nbsp; Version 3.15.5 is installed in two modules: protobuf/3.15.5 is compiled with the system gcc, at installation this is version 4.8.5; and protobuf/3.15.5-gcc9.3.0 is compiled with module gcc/9.3.0.<br /> &nbsp;</p> Tue, 09 Mar 2021 11:14:00 GMT https://www.uppmax.uu.se/changelog 2021-03-09T11:14:00Z [bio] Rcorrector/1.0.4 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/mourisl/Rcorrector">Rcorrector</a> (Rcorrector(RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data.) version 1.0.4 installed on all systems as module Rcorrector/1.0.4.<br /> &nbsp;</p> Mon, 08 Mar 2021 14:31:00 GMT https://www.uppmax.uu.se/changelog 2021-03-08T14:31:00Z [bio] beast2/2.6.3 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/CompEvol/beast2">beast2</a> (Bayesian Evolutionary Analysis by Sampling Trees) version 2.6.3 installed on all systems as module beast2/2.6.3.&nbsp; All packages as available 2021-03-08 are also installed.</p> Mon, 08 Mar 2021 13:29:00 GMT https://www.uppmax.uu.se/changelog 2021-03-08T13:29:00Z [libs] libsodium/1.0.18-stable installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://doc.libsodium.org/">libsodium</a> (Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, password hashing and more.) version 1.0.18-stable installed on all systems as module libsodium/1.0.18-stable.<br /> &nbsp;</p> Mon, 08 Mar 2021 12:03:00 GMT https://www.uppmax.uu.se/changelog 2021-03-08T12:03:00Z [libs] libzmq/4.3.4 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/zeromq/libzmq">libzmq</a> (the ZeroMQ lightweight messaging kernel is a library which extends the standard socket interfaces with features traditionally provided by specialised messaging middleware products. ZeroMQ sockets provide an abstraction of asynchronous message queues, multiple messaging patterns, message filtering (subscriptions), seamless access to multiple transport protocols and more.) version 4.3.4 installed on all systems as module libzmq/4.3.4.<br /> &nbsp;</p> Mon, 08 Mar 2021 11:34:00 GMT https://www.uppmax.uu.se/changelog 2021-03-08T11:34:00Z [libs] libwebp/1.2.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/webmproject/libwebp">libwebp</a> (library to encode and decode images in WebP format) version 1.2.0 installed on all systems as module libwebp/1.2.0.<br /> &nbsp;</p> Fri, 05 Mar 2021 13:04:00 GMT https://www.uppmax.uu.se/changelog 2021-03-05T13:04:00Z [apps] RStudio/1.4.1106 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://rstudio.com">RStudio</a> (Integrated development environment for the R language) version 1.4.1106 installed on all systems as module RStudio/1.4.1106.</p> Fri, 05 Mar 2021 12:47:00 GMT https://www.uppmax.uu.se/changelog 2021-03-05T12:47:00Z [bio] snpAD/0.3.4 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://bioinf.eva.mpg.de/snpAD">snpAD</a> (an ancient-DNA aware genotyper) version 0.3.4 installed on all systems as module snpAD/0.3.4.</p> Tue, 02 Mar 2021 13:53:00 GMT https://www.uppmax.uu.se/changelog 2021-03-02T13:53:00Z [apps] gromacs/2021.1.th installed on Rackham and Snowy https://www.uppmax.uu.se/changelog Fri, 26 Feb 2021 07:57:00 GMT https://www.uppmax.uu.se/changelog 2021-02-26T07:57:00Z [apps] Vapor/3.3.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.vapor.ucar.edu/">Vapor</a> (VAPOR is the Visualization and Analysis Platform for Ocean\, Atmosphere\, and Solar Researchers. VAPOR provides an interactive 3D visualization environment that can also produce animations and still frame images.) version 3.3.0 installed on all systems as module Vapor/3.3.0.</p> Mon, 22 Feb 2021 10:45:00 GMT https://www.uppmax.uu.se/changelog 2021-02-22T10:45:00Z [bio] Shasta/0.7.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/chanzuckerberg/shasta">Shasta </a>(The goal of the Shasta long read assembler is to rapidly produce accurate assembled sequence using as input DNA reads generated by Oxford Nanopore flow cells.) version 0.7.0 installed on all systems as module Shasta/0.7.0.<br /> &nbsp;</p> <p></p> Thu, 11 Feb 2021 13:16:00 GMT https://www.uppmax.uu.se/changelog 2021-02-11T13:16:00Z [bio] FastML/3.11 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://fastml.tau.ac.il">FastML</a> (tool for the reconstruction of ancestral sequences based on the phylogenetic relations between homologous sequences) version 3.11 installed on all systems as module FastML/3.11.<br /> &nbsp;</p> Wed, 10 Feb 2021 15:09:00 GMT https://www.uppmax.uu.se/changelog 2021-02-10T15:09:00Z [bio] FastME/2.1.6.2 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://gite.lirmm.fr/atgc/FastME">FastME</a> (comprehensive, accurate and fast distance-based phylogeny inference program) version 2.1.6.2 installed on all systems as module FastME/2.1.6.2.</p> Wed, 10 Feb 2021 14:20:00 GMT https://www.uppmax.uu.se/changelog 2021-02-10T14:20:00Z [bio] mrbayes/3.2.7a/-mpi installed on all systems (-gpu on Snowy) https://www.uppmax.uu.se/changelog <p><a href="https://github.com/NBISweden/MrBayes">mrbayes </a>(A program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models.) version 3.2.7a installed on all systems as module mrbayes/3.2.7a. MPI version is&nbsp;installed on all systems&nbsp;<span style="font-size:1em">as&nbsp;mrbayes/3.2.7a-mpi. GPU version is installed on Snowy as&nbsp;mrbayes/3.2.7a-gpu.</span></p> <p></p> Wed, 10 Feb 2021 09:08:00 GMT https://www.uppmax.uu.se/changelog 2021-02-10T09:08:00Z [bio] blast/2.11.0+ installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://blast.ncbi.nlm.nih.gov/Blast.cgi">BLAST</a> version 2.11.0+ installed on all systems as module blast/2.11.0+.<br /> &nbsp;</p> Mon, 08 Feb 2021 11:07:00 GMT https://www.uppmax.uu.se/changelog 2021-02-08T11:07:00Z [apps] vmtouch/1.3.1-20200309-4b70a9f installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://hoytech.com/vmtouch">vmtouch</a> (a tool for learning about and controlling the file system cache of unix and unix-like systems) version 1.3.1-20200309-4b70a9f installed on all systems as module vmtouch/1.3.1-20200309-4b70a9f.</p> <p>vmtouch can be particularly helpful for managing large, randomly accessed files over networked filesystems such as crex.&nbsp; See 'module help vmtouch/1.3.1-20200309-4b70a9f' for more information.</p> Mon, 08 Feb 2021 10:39:00 GMT https://www.uppmax.uu.se/changelog 2021-02-08T10:39:00Z [comp] python/3.8.7 and python3/3.8.7 installed on all systems https://www.uppmax.uu.se/changelog <p>Python 3.8.7 is now installed as module python/3.8.7 and python3/3.8.7 on all systems.&nbsp; The python3 module versions do not provide a 'python' name and do not conflict with python/2.x.y modules.</p> <p>As usual, a number of Python packages are included with the module, including numpy, scipy, jupyter, pandas, and matplotlib.</p> Mon, 01 Feb 2021 12:48:00 GMT https://www.uppmax.uu.se/changelog 2021-02-01T12:48:00Z [bio] cellranger/5.0.1 and the databases cellranger-data/2020-A and cellranger-VDJ-data/5.0.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/what-is-cell-ranger">10X Chromium Cellranger </a>(Cell line analysis system) version 5.0.1&nbsp;installed on all systems as module cellranger/5.0.1. Also installed are Cellranger single cell gene expression reference data as cellranger-data/2020-A, and Cellranger single cell V(D)J immune profiling reference data as cellranger-VDJ-data/5.0.0. These are both loaded by the new cellranger/5.0.1 module as prerequisites. For more information, see 'module help' for the newly installed modules.</p> Fri, 22 Jan 2021 13:08:00 GMT https://www.uppmax.uu.se/changelog 2021-01-22T13:08:00Z [bio] kallisto/0.46.2 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/pachterlab/kallisto">kallisto </a>(a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.) version 0.46.2 installed on all systems as module kallisto/0.46.2.<br /> &nbsp;</p> Mon, 18 Jan 2021 13:39:00 GMT https://www.uppmax.uu.se/changelog 2021-01-18T13:39:00Z [bio] SACRA/1.0.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/hattori-lab/SACRA">SACRA </a>(SACRA splits the chimeric reads to the non-chimeric reads in PacBio long reads of MDA-treated virome sample.) version 1.0.0 installed on all systems as module SACRA/1.0.0.<br /> &nbsp;</p> Mon, 18 Jan 2021 12:37:00 GMT https://www.uppmax.uu.se/changelog 2021-01-18T12:37:00Z [bio] SeqKit/0.15.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://bioinf.shenwei.me/seqkit/">SeqKit </a>(A cross-platform and ultrafast toolkit for FASTA/Q file manipulation) version 0.15.0 installed on all systems as module SeqKit/0.15.0.<br /> &nbsp;</p> <p></p> Mon, 18 Jan 2021 12:35:00 GMT https://www.uppmax.uu.se/changelog 2021-01-18T12:35:00Z [bio] last/963 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://last.cbrc.jp/">last </a>(finds similar regions between sequences.) version 963 installed on all systems as module last/963.<br /> &nbsp;</p> <p></p> Mon, 18 Jan 2021 12:33:00 GMT https://www.uppmax.uu.se/changelog 2021-01-18T12:33:00Z [bio] GUSHR/1.0.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/Gaius-Augustus/GUSHR">GUSHR</a> (Assembly-free construction of UTRs from short read RNA-Seq data on the basis of coding sequence annotation) version 1.0.0 installed on all systems as module GUSHR/1.0.0.<br /> &nbsp;</p> Mon, 18 Jan 2021 11:08:00 GMT https://www.uppmax.uu.se/changelog 2021-01-18T11:08:00Z [bio] GeneMark/4.62-es installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://topaz.gatech.edu/GeneMark/index.html">GeneMark</a> (de novo gene prediction) version 4.62-ES is now installed as module GeneMark/4.62-es on all systems.&nbsp; The key file is also updated as of today's date, 17-Jan-2021.</p> Sun, 17 Jan 2021 15:36:00 GMT https://www.uppmax.uu.se/changelog 2021-01-17T15:36:00Z [bio] ProtHint/2.5.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/gatech-genemark/ProtHint">ProtHint</a> (pipeline for predicting and scoring hints (in the form of introns, start and stop codons) in the genome of interest by mapping and spliced aligning predicted genes to a database of reference protein sequences) version 2.5.0 installed on all systems as module ProtHint/2.5.0.<br /> &nbsp;</p> Thu, 14 Jan 2021 13:44:00 GMT https://www.uppmax.uu.se/changelog 2021-01-14T13:44:00Z [bio] Sniffles/1.0.12-201218-4ff6ecb installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/fritzsedlazeck/Sniffles">Sniffles</a> (Sniffles is a structural variation caller using third generation sequencing (PacBio or Oxford Nanopore)) version 1.0.12-201218-4ff6ecb installed on all systems as module Sniffles/1.0.12-201218-4ff6ecb.<br /> &nbsp;</p> <p></p> Thu, 14 Jan 2021 10:38:00 GMT https://www.uppmax.uu.se/changelog 2021-01-14T10:38:00Z [bio] DelGet/5.4 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/4ureliek/DelGet">DelGet</a> (finds micro- and midsize deletions (using gaps of 1-30 nt and &gt;30 nt respectively) between orthologous regions of 3 or more species) version 5.4 installed on all systems as module DelGet/5.4.<br /> &nbsp;</p> Wed, 13 Jan 2021 14:22:00 GMT https://www.uppmax.uu.se/changelog 2021-01-13T14:22:00Z [bio] Kalign/1.04 and Kalign/2.04 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://msa.sbc.su.se/cgi-bin/msa.cgi">Kalign</a> (fast and accurate multiple sequence alignment algorithm) versions 1.04 and 2.04 installed on all systems as modules Kalign/1.04 and Kalign/2.04.<br /> &nbsp;</p> Wed, 13 Jan 2021 13:33:00 GMT https://www.uppmax.uu.se/changelog 2021-01-13T13:33:00Z [bio] minimap2/2.17-r941 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/lh3/minimap2">minimap2</a> (versatile pairwise aligner for genomic and spliced nucleotide sequences) version 2.17-r941 installed on all systems as module minimap2/2.17-r941.<br /> &nbsp;</p> Tue, 12 Jan 2021 10:00:00 GMT https://www.uppmax.uu.se/changelog 2021-01-12T10:00:00Z [bio] ANGSD/0.933 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://www.popgen.dk/angsd/index.php/ANGSD">ANGSD</a> (software for analyzing next generation sequencing data) version 0.933 installed on all systems as module ANGSD/0.933.<br /> &nbsp;</p> Mon, 04 Jan 2021 15:20:00 GMT https://www.uppmax.uu.se/changelog 2021-01-04T15:20:00Z [apps] lammps/29Oct2020_gcc_openmpi installed on Rackham https://www.uppmax.uu.se/changelog <p>lammps (LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel) version 29Oct2020_gcc_openmpi installed on Rackham&nbsp;as module lammps/29Oct2020_gcc_openmpi.<br /> https://lammps.sandia.gov/</p> Mon, 04 Jan 2021 13:00:00 GMT https://www.uppmax.uu.se/changelog 2021-01-04T13:00:00Z [libs] lpsolve/5.5.2.9 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://sourceforge.net/projects/lpsolve/">lp_solve</a> (Mixed Integer Linear Programming (MILP) solver) version 5.5.2.9 installed on all systems as module lpsolve/5.5.2.9.<br /> &nbsp;</p> Wed, 16 Dec 2020 15:03:00 GMT https://www.uppmax.uu.se/changelog 2020-12-16T15:03:00Z [apps] sqlite/3.34.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.sqlite.org">SQLite</a> (C-language library that implements a small, fast, self-contained, high-reliability, full-featured, SQL database engine) version 3.34.0 installed on all systems as module sqlite/3.34.0.</p> Tue, 15 Dec 2020 14:24:00 GMT https://www.uppmax.uu.se/changelog 2020-12-15T14:24:00Z [bio] augustus/3.3.3-CGP installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://bioinf.uni-greifswald.de/webaugustus/">AUGUSTUS</a> (gene prediction) version 3.3.3 with Comparative Gene Prediction support is installed as module augustus/3.3.3-CGP on all systems.&nbsp; This specific module is largely a wrapper around an EasyBuild-built module, with UPPMAX additions for copying the config directory.&nbsp; See 'module help augustus/3.3.3-CGP' for more.</p> Tue, 15 Dec 2020 11:01:00 GMT https://www.uppmax.uu.se/changelog 2020-12-15T11:01:00Z [bio] NeEstimator/2.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://www.molecularfisherieslaboratory.com.au/neestimator-software/">NeEstimator</a> (The NeEstimator software estimates genetic effective population sizes (Ne) from genotype data.) version 2.1 installed on all systems as module NeEstimator/2.1.</p> Fri, 11 Dec 2020 22:13:00 GMT https://www.uppmax.uu.se/changelog 2020-12-11T22:13:00Z [bio] RAisD/2.9 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://bioinformaticshome.com/tools/descriptions/RAiSD.html">RAisD</a> (A parameter free tool to detect selective sweeps using multiple signatures and enumeration of single nucleotide polymorphism (NP) vectors. ) version 2.9 installed on all systems as module RAisD/2.9.</p> Fri, 11 Dec 2020 22:12:00 GMT https://www.uppmax.uu.se/changelog 2020-12-11T22:12:00Z [bio] SNeP/1.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://bioinformaticshome.com/tools/descriptions/SNeP.html">SNeP</a> (Estimates trends in effective population size trajectories using genome-wide SNP data. A user can adjust parameters for sample size, mutation, phasing, and recombination rate.) version 1.1 installed on all systems as module SNeP/1.1.</p> Fri, 11 Dec 2020 22:11:00 GMT https://www.uppmax.uu.se/changelog 2020-12-11T22:11:00Z [bio] IGV/2.8.13 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://software.broadinstitute.org/software/igv/home">IGV</a> (high-performance, easy-to-use, interactive tool for the visual exploration of genomic data) version 2.8.13 installed on all systems as module IGV/2.8.13.&nbsp; The corresponding IGVtools are available in IGVtools/2.8.13.</p> Fri, 11 Dec 2020 14:29:00 GMT https://www.uppmax.uu.se/changelog 2020-12-11T14:29:00Z [bio] IGVtools/2.8.13 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://software.broadinstitute.org/software/igv/home">IGVtools</a> (tools for preparing data for IGV display) version 2.8.13 installed on all systems as module IGVtools/2.8.13.</p> Fri, 11 Dec 2020 10:55:00 GMT https://www.uppmax.uu.se/changelog 2020-12-11T10:55:00Z [bio] SHAPEIT/v4.1.3 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/odelaneau/shapeit4">SHAPEIT</a> (fast and accurate method for estimation of haplotypes (aka phasing) for SNP array and sequencing data; version 4 is a refactored and improved version of the SHAPEIT algorithm with multiple key additional features) version v4.1.3 installed on all systems as module SHAPEIT/v4.1.3.<br /> &nbsp;</p> Wed, 09 Dec 2020 09:39:00 GMT https://www.uppmax.uu.se/changelog 2020-12-09T09:39:00Z [apps] ORCA/4.2.1 installed on all systems https://www.uppmax.uu.se/changelog <p>ORCA version 4.2.1 installed on all systems as module ORCA/4.2.1.</p> Tue, 08 Dec 2020 18:17:00 GMT https://www.uppmax.uu.se/changelog 2020-12-08T18:17:00Z [bio] cyvcf2/0.30.1 installed on all systems https://www.uppmax.uu.se/changelog <p>cyvcf2 version 0.30.1 installed on all systems as module cyvcf2/0.30.1.</p> <p>https://github.com/brentp/cyvcf2</p> Tue, 08 Dec 2020 13:15:00 GMT https://www.uppmax.uu.se/changelog 2020-12-08T13:15:00Z [apps] wrf-python/1.3.1 installed on Rackham and Snowy https://www.uppmax.uu.se/changelog <p><a href="https://wrf-python.readthedocs.io/en/latest/">wrf-python </a>(A collection of diagnostic and interpolation routines for use with output from the Weather Research and Forecasting (WRF-ARW) Model.) version 1.3.1 installed on&nbsp;Rackham and Snowy as module wrf-python/1.3.1.<br /> &nbsp;</p> Mon, 07 Dec 2020 20:53:00 GMT https://www.uppmax.uu.se/changelog 2020-12-07T20:53:00Z [bio] IntaRNA/3.2.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://backofenlab.github.io/IntaRNA/">IntaRNA</a> (efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites) version 3.2.1 installed on all systems as module IntaRNA/3.2.1.<br /> &nbsp;</p> Mon, 07 Dec 2020 16:06:00 GMT https://www.uppmax.uu.se/changelog 2020-12-07T16:06:00Z [bio] RNAfold/2.4.17 aka ViennaRNA/2.4.17 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.tbi.univie.ac.at/RNA/">RNAfold</a>, also known as <a href="https://www.tbi.univie.ac.at/RNA/">ViennaRNA</a> (a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures) version 2.4.17 is now installed on all systems as the modules RNAfold/2.4.17 and ViennaRNA/2.4.17.&nbsp; These are different names for the same module.<br /> &nbsp;</p> Mon, 07 Dec 2020 15:02:00 GMT https://www.uppmax.uu.se/changelog 2020-12-07T15:02:00Z [bio] MEGAN/6.20.17 installed on all systems https://www.uppmax.uu.se/changelog <p>MEGAN version 6.20.17 installed on all systems as module MEGAN/6.20.17.</p> Mon, 07 Dec 2020 14:45:00 GMT https://www.uppmax.uu.se/changelog 2020-12-07T14:45:00Z [bio] cutadapt/3.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://cutadapt.readthedocs.io/en/stable/index.html">cutadapt</a> (finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads) version 3.1 installed on all systems as module cutadapt/3.1.</p> Mon, 07 Dec 2020 14:04:00 GMT https://www.uppmax.uu.se/changelog 2020-12-07T14:04:00Z [bio] HISAT2/2.2.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://daehwankimlab.github.io/hisat2/">HISAT2</a> (fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes as well as to a single reference genome) version 2.2.1 installed on all systems as module HISAT2/2.2.1.<br /> &nbsp;</p> Thu, 03 Dec 2020 15:43:00 GMT https://www.uppmax.uu.se/changelog 2020-12-03T15:43:00Z [bio] Unicycler/0.4.8 installed on all clusters https://www.uppmax.uu.se/changelog <p><a href="https://github.com/rrwick/Unicycler">Unicycler</a> (assembly pipeline for bacterial genomes) version 0.4.8 is now installed as module Unicycler/0.4.8 on all clusters.&nbsp; This is an alias module for the EasyBuild module Unicycler/0.4.8-gompi-2020a-Python-3.8.2.</p> Wed, 02 Dec 2020 12:54:00 GMT https://www.uppmax.uu.se/changelog 2020-12-02T12:54:00Z [bio] SHAPEIT/v3.r884.2 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://jmarchini.org/shapeit3/">SHAPEIT</a> (haplotype estimation for biobank scale datasets) v3.r884.2 (aka SHAPEIT3) is now installed as module SHAPEIT/v3.r884.2.</p> Wed, 02 Dec 2020 11:19:00 GMT https://www.uppmax.uu.se/changelog 2020-12-02T11:19:00Z [apps] NCO/4.9.3 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://nco.sourceforge.net/">NCO</a> (The NCO toolkit manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5) version 4.9.3 installed on all systems as module NCO/4.9.3.<br /> &nbsp;</p> <p></p> Tue, 01 Dec 2020 13:47:00 GMT https://www.uppmax.uu.se/changelog 2020-12-01T13:47:00Z [bio] quast/5.0.2 installed on all systems https://www.uppmax.uu.se/changelog <p>quast (Quality Assessment Tool for Genome Assemblies) version 5.0.2 installed on all systems as module quast/5.0.2.</p> Mon, 30 Nov 2020 13:07:00 GMT https://www.uppmax.uu.se/changelog 2020-11-30T13:07:00Z [apps] ncview/2.1.7 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://meteora.ucsd.edu/~pierce/ncview_home_page.html">ncview</a> (A netCDF visual browser) version 2.1.7 installed on all systems as module ncview/2.1.7.</p> Thu, 26 Nov 2020 20:28:00 GMT https://www.uppmax.uu.se/changelog 2020-11-26T20:28:00Z [bio] MaSuRCA/3.4.2 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/alekseyzimin/masurca">MaSuRCA</a> (genome assembly and analysis toolkit) version 3.4.2 installed on all systems as module MaSuRCA/3.4.2.<br /> &nbsp;</p> Wed, 25 Nov 2020 11:07:00 GMT https://www.uppmax.uu.se/changelog 2020-11-25T11:07:00Z [bio] MUMmer/4.0.0rc1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/mummer4/mummer">MUMmer</a> (versatile alignment tool for DNA and protein sequences) version 4.0.0rc1 installed on all systems as module MUMmer/4.0.0rc1.<br /> &nbsp;</p> Wed, 25 Nov 2020 09:15:00 GMT https://www.uppmax.uu.se/changelog 2020-11-25T09:15:00Z [bio] schmutzi/20200706-597c6bc installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/grenaud/schmutzi">schmutzi</a> (Bayesian maximum a posteriori contamination estimate for ancient samples) version 20200706-597c6bc installed on all systems as module schmutzi/20200706-597c6bc.&nbsp; The previously installed older version schmutzi/20160424 is also enabled.</p> Wed, 25 Nov 2020 08:59:00 GMT https://www.uppmax.uu.se/changelog 2020-11-25T08:59:00Z [bio] gcta/1.93.2beta installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://cnsgenomics.com/software/gcta/">gcta</a> (analyses to better understand the genetic architecture of complex traits) version 1.93.2beta installed on all systems as module gcta/1.93.2beta.<br /> &nbsp;</p> Tue, 24 Nov 2020 10:18:00 GMT https://www.uppmax.uu.se/changelog 2020-11-24T10:18:00Z [bio] trinity/2.11.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/trinityrnaseq/trinityrnaseq/wiki">Trinity</a> (assembles transcript sequences from Illumina RNA-Seq data) version 2.11.0 installed on all systems as module trinity/2.11.0.<br /> &nbsp;</p> Mon, 23 Nov 2020 14:18:00 GMT https://www.uppmax.uu.se/changelog 2020-11-23T14:18:00Z [bio] TargetP/2.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://www.cbs.dtu.dk/services/TargetP">TargetP</a> (predicts the presence of N-terminal presequences: signal peptide (SP), mitochondrial transit peptide (mTP), chloroplast transit peptide (cTP) or thylakoid luminal transit peptide (luTP)) version 2.0 installed on all systems as module TargetP/2.0.</p> Mon, 23 Nov 2020 12:48:00 GMT https://www.uppmax.uu.se/changelog 2020-11-23T12:48:00Z [bio] TransDecoder/5.5.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/TransDecoder/TransDecoder/wiki">TransDecoder</a> (identifies candidate coding regions within transcript sequences) version 5.5.0 installed on all systems as module TransDecoder/5.5.0.<br /> &nbsp;</p> Mon, 23 Nov 2020 11:51:00 GMT https://www.uppmax.uu.se/changelog 2020-11-23T11:51:00Z [bio] MAGeCK/0.5.9.4 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://sourceforge.net/p/mageck/wiki/Home/">MAGeCK</a> (Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout) version 0.5.9.4 installed on all systems as module MAGeCK/0.5.9.4.<br /> &nbsp;</p> Thu, 19 Nov 2020 17:18:00 GMT https://www.uppmax.uu.se/changelog 2020-11-19T17:18:00Z [bio] selscan/1.3.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/szpiech/selscan/releases/tag/v1.3.0">selscan</a> (Positive selection scans on haplotypes.) version 1.3.0 installed on all systems as module selscan/1.3.0.</p> <p></p> Wed, 18 Nov 2020 12:07:00 GMT https://www.uppmax.uu.se/changelog 2020-11-18T12:07:00Z [bio] SweeD/4.0.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://pop-gen.eu/wordpress/software/sweed">SweeD</a> (Likelihood-based Selective Sweep Detection) version 4.0.0 installed on all systems as module SweeD/4.0.0.</p> <p></p> Wed, 18 Nov 2020 12:06:00 GMT https://www.uppmax.uu.se/changelog 2020-11-18T12:06:00Z [bio] cellranger-ARC/1.0.0 and cellranger-ARC-data/2020-A installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/downloads/latest">10X Chromium Cellranger ARC</a> (Cell Ranger single-cell multiome ATAC + Gene Exp.) version 1.0.0 installed on all systems as module cellranger-ARC/1.0.0.&nbsp; Also installed are Cellranger ARC reference data in cellranger-ARC-data/2020-A.</p> Mon, 16 Nov 2020 15:06:00 GMT https://www.uppmax.uu.se/changelog 2020-11-16T15:06:00Z [bio] cellranger-DNA/1.1.0 and cellranger-DNA-data/1.0.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://support.10xgenomics.com/single-cell-dna/software/downloads/latest">10X Chromium Cellranger DNA</a> (Cell Ranger DNA single-cell analysis system) version 1.1.0 installed on all systems as module cellranger-DNA/1.1.0.&nbsp; Also installed are reference data as cellranger-DNA-data/1.0.0.</p> Mon, 16 Nov 2020 14:57:00 GMT https://www.uppmax.uu.se/changelog 2020-11-16T14:57:00Z [bio] cellranger/4.0.0 and cellranger-data/4.0.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/what-is-cell-ranger">10X Chromium Cellranger</a> (Cell line analysis system) version 4.0.0 installed on all systems as module cellranger/4.0.0.&nbsp; Also installed is Cellranger reference data as cellranger-data/4.0.0.<br /> &nbsp;</p> Mon, 16 Nov 2020 14:53:00 GMT https://www.uppmax.uu.se/changelog 2020-11-16T14:53:00Z [bio] spaceranger/1.2.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger">Chromium spaceranger</a> (set of analysis pipelines that process Visium spatial RNA-seq output and brightfield microscope images in order to detect tissue, align reads, generate feature-spot matrices, perform clustering and gene expression analysis, and place spots in spatial context on the slide image) version 1.2.0 installed on all systems as module spaceranger/1.2.0.</p> <p>Also installed, and loaded by this module as a prerequisite, is <a href="https://support.10xgenomics.com/spatial-gene-expression/software/downloads/latest">Spatial Expression Reference data</a> as module spaceranger-data/2020-A.</p> Mon, 16 Nov 2020 14:49:00 GMT https://www.uppmax.uu.se/changelog 2020-11-16T14:49:00Z [bio] NanoPlot/1.33.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://pypi.org/project/NanoPlot/">NanoPlot</a> (Plotting tool for long read sequencing data and alignments.) version 1.33.1 installed on all systems as module NanoPlot/1.33.1.<br /> &nbsp;</p> Mon, 16 Nov 2020 12:19:00 GMT https://www.uppmax.uu.se/changelog 2020-11-16T12:19:00Z [bio] megahit/1.2.9 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/voutcn/megahit">megahit</a> (MEGAHIT is an ultra-fast and memory-efficient NGS assembler. It is optimized for metagenomes, but also works well on generic single genome assembly (small or mammalian size) and single-cell assembly.) version 1.2.9 installed on all systems as module megahit/1.2.9</p> Thu, 12 Nov 2020 20:34:00 GMT https://www.uppmax.uu.se/changelog 2020-11-12T20:34:00Z [bio] diamond/2.0.4 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/bbuchfink/diamond">diamond</a> (sequence aligner for protein and translated DNA searches, designed for high performance analysis of big sequence data) version 2.0.4 installed on all systems as module diamond/2.0.4.<br /> &nbsp;</p> Thu, 12 Nov 2020 14:05:00 GMT https://www.uppmax.uu.se/changelog 2020-11-12T14:05:00Z [bio] mafTools/20170914-82077ac installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/dentearl/mafTools">mafTools</a> (collection of tools that operate on Multiple Alignment Format (maf) files) version 20170914-82077ac installed on all systems as module mafTools/20170914-82077ac.<br /> &nbsp;</p> Thu, 12 Nov 2020 14:05:00 GMT https://www.uppmax.uu.se/changelog 2020-11-12T14:05:00Z [apps] QGIS/3.4.12 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://qgis.org/en/site/">QGIS</a> (Create, edit, visualise, analyse and publish geospatial information) version 3.4.12 installed on all systems as module QGIS/3.4.12.<br /> &nbsp;</p> Tue, 10 Nov 2020 14:33:00 GMT https://www.uppmax.uu.se/changelog 2020-11-10T14:33:00Z [bio] Beagle/5.1 installed on all systems https://www.uppmax.uu.se/changelog <p>Beagle (Beagle is a software package for phasing genotypes and for imputing ungenotyped markers.) version 5.1 installed on all systems as module Beagle/5.1.<br /> https://faculty.washington.edu/browning/beagle/beagle.html</p> Mon, 09 Nov 2020 10:33:00 GMT https://www.uppmax.uu.se/changelog 2020-11-09T10:33:00Z [bio] FastQC/0.11.9 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.bioinformatics.babraham.ac.uk/projects/fastqc/">FastQC</a> (A quality control tool for high throughput sequence data) version 0.11.9 installed on all systems as module FastQC/0.11.9.</p> <p></p> Mon, 09 Nov 2020 10:23:00 GMT https://www.uppmax.uu.se/changelog 2020-11-09T10:23:00Z [bio] spades/3.14.1 installed on all systems https://www.uppmax.uu.se/changelog <p>spades (SPAdes --&nbsp; St. Petersburg genome assembler -- is an assembly toolkit containing various assembly pipelines.) version 3.14.1 installed on all systems as module spades/3.14.1.</p> <p></p> Thu, 29 Oct 2020 10:47:00 GMT https://www.uppmax.uu.se/changelog 2020-10-29T10:47:00Z [bio] cactus/1.2.3 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/ComparativeGenomicsToolkit/cactus">cactus</a> (whole genome alignment) version 1.2.3 installed on all systems as module cactus/1.2.3.&nbsp; Both the prebuilt Singularity image and locally-built binaries are available.</p> <p>This is a complicated tool to run.&nbsp; Please contact support@uppmax.uu.se for additional help.</p> Wed, 28 Oct 2020 15:12:00 GMT https://www.uppmax.uu.se/changelog 2020-10-28T15:12:00Z [apps] SAIGE/0.42.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/weizhouUMICH/SAIGE">SAIGE</a> (R package with Scalable and Accurate Implementation of Generalized mixed model (Chen, H. et al. 2016). It accounts for sample relatedness and is feasible for genetic association tests in large cohorts and biobanks (N &gt; 400,000).) version 0.42.1 installed on all systems as module SAIGE/0.42.1.</p> <p>The R package SAIGE was removed from R_packages/4.0.0 and moved to this separate module.</p> Wed, 28 Oct 2020 15:10:00 GMT https://www.uppmax.uu.se/changelog 2020-10-28T15:10:00Z [bio] jellyfish/2.3.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/gmarcais/Jellyfish">jellyfish</a> (tool for fast, memory-efficient counting of k-mers in DNA) version 2.3.0 installed on all systems as module jellyfish/2.3.0.</p> Wed, 28 Oct 2020 15:03:00 GMT https://www.uppmax.uu.se/changelog 2020-10-28T15:03:00Z [bio] jellyfish/1.1.12 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/gmarcais/Jellyfish">jellyfish</a> (tool for fast, memory-efficient counting of k-mers in DNA) version 1.1.12 installed on all systems as module jellyfish/1.1.12.</p> Wed, 28 Oct 2020 15:02:00 GMT https://www.uppmax.uu.se/changelog 2020-10-28T15:02:00Z [apps] PRISMS-PF/2.1.1 installed on Rackham and Snowy https://www.uppmax.uu.se/changelog <p>PRISMS-PF (PRedictive Integrated Structural Materials Science&ndash;Phase Field) version 2.1.1 is installed on Rackham and Snowy as module PRISMS-PF/2.1.1.<br /> It is a powerful, massively parallel finite element code for conducting phase field and other related simulations of microstructural evolution.</p> Fri, 23 Oct 2020 09:05:00 GMT https://www.uppmax.uu.se/changelog 2020-10-23T09:05:00Z [apps] NCL/6.6.2 installed on Rackham https://www.uppmax.uu.se/changelog <p><a href="https://www.ncl.ucar.edu/">NCL</a> (The NCAR Command Language) version 6.6.2 is installed on Rackham as module NCL-graphics/6.6.2.<br /> It is a free interpreted language designed specifically for scientific data processing and visualization. It can read and write netCDF-3, netCDF-4 classic, netCDF-4, HDF4, binary, and ASCII data. It can read HDF-EOS2, HDF-EOS5, GRIB1, GRIB2, and OGR files (shapefiles, MapInfo, GMT, Tiger).</p> Tue, 06 Oct 2020 12:37:00 GMT https://www.uppmax.uu.se/changelog 2020-10-06T12:37:00Z [bio] StringTie/2.1.4 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://ccb.jhu.edu/software/stringtie/">StringTie</a> (fast and highly efficient assembler of RNA-Seq alignments into potential transcripts) version 2.1.4 installed on all systems as module StringTie/2.1.4.<br /> &nbsp;</p> Thu, 01 Oct 2020 12:52:00 GMT https://www.uppmax.uu.se/changelog 2020-10-01T12:52:00Z [bio] segemehl/0.3.4 installed on all systems https://www.uppmax.uu.se/changelog <p>segemehl (segemehl is a software to map short sequencer reads to reference genomes) version 0.3.4 installed on all systems as module segemehl/0.3.4.</p> Mon, 28 Sep 2020 09:18:00 GMT https://www.uppmax.uu.se/changelog 2020-09-28T09:18:00Z [apps] WRF/WPS-4.1.3 installed on Rackham and Snowy https://www.uppmax.uu.se/changelog <p><a href="https://www.mmm.ucar.edu/weather-research-and-forecasting-model">WRF </a>(The Weather Research and Forecasting Model) and its pre-processing system (WPS) are installed on Rackham and Snowy as module WRF/4.1.3 and WPS/4.1.3. For usage, run 'module show WRF' or '...WPS'.</p> Fri, 25 Sep 2020 11:50:00 GMT https://www.uppmax.uu.se/changelog 2020-09-25T11:50:00Z [bio] vcflib/1.0.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/vcflib/vcflib">vcflib</a> (C++ library for parsing and manipulating VCF files) version 1.0.1 installed on all systems as module vcflib/1.0.1.<br /> &nbsp;</p> Wed, 16 Sep 2020 13:38:00 GMT https://www.uppmax.uu.se/changelog 2020-09-16T13:38:00Z [bio] plink2/2.00-alpha-2.3-20200124 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.cog-genomics.org/plink/2.0/">plink2</a> (association analysis toolset) version 2.00-alpha-2.3-20200124 installed on all systems as module plink2/2.00-alpha-2.3-20200124.<br /> &nbsp;</p> Wed, 16 Sep 2020 09:42:00 GMT https://www.uppmax.uu.se/changelog 2020-09-16T09:42:00Z [bio] picard/2.23.4 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://broadinstitute.github.io/picard/">picard</a> (a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF) version 2.23.4 installed on all systems as module picard/2.23.4.</p> Wed, 16 Sep 2020 08:49:00 GMT https://www.uppmax.uu.se/changelog 2020-09-16T08:49:00Z [bio] AdmixTools/7.0.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/DReichLab/AdmixTools">AdmixTools</a> (implements five methods described in Patterson et al. (2012) Ancient admixture in human history) version 7.0.1 installed on all systems as module AdmixTools/7.0.1.<br /> &nbsp;</p> Tue, 15 Sep 2020 13:06:00 GMT https://www.uppmax.uu.se/changelog 2020-09-15T13:06:00Z [bio] msmc/1.1.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/stschiff/msmc">MSMC</a> (implements MSMC, a method to infer population size and gene flow from multiple genome sequences) version 1.1.0 installed on all systems as module msmc/1.1.0.</p> Thu, 10 Sep 2020 11:40:00 GMT https://www.uppmax.uu.se/changelog 2020-09-10T11:40:00Z [apps] SPRKKR versions 7.7.1 and 7.7.3 installed on Rackham and Snowy https://www.uppmax.uu.se/changelog <p><a href="https://www.ebert.cup.uni-muenchen.de/index.php/en/software-en/13-sprkkr" title="SPRKKR">SPRKKR</a>&nbsp;-&nbsp;a spin polarized relativistic Korringa-Kohn-Rostoker (SPR-KKR) code for calculating solid state properties - versions 7.7.1 and 7.7.3 are&nbsp;installed on Rackham and Snowy as modules SPRKKR/7.7.1 and SPRKKR/7.7.3.</p> Thu, 10 Sep 2020 10:38:00 GMT https://www.uppmax.uu.se/changelog 2020-09-10T10:38:00Z [bio] ms/20071014 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://home.uchicago.edu/~rhudson1/source/mksamples.html">ms</a> (generating samples under a Wright-Fisher neutral model) version 20071014 installed on all systems as module ms/20071014.<br /> &nbsp;</p> Wed, 09 Sep 2020 13:58:00 GMT https://www.uppmax.uu.se/changelog 2020-09-09T13:58:00Z [bio] METAL/2011-03-25 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://csg.sph.umich.edu/abecasis/Metal/">METAL</a> (facilitate meta-analysis of large datasets, such as several whole genome scans) version 2011-03-25 installed on all systems as module METAL/2011-03-25.<br /> &nbsp;</p> Tue, 08 Sep 2020 08:49:00 GMT https://www.uppmax.uu.se/changelog 2020-09-08T08:49:00Z [bio] GenomeTools/1.6.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://genometools.org/">GenomeTools</a> (free collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary named gt) version 1.6.1 installed on all systems as module GenomeTools/1.6.1.<br /> &nbsp;</p> Thu, 27 Aug 2020 11:11:00 GMT https://www.uppmax.uu.se/changelog 2020-08-27T11:11:00Z [bio] RECON/1.08 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://eddylab.org/software/recon/">RECON</a> (package for automated de novo identification of repeat families from genomic sequences) version 1.08 installed on all systems as module RECON/1.08.&nbsp; This version uses an <a href="http://www.repeatmasker.org/RepeatModeler/RECON-1.08.tar.gz">updated version of the source</a>.</p> Mon, 24 Aug 2020 12:06:00 GMT https://www.uppmax.uu.se/changelog 2020-08-24T12:06:00Z [bio] RepeatScout/1.0.6 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/mmcco/RepeatScout">RepeatScout</a> (tool to discover repetitive substrings in DNA) version 1.0.6 installed on all systems as module RepeatScout/1.0.6.&nbsp; This version is <a href="http://www.repeatmasker.org/RepeatScout-1.0.6.tar.gz">specially modified</a> to handle multiple sequences.</p> Mon, 24 Aug 2020 11:41:00 GMT https://www.uppmax.uu.se/changelog 2020-08-24T11:41:00Z [bio] RepeatScout/1.0.5 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/mmcco/RepeatScout">RepeatScout</a> (tool to discover repetitive substrings in DNA) version 1.0.5 installed on all systems as module RepeatScout/1.0.5.<br /> &nbsp;</p> Mon, 24 Aug 2020 11:08:00 GMT https://www.uppmax.uu.se/changelog 2020-08-24T11:08:00Z [bio] nseg/1.0.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/jebrosen/nseg">nseg</a> (identifies and masks regions of low complexity in nucleic acid sequences) version 1.0.1 installed on all systems as module nseg/1.0.1.&nbsp; This is compiled from an updated version of the source originally available from <a href="ftp://ftp.ncbi.nih.gov/pub/seg/nseg">here</a>.<br /> &nbsp;</p> Mon, 24 Aug 2020 10:59:00 GMT https://www.uppmax.uu.se/changelog 2020-08-24T10:59:00Z [bio] trf/4.09.1 installed on all system https://www.uppmax.uu.se/changelog <p><a href="https://github.com/Benson-Genomics-Lab/TRF">TRF</a> (Tandem Repeat Finder, a program to locate and display tandem repeats in DNA sequences) version 4.09.1 installed on all systems as module trf/4.09.1.</p> Mon, 24 Aug 2020 10:26:00 GMT https://www.uppmax.uu.se/changelog 2020-08-24T10:26:00Z [apps] tmux/3.1b installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/tmux/tmux/wiki">tmux</a> (terminal multiplexer) version 3.1b installed on all systems as module tmux/3.1b.</p> <p>Also provided are older versions tmux/1.9a and tmux/2.5.<br /> &nbsp;</p> Fri, 21 Aug 2020 12:53:00 GMT https://www.uppmax.uu.se/changelog 2020-08-21T12:53:00Z [bio] ont_fast5_api/3.1.6 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/nanoporetech/ont_fast5_api">ont_fast5_api</a> (simple interface to HDF5 files of the Oxford Nanopore .fast5 file format) version 3.1.6 installed on all systems as module ont_fast5_api/3.1.6.<br /> &nbsp;</p> Fri, 21 Aug 2020 08:56:00 GMT https://www.uppmax.uu.se/changelog 2020-08-21T08:56:00Z [bio] MethPipe/4.1.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://smithlabresearch.org/software/methpipe/">MethPipe</a> (computational pipeline for analyzing bisulfite sequencing data (WGBS and RRBS)) version 4.1.1 installed on all systems as module MethPipe/4.1.1.&nbsp; <a href="http://smithlabresearch.org/software/radmeth/">RADmeth</a>&nbsp;is now included in MethPipe.</p> Thu, 20 Aug 2020 10:52:00 GMT https://www.uppmax.uu.se/changelog 2020-08-20T10:52:00Z [apps] nonmem/7.4.4 and nonmem/7.4.4-intel installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.iconplc.com/innovation/nonmem/">NONMEM</a> (very general (non-interactive) model analysis program that can be used to fit models to many different types of data) version 7.4.4 installed on all systems as module nonmem/7.4.4, which compiles with gfortran from gcc/8.3.0, and module nonmem/7.4.4-intel, which compiles with ifort from intel/19.5.&nbsp; The '-intel' module cannot be used on Bianca.</p> Thu, 20 Aug 2020 10:43:00 GMT https://www.uppmax.uu.se/changelog 2020-08-20T10:43:00Z [apps] PsN/5.0.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://uupharmacometrics.github.io/PsN/">PsN</a> (Perl-speaks-NONMEM is a collection of Perl modules and programs aiding in the development of non-linear mixed effect models using NONMEM) version 5.0.0 installed on all systems as module PsN/5.0.0.&nbsp; This is configured to use either nonmem/7.4.3 (PsN name is 7_4_3), nonmem/7.4.3-intel (PsN name is 7_4_3_intel), nonmem/7.4.4 (PsN name is 7_4_4) or&nbsp;nonmem/7.4.4-intel (PsN name is 7_4_4_intel).&nbsp; 7_4_4 is the default.&nbsp; 7_4_3_intel and 7.4.4_intel, like nonmem/7.4.3-intel and nonmem/7.4.4-intel, will not work on bianca.</p> Tue, 18 Aug 2020 15:18:00 GMT https://www.uppmax.uu.se/changelog 2020-08-18T15:18:00Z [apps] pandoc/2.10.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://pandoc.org/">Pandoc</a> (a Haskell library for converting from one markup format to another, and a command-line tool that uses this library.) version 2.10.1 installed on all systems as module pandoc/2.10.1.<br /> &nbsp;</p> Mon, 17 Aug 2020 12:32:00 GMT https://www.uppmax.uu.se/changelog 2020-08-17T12:32:00Z [comp] git/2.28.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://git-scm.com/">Git</a> (Source control management) version 2.28.0 installed on all systems as module git/2.28.0.</p> Mon, 17 Aug 2020 11:23:00 GMT https://www.uppmax.uu.se/changelog 2020-08-17T11:23:00Z [comp] git/2.24.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://git-scm.com/">Git</a> (Source control management) version 2.24.0 installed on all systems as module git/2.24.0.<br /> &nbsp;</p> Mon, 17 Aug 2020 11:16:00 GMT https://www.uppmax.uu.se/changelog 2020-08-17T11:16:00Z [bio] Tombo/1.5.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/nanoporetech/tombo">Tombo</a> (suite of tools primarily for the identification of modified nucleotides from nanopore sequencing data) version 1.5.1 installed on all systems as module Tombo/1.5.1.<br /> &nbsp;</p> Wed, 12 Aug 2020 11:01:00 GMT https://www.uppmax.uu.se/changelog 2020-08-12T11:01:00Z [bio] freebayes/1.3.2 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/ekg/freebayes">freebayes</a> (haplotype-based variant detector) version 1.3.2 installed on all systems as module freebayes/1.3.2.<br /> &nbsp;</p> Wed, 12 Aug 2020 11:00:00 GMT https://www.uppmax.uu.se/changelog 2020-08-12T11:00:00Z [bio] Redundans/0.14a-20190509-ffae69e installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/lpryszcz/redundans">Redundans</a> version&nbsp;0.14a including commits through ffae69e dated 2019 May 09 is now&nbsp;installed on all systems as module Redundans/0.14a-20190509-ffae69e.</p> Wed, 12 Aug 2020 10:57:00 GMT https://www.uppmax.uu.se/changelog 2020-08-12T10:57:00Z [bio] blast/2.10.1+ installed on all systems https://www.uppmax.uu.se/changelog <p>LAST finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance. this is the 2.10.1+ update of the local BlastDB tool &quot; 1&gt;&amp;2<br /> BLAST finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance. this is the 2.10.1+ update of the local BlastDB tool</p> Mon, 10 Aug 2020 08:33:00 GMT https://www.uppmax.uu.se/changelog 2020-08-10T08:33:00Z [bio] EnsEMBL-API/94 installed on all systems https://www.uppmax.uu.se/changelog <p>EnsEMBL-API (The Ensembl Core API (Application Programming Interface) serves as a middle layer between the underlying MySQL database and the user's script. It aims to encapsulate the database layer by providing high level access to the database.) version 94 installed on all systems as module EnsEMBL-API/94.<br /> http://www.ensembl.org/info/docs/api/core/</p> <p></p> Tue, 28 Jul 2020 08:39:00 GMT https://www.uppmax.uu.se/changelog 2020-07-28T08:39:00Z [bio] LDpred/1.0.10 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/bvilhjal/ldpred">LDpred</a> (Python based software package that adjusts GWAS summary statistics for the effects of linkage disequilibrium) version 1.0.10 installed on all systems as module LDpred/1.0.10.<br /> &nbsp;</p> Tue, 21 Jul 2020 10:33:00 GMT https://www.uppmax.uu.se/changelog 2020-07-21T10:33:00Z [bio] CITE-seq-Count/1.4.3 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://hoohm.github.io/CITE-seq-Count/">CITE-seq-Count</a> (python package that allows to count antibody TAGS from a CITE-seq and/or cell hashing experiment) version 1.4.3 installed on all systems as module CITE-seq-Count/1.4.3.<br /> &nbsp;</p> Mon, 20 Jul 2020 13:23:00 GMT https://www.uppmax.uu.se/changelog 2020-07-20T13:23:00Z [bio] htseq/0.12.4 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://htseq.readthedocs.io">HTSeq</a> (Analysing high-throughput sequencing data with Python) version 0.12.4 installed on all systems as module htseq/0.12.4.<br /> &nbsp;</p> Mon, 20 Jul 2020 11:47:00 GMT https://www.uppmax.uu.se/changelog 2020-07-20T11:47:00Z [build] cmake/3.17.3 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://cmake.org/">CMake</a> (open-source, cross-platform family of tools designed to build, test and package software) version 3.17.3 installed on all systems as module cmake/3.17.3.<br /> &nbsp;</p> Mon, 13 Jul 2020 12:21:00 GMT https://www.uppmax.uu.se/changelog 2020-07-13T12:21:00Z [bio] vawk/0.0.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/cc2qe/vawk">vawk</a> (awk-like VCF parser) version 0.0.1 installed on all systems as module vawk/0.0.1.<br /> &nbsp;</p> Tue, 30 Jun 2020 14:34:00 GMT https://www.uppmax.uu.se/changelog 2020-06-30T14:34:00Z [bio] RepeatMasker/4.1.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://www.repeatmasker.org/">RepeatMasker</a> (screens DNA sequences for interspersed repeats and low complexity DNA sequences) version 4.1.0 installed on all systems as module RepeatMasker/4.1.0.<br /> &nbsp;</p> Tue, 30 Jun 2020 14:32:00 GMT https://www.uppmax.uu.se/changelog 2020-06-30T14:32:00Z [bio] bwa-meth/0.2.2 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/brentp/bwa-meth">bwa-meth</a> (fast and accurate alignment of BS-Seq reads) version 0.2.2 installed on all systems as module bwa-meth/0.2.2.<br /> &nbsp;</p> Thu, 18 Jun 2020 13:01:00 GMT https://www.uppmax.uu.se/changelog 2020-06-18T13:01:00Z [bio] MethylDackel/0.5.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/dpryan79/MethylDackel">MethylDackel</a> (A (mostly) universal methylation extractor for BS-seq experiments) version 0.5.1 installed on all systems as module MethylDackel/0.5.1.<br /> &nbsp;</p> Thu, 18 Jun 2020 12:34:00 GMT https://www.uppmax.uu.se/changelog 2020-06-18T12:34:00Z [bio] libBigWig/0.4.4 installed on all systems https://www.uppmax.uu.se/changelog Thu, 18 Jun 2020 12:12:00 GMT https://www.uppmax.uu.se/changelog 2020-06-18T12:12:00Z [bio] BEDTools/2.29.2 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://bedtools.readthedocs.io">BEDTools</a> (the swiss army knife for genome arithmetic) version 2.29.2 installed on all systems as module BEDTools/2.29.2.<br /> &nbsp;</p> Thu, 04 Jun 2020 13:42:00 GMT https://www.uppmax.uu.se/changelog 2020-06-04T13:42:00Z [bio] braker/2.1.5 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/Gaius-Augustus/BRAKER">BRAKER</a> (pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes) version 2.1.5 installed on all systems as module braker/2.1.5.</p> <p>Note that a copy of the GeneMark licence in the user home directory and a local, writable copy of the augustus config directory are both required to run braker. Help for both is available by following 'module&nbsp;help braker/2.1.5'.</p> Thu, 04 Jun 2020 12:53:00 GMT https://www.uppmax.uu.se/changelog 2020-06-04T12:53:00Z [bio] MaxBin/2.2.7 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://downloads.jbei.org/data/MaxBin.html">MaxBin</a> (software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm) version 2.2.7 installed on all systems as module MaxBin/2.2.7.<br /> &nbsp;</p> Tue, 02 Jun 2020 18:23:00 GMT https://www.uppmax.uu.se/changelog 2020-06-02T18:23:00Z [bio] CONCOCT/1.1.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/BinPro/CONCOCT">CONCOCT</a> (Clustering cONtigs with COverage and ComposiTion) version 1.1.0 installed on all systems as module CONCOCT/1.1.0.<br /> &nbsp;</p> Tue, 02 Jun 2020 16:35:00 GMT https://www.uppmax.uu.se/changelog 2020-06-02T16:35:00Z [bio] CheckM/1.1.2 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/Ecogenomics/CheckM">CheckM</a> (assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes) version 1.1.2 installed on all systems as module CheckM/1.1.2.<br /> &nbsp;</p> Tue, 02 Jun 2020 08:47:00 GMT https://www.uppmax.uu.se/changelog 2020-06-02T08:47:00Z [bio] MultiQC/1.9 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://multiqc.info">MultiQC</a> (aggregate results from bioinformatics analyses across many samples into a single report) version 1.9 installed on all systems as module MultiQC/1.9.<br /> &nbsp;</p> Mon, 01 Jun 2020 09:31:00 GMT https://www.uppmax.uu.se/changelog 2020-06-01T09:31:00Z [bio] MakeHub/1.0.5-1ecd6bb installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/Gaius-Augustus/MakeHub">MakeHub</a> (Fully automated generation of UCSC assembly hubs) version 1.0.5-1ecd6bb installed on all systems as module MakeHub/1.0.5-1ecd6bb.</p> Fri, 29 May 2020 16:10:00 GMT https://www.uppmax.uu.se/changelog 2020-05-29T16:10:00Z [bio] ucsc-utilities/v398 installed on all systems https://www.uppmax.uu.se/changelog <p>The <a href="http://hgdownload.soe.ucsc.edu/admin/exe/">UCSC Kent utilities</a> (Kent bioinformatics utilities) version v398 installed on all systems as module ucsc-utilities/v398.<br /> &nbsp;</p> Fri, 29 May 2020 15:51:00 GMT https://www.uppmax.uu.se/changelog 2020-05-29T15:51:00Z [bio] GenomeThreader/1.7.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://genomethreader.org/">GenomeThreader</a> (software tool to compute gene structure predictions) version 1.7.1 installed on all systems as module GenomeThreader/1.7.1.<br /> &nbsp;</p> Thu, 28 May 2020 13:54:00 GMT https://www.uppmax.uu.se/changelog 2020-05-28T13:54:00Z [bio] cdbfasta/1.00 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/gpertea/cdbfasta">cdbfasta</a> (Constant DataBase tools for indexing and retrieving records from multi-FASTA or similarly structured files) version 1.00 installed on all systems as module cdbfasta/1.00.<br /> &nbsp;</p> Thu, 28 May 2020 13:07:00 GMT https://www.uppmax.uu.se/changelog 2020-05-28T13:07:00Z [bio] ProtHint/2.4.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/gatech-genemark/ProtHint">ProtHint</a> (pipeline for predicting and scoring hints [in the form of introns, start and stop codons] in the genome of interest by mapping and spliced aligning predicted genes to a database of reference protein sequences) version 2.4.0 installed on all systems as module ProtHint/2.4.0.<br /> &nbsp;</p> Thu, 28 May 2020 11:08:00 GMT https://www.uppmax.uu.se/changelog 2020-05-28T11:08:00Z [bio] spaln/2.4.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln">spaln</a> (stand-alone program that maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence in a single job) version 2.4.0 installed on all systems as module spaln/2.4.0.<br /> &nbsp;</p> Wed, 27 May 2020 15:43:00 GMT https://www.uppmax.uu.se/changelog 2020-05-27T15:43:00Z [bio] HOMER/4.11 with all data installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://homer.ucsd.edu/homer/">HOMER</a> ((Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and ChIP-Seq analysis) version 4.11 installed on all systems as module HOMER/4.11.&nbsp; All available data sources are also installed.</p> Mon, 25 May 2020 14:27:00 GMT https://www.uppmax.uu.se/changelog 2020-05-25T14:27:00Z [apps] RStudio/1.2.5042 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://rstudio.com">RStudio</a> (Integrated development environment for the R language) version 1.2.5042 installed on all systems as module RStudio/1.2.5042.<br /> &nbsp;</p> Wed, 20 May 2020 08:20:00 GMT https://www.uppmax.uu.se/changelog 2020-05-20T08:20:00Z [apps] GDAL/3.1.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.gdal.org">GDAL</a> (translator library for raster and vector geospatial data formats) version 3.1.0 installed on all systems as module GDAL/3.1.0.<br /> &nbsp;</p> Tue, 19 May 2020 12:05:00 GMT https://www.uppmax.uu.se/changelog 2020-05-19T12:05:00Z [apps] ROOT/6.20.04 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://root.cern.ch/">ROOT</a> (modular scientific software toolkit. It provides all the functionalities needed to deal with big data processing, statistical analysis, visualisation and storage) version 6.20.04 installed on all systems as module ROOT/6.20.04.</p> Tue, 19 May 2020 12:04:00 GMT https://www.uppmax.uu.se/changelog 2020-05-19T12:04:00Z [libs] PROJ/6.3.2 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://proj.org">PROJ</a> (Cartographic Projections and Coordinate Transformations Library) version 6.3.2 installed on all systems as module PROJ/6.3.2.</p> Mon, 18 May 2020 14:49:00 GMT https://www.uppmax.uu.se/changelog 2020-05-18T14:49:00Z [bio] rsem/1.3.3 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/deweylab/RSEM">rsem</a> (accurate quantification of gene and isoform expression from RNA-Seq data) version 1.3.3 installed on all systems as module rsem/1.3.3.</p> Mon, 18 May 2020 09:19:00 GMT https://www.uppmax.uu.se/changelog 2020-05-18T09:19:00Z [bio] Stacks/2.53 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://catchenlab.life.illinois.edu/stacks/">Stacks</a> (Software pipeline for building loci from short-read sequences) version 2.53 installed on all systems as module Stacks/2.53.</p> Mon, 11 May 2020 12:49:00 GMT https://www.uppmax.uu.se/changelog 2020-05-11T12:49:00Z [comp] rust/1.43.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.rust-lang.org/">Rust</a> (the Rust programming language and Cargo tools) version 1.43.1 installed on all systems as module rust/1.43.1.</p> Fri, 08 May 2020 08:46:00 GMT https://www.uppmax.uu.se/changelog 2020-05-08T08:46:00Z [apps] Armadillo/9.700.2 installed on all systems https://www.uppmax.uu.se/changelog <p><strong>Armadillo</strong> version 9.700.2 installed on all systems as <strong>module Armadillo/9.700.2</strong>. Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions. <a href="https://sourceforge.net/projects/arma/" title="https://sourceforge.net/projects/arma/">https://sourceforge.net/projects/arma/</a></p> Fri, 24 Apr 2020 15:24:00 GMT https://www.uppmax.uu.se/changelog 2020-04-24T15:24:00Z [apps] Singular/4.1.2 installed on all systems https://www.uppmax.uu.se/changelog <p><strong>Singular</strong> (a computer algebra system for polynomial computations, with special emphasis on commutative and non-commutative algebra, algebraic geometry, and singularity theory.) version 4.1.2 installed on all systems as <strong>module Singular/4.1.2</strong>.&nbsp;<a href="https://www.singular.uni-kl.de" title="https://www.singular.uni-kl.de">https://www.singular.uni-kl.de</a></p> <p></p> Fri, 24 Apr 2020 14:51:00 GMT https://www.uppmax.uu.se/changelog 2020-04-24T14:51:00Z [apps] gromacs/2020-GPU installed on Snowy hybrid nodes https://www.uppmax.uu.se/changelog <p>GROMACS 2020 installed on Snowy as module <strong>gromacs/2020-GPU</strong>. GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. This is a <strong>GPU enabled build</strong>, containing both MPI and threadMPI binaries. <a href="http://www.gromacs.org" title="http://www.gromacs.org">http://www.gromacs.org</a></p> <p></p> Thu, 23 Apr 2020 19:57:00 GMT https://www.uppmax.uu.se/changelog 2020-04-23T19:57:00Z [bio] phylobayesmpi/1.8b installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/bayesiancook/pbmpi">PhyloBayes MPI</a>&nbsp;(PhyloBayes with MPI support) version 1.8b installed on all systems as module phylobayesmpi/1.8b.&nbsp; This module loads gcc/9.2.0 and openmpi/3.1.4 and should work equally well on all clusters.<br /> &nbsp;</p> Wed, 22 Apr 2020 16:28:00 GMT https://www.uppmax.uu.se/changelog 2020-04-22T16:28:00Z [apps] Ansys/2020R1 installed on Rackham https://www.uppmax.uu.se/changelog <p>ANSYS (engineering simulation software) 2020R1 suite is installed on Rackham as module <strong>Ansys/2020R1</strong>. ANSYS Fluent, CFX, CEI, ANSYS workbench, and more,&nbsp;are installed. <a href="https://www.ansys.com/products/release-highlights" title="https://www.ansys.com/products/release-highlights">https://www.ansys.com/products/release-highlights</a></p> Wed, 22 Apr 2020 15:24:00 GMT https://www.uppmax.uu.se/changelog 2020-04-22T15:24:00Z [bio] biopython/1.76-py3 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://biopython.org">BioPython</a>&nbsp;(Python packages for doing bioinformatics tasks) version 1.76-py3 installed on all systems as module biopython/1.76-py3.&nbsp; This module loads python/3.7.2 as a prerequisite.</p> Mon, 20 Apr 2020 16:22:00 GMT https://www.uppmax.uu.se/changelog 2020-04-20T16:22:00Z [comp] fpc/3.0.4 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.freepascal.org/">fpc</a> (Free Pascal Compiler) version 3.0.4 installed on all systems as module fpc/3.0.4.</p> Mon, 20 Apr 2020 16:20:00 GMT https://www.uppmax.uu.se/changelog 2020-04-20T16:20:00Z [apps] OpenFOAM version v1912 installed on all systems https://www.uppmax.uu.se/changelog <p style="margin-left:0px"><strong>OpenFOAM</strong> (a free, open source computational fluid&nbsp; software package) version v1912 installed on all systems as module <strong>OpenFOAM/v1912</strong>. <a href="https://www.openfoam.com/" title="https://www.openfoam.com/">https://www.openfoam.com/</a></p> Mon, 20 Apr 2020 15:41:00 GMT https://www.uppmax.uu.se/changelog 2020-04-20T15:41:00Z [apps] OpenFOAM versions 6 and 7 installed on all systems https://www.uppmax.uu.se/changelog <p style="margin-left:0px"><strong>OpenFOAM</strong> (a free, open source computational fluid&nbsp; software package) versions 6 and 7 installed on all systems as modules <strong>OpenFOAM/6</strong> and <strong>OpenFOAM/7</strong>. <a href="https://www.openfoam.org/" title="https://www.openfoam.org">https://www.openfoam.org</a></p> Mon, 20 Apr 2020 15:37:00 GMT https://www.uppmax.uu.se/changelog 2020-04-20T15:37:00Z [bio] Genepop/4.7 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://kimura.univ-montp2.fr/~rousset/Genepop.htm">Genepop</a> (population genetics software package) version 4.7 installed on all systems as module Genepop/4.7.</p> Mon, 20 Apr 2020 15:19:00 GMT https://www.uppmax.uu.se/changelog 2020-04-20T15:19:00Z [apps] XCrySDen versions 1.5.60 and 1.6.2 installed on Rackham https://www.uppmax.uu.se/changelog <p>XCrySDen (a crystalline and molecular structure visualisation program)&nbsp;versions 1.5.60 and 1.6.2 installed on Rackham as modules <strong>XCrySDen/1.5.60</strong> and <strong>XCrySDen/1.6.2</strong>.&nbsp;<a href="http://www.xcrysden.org" title="http://www.xcrysden.org">http://www.xcrysden.org</a></p> <p></p> Fri, 17 Apr 2020 08:38:00 GMT https://www.uppmax.uu.se/changelog 2020-04-17T08:38:00Z [apps] Siesta version 4.1-MaX-1.0 installed on all systems https://www.uppmax.uu.se/changelog <p>Siesta (SIESTA is both a method and its computer program implementation, to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids.) version 4.1-MaX-1.0 installed on all systems as module <strong>Siesta/4.1-MaX-1.0</strong>.&nbsp;<a href="https://gitlab.com/siesta-project/siesta/-/tree/MaX-1.0" title="https://gitlab.com/siesta-project/siesta/-/tree/MaX-1.0">https://gitlab.com/siesta-project/siesta/-/tree/MaX-1.0</a></p> Thu, 16 Apr 2020 10:20:00 GMT https://www.uppmax.uu.se/changelog 2020-04-16T10:20:00Z [apps] Siesta version 4.1-b4 installed on all systems https://www.uppmax.uu.se/changelog <p style="margin-left:0px">Siesta (SIESTA is both a method and its computer program implementation, to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids.) version 4.1-b4 installed on all systems as module <strong>Siesta/4.1-b4</strong>.&nbsp;<a href="https://gitlab.com/siesta-project/siesta/-/tree/v4.1-b4" title="https://gitlab.com/siesta-project/siesta/-/tree/v4.1-b4">https://gitlab.com/siesta-project/siesta/-/tree/v4.1-b4</a></p> <div></div> Thu, 16 Apr 2020 10:10:00 GMT https://www.uppmax.uu.se/changelog 2020-04-16T10:10:00Z [bio] diamond/0.931 is installed on all systems https://www.uppmax.uu.se/changelog <p>diamond (sequence aligner for protein and translated DNA searches, designed for high performance analysis of big sequence data) version 0.9.31 installed on all systems as module diamond/0.9.31. https://github.com/bbuchfink/diamond</p> Fri, 10 Apr 2020 08:25:00 GMT https://www.uppmax.uu.se/changelog 2020-04-10T08:25:00Z [bio] canu/2.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://canu.readthedocs.org/">Canu</a> (a fork of the Celera Assembler, designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION)) version 2.0 installed on all systems as module canu/2.0.&nbsp; Note that assemblies begun with previous version of Canu (canu/1.x) cannot be continued by canu/2.0.</p> Thu, 09 Apr 2020 13:10:00 GMT https://www.uppmax.uu.se/changelog 2020-04-09T13:10:00Z [bio] SpeedSeq/0.1.2-20180208-4e60002 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/hall-lab/speedseq">SpeedSeq</a> (flexible framework for rapid genome analysis and interpretation) version 0.1.2 as of commit 4e60002 on 2018-02-08, is now installed as module SpeedSeq/0.1.2-20180208-4e60002 on all systems.</p> Mon, 06 Apr 2020 09:20:00 GMT https://www.uppmax.uu.se/changelog 2020-04-06T09:20:00Z [bio] raxml/8.2.12-gcc iand raxml/8.2.12-gcc-mpi nstalled on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/stamatak/standard-RAxML">RAxML</a> (A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies) version 8.2.12-gcc installed on all systems as module raxml/8.2.12-gcc, and with MPI support as raxml/8.2.12-gcc-mpi.</p> Wed, 01 Apr 2020 09:47:00 GMT https://www.uppmax.uu.se/changelog 2020-04-01T09:47:00Z [bio] DATES/753 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/priyamoorjani/DATES">DATES</a> (DATES (Distribution of Ancestry Tracts of Evolutionary Signals) is a method to estimate the time of admixture in ancient DNA samples described in Narasimhan, Patterson et al. 2018) version 753 installed on all systems as module DATES/753.</p> Tue, 31 Mar 2020 14:46:00 GMT https://www.uppmax.uu.se/changelog 2020-03-31T14:46:00Z [libs] gsl/2.5 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.gnu.org/software/gsl/">GSL</a> (Gnu Scientific Library, a numerical library for C and C++ programmers) version 2.5 installed on all systems as module gsl/2.5.</p> Tue, 31 Mar 2020 13:37:00 GMT https://www.uppmax.uu.se/changelog 2020-03-31T13:37:00Z [libs] openblas/0.2.20 and openblas/0.2.20-singlethread installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/xianyi/OpenBLAS">OpenBLAS</a> (&nbsp;an optimized Basic Linear Algebra Subprograms [BLAS] library based on&nbsp;<a href="https://www.tacc.utexas.edu/research-development/tacc-software/gotoblas2">GotoBLAS2</a>&nbsp;1.13 BSD version) version 0.2.20 is build in multithreaded and singlethreaded versions and is installed as modules openblas/0.2.20 and openblas/0.2.20-singlethread, respectively,&nbsp;on all systems.</p> Tue, 31 Mar 2020 13:33:00 GMT https://www.uppmax.uu.se/changelog 2020-03-31T13:33:00Z [libs] fftw/3.3.8 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://www.fftw.org">FFTW</a> (C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data) version 3.3.8 installed on all systems as module fftw/3.3.8.</p> Tue, 31 Mar 2020 13:27:00 GMT https://www.uppmax.uu.se/changelog 2020-03-31T13:27:00Z [bio] iqtree/2.0-rc2-omp-mpi installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://www.iqtree.org">IQ-Tree</a> (efficient software for phylogenomic inference) version 2.0-rc2-omp-mpi installed on all systems as module iqtree/2.0-rc2-omp-mpi.</p> Thu, 26 Mar 2020 13:43:00 GMT https://www.uppmax.uu.se/changelog 2020-03-26T13:43:00Z [bio] barrnap/0.9 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/tseemann/barrnap">Barrnap</a> (detect rRNA genes in diverse genomes) version 0.9 installed on all systems as module barrnap/0.9.<br /> &nbsp;</p> Mon, 23 Mar 2020 12:16:00 GMT https://www.uppmax.uu.se/changelog 2020-03-23T12:16:00Z [bio] LUMPY/0.3.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/arq5x/lumpy-sv">LUMPY</a> (a general probabilistic framework for structural variant discovery) version 0.3.0 installed on all systems as module LUMPY/0.3.0.</p> Fri, 13 Mar 2020 16:18:00 GMT https://www.uppmax.uu.se/changelog 2020-03-13T16:18:00Z [bio] sambamba/0.7.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://lomereiter.github.io/sambamba">sambamba</a> (SAM file processing) version 0.7.1 installed on all systems as module sambamba/0.7.1.</p> Fri, 13 Mar 2020 15:08:00 GMT https://www.uppmax.uu.se/changelog 2020-03-13T15:08:00Z [bio] fastp/0.20.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/OpenGene/fastp">fastp</a> (fast all-in-one preprocessing for FastQ files) version 0.20.0 installed on all systems as module fastp/0.20.0.<br /> &nbsp;</p> Tue, 10 Mar 2020 10:52:00 GMT https://www.uppmax.uu.se/changelog 2020-03-10T10:52:00Z [bio] LINKS/1.8.7 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/bcgsc/links">LINKS</a> (Long Interval Nucleotide K-mer Scaffolder) version 1.8.7 installed on all systems as module LINKS/1.8.7.</p> Fri, 06 Mar 2020 10:29:00 GMT https://www.uppmax.uu.se/changelog 2020-03-06T10:29:00Z [bio] ARCS/1.1.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/bcgsc/arcs">ARCS</a> (scaffold genome sequence assemblies using linked read sequencing data) version 1.1.1 installed on all systems as module ARCS/1.1.1.&nbsp; This module also loads LINKS/1.8.7 and tigmint/1.1.2.</p> Fri, 06 Mar 2020 10:26:00 GMT https://www.uppmax.uu.se/changelog 2020-03-06T10:26:00Z [apps] swig/3.0.12 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://sourceforge.net/projects/swig/">swig</a> (code generator for connecting C/C++ with other programming languages) version 3.0.12 installed on all systems as module swig/3.0.12.</p> Thu, 05 Mar 2020 13:13:00 GMT https://www.uppmax.uu.se/changelog 2020-03-05T13:13:00Z [bio] GAA/1.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://sourceforge.net/projects/gaa-wugi">GAA</a> (merge assemblies) version 1.1 installed on all systems as module GAA/1.1.</p> Thu, 05 Mar 2020 12:33:00 GMT https://www.uppmax.uu.se/changelog 2020-03-05T12:33:00Z [apps] NCO/4.8.1 and NCO/4.9.2 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://nco.sourceforge.net/">NCO</a> (toolkit manipulates and analyzes data stored in&nbsp;<a href="http://www.unidata.ucar.edu/netcdf">netCDF</a>-accessible formats) versions 4.8.1 and 4.9.2 are now available as modules NCO/4.8.1 and NCO/4.9.2 on all systems.</p> Thu, 05 Mar 2020 09:59:00 GMT https://www.uppmax.uu.se/changelog 2020-03-05T09:59:00Z [apps] ABINIT/8.10.3 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.abinit.org/">ABINIT</a> (software suite to calculate the optical, mechanical, vibrational, and other observable properties of materials) version 8.10.3 is now installed as module ABINIT/8.10.3 on all systems.</p> Thu, 27 Feb 2020 15:54:00 GMT https://www.uppmax.uu.se/changelog 2020-02-27T15:54:00Z [libs] NLopt/2.6.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/stevengj/nlopt">NLopt</a> (a library for nonlinear local and global optimization, for functions with and without gradient information. It is designed as a simple, unified interface and packaging of several free/open-source nonlinear optimization libraries.) version 2.6.1 installed on all systems as module NLopt/2.6.1.</p> Tue, 25 Feb 2020 14:38:00 GMT https://www.uppmax.uu.se/changelog 2020-02-25T14:38:00Z [bio] deepTools/3.3.2 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/deeptools/deepTools">deepTools</a> (tools to process and analyze deep sequencing data)&nbsp;version 3.3.2 installed on all systems as module deepTools/3.3.2.</p> Mon, 24 Feb 2020 15:16:00 GMT https://www.uppmax.uu.se/changelog 2020-02-24T15:16:00Z [bio] MACS/2.2.6 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://taoliu.github.io/MACS/">MACS</a> (Model-based Analysis of ChIP-Seq) version 2.2.6 is now installed as module MACS/2.2.6 on all systems.</p> Mon, 24 Feb 2020 15:00:00 GMT https://www.uppmax.uu.se/changelog 2020-02-24T15:00:00Z [bio] PCAngsd/0.982 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/Rosemeis/pcangsd">PCAngsd</a> (framework for analyzing low depth NGS data in heterogeneous populations using PCA) version 0.982 installed on all systems as module PCAngsd/0.982.</p> Thu, 20 Feb 2020 13:11:00 GMT https://www.uppmax.uu.se/changelog 2020-02-20T13:11:00Z [bio] SLiM/3.3.2 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://messerlab.org/slim/">SLiM</a> (evolutionary genetic forward simulations) version 3.3.2 is now installed as module SLiM/3.3.2 on all systems.</p> Tue, 11 Feb 2020 19:20:00 GMT https://www.uppmax.uu.se/changelog 2020-02-11T19:20:00Z [bio] SLiM/2.6 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://messerlab.org/slim/">SLiM</a> (evolutionary genetic forward simulations) 2.6 has been installed as module SLiM/2.6 on all systems.</p> Tue, 11 Feb 2020 19:06:00 GMT https://www.uppmax.uu.se/changelog 2020-02-11T19:06:00Z [bio] beagle/3.1.2 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/beagle-dev/beagle-lib">Beagle</a> (general purpose library for evaluating the likelihood of sequence evolution on trees) version 3.1.2 installed on all systems as module beagle/3.1.2.</p> Tue, 11 Feb 2020 16:28:00 GMT https://www.uppmax.uu.se/changelog 2020-02-11T16:28:00Z [bio] beast2/2.6.2pre installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/CompEvol/beast2">Beast2</a> (Bayesian Evolutionary Analysis by Sampling Trees) version 2.6.2pre installed on all systems as module beast2/2.6.2pre.</p> Tue, 11 Feb 2020 10:37:00 GMT https://www.uppmax.uu.se/changelog 2020-02-11T10:37:00Z [bio] PRSice version 2.2.11.b installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.prsice.info/">PRSice</a> (A software package for calculating, applying, evaluating and plotting the results of polygenic risk scores) version 2.2.11.b installed on all systems as module PRSice/2.2.11.b.</p> Mon, 10 Feb 2020 15:07:00 GMT https://www.uppmax.uu.se/changelog 2020-02-10T15:07:00Z [bio] cd-hit/4.8.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/weizhongli/cdhit">CD-Hit</a> (clustering and deduplication of a wide variety of sequence data) version 4.8.1 installed on all systems as module cd-hit/4.8.1.</p> Tue, 04 Feb 2020 10:31:00 GMT https://www.uppmax.uu.se/changelog 2020-02-04T10:31:00Z [bio] MaSuRCA/3.3.5 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/alekseyzimin/masurca">MaSuRCA</a> (assembler for short reads, long reads, and hybrid datasets) version 3.3.5 installed on all systems as module MaSuRCA/3.3.5.</p> Thu, 30 Jan 2020 12:24:00 GMT https://www.uppmax.uu.se/changelog 2020-01-30T12:24:00Z [bio] quickmerge/0.3-9233726 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/mahulchak/quickmerge">Quickmerge</a> (simple and fast metassembler and assembly gap filler designed for long molecule based assemblies) version 0.3-9233726 installed on all systems as module quickmerge/0.3-9233726.&nbsp; By default, the module loads MUMmer74.0.0beta2 for alignment, to enable multithreading.&nbsp; If an earlier, nonmultithreaded MUMmer is desired, load the appropriate MUMmer module after loading this module.</p> Thu, 30 Jan 2020 12:22:00 GMT https://www.uppmax.uu.se/changelog 2020-01-30T12:22:00Z [bio] bam2fastx/1.3.0-80dbf79 installed on all systems https://www.uppmax.uu.se/changelog <p>Pacific Biosciences' <a href="https://github.com/PacificBiosciences/bam2fastx">bam2fastq</a> (converting and demultiplexing of PacBio BAM files into gzipped fasta and fastq files)&nbsp;version 1.3.0-80dbf79 (release 1.3.0 updated through git commit 80dbf79) installed on all systems as module bam2fastx/1.3.0-80dbf79.</p> Wed, 29 Jan 2020 11:35:00 GMT https://www.uppmax.uu.se/changelog 2020-01-29T11:35:00Z [bio] augustus/3.3.3 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://bioinf.uni-greifswald.de/augustus">AUGUSTUS</a> (find genes and their structures in one or more genomes) version 3.3.3 installed on all systems as module augustus/3.3.3.</p> Mon, 27 Jan 2020 18:25:00 GMT https://www.uppmax.uu.se/changelog 2020-01-27T18:25:00Z [bio] Salmon/1.1.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://salmon.readthedocs.io/en/latest/salmon.html">Salmon</a> version 1.1.0, a tool for&nbsp;transcript quantification from RNA-seq data, has been installed on all systems as module Salmon/1.1.0&nbsp;.&nbsp;</p> Fri, 24 Jan 2020 11:40:00 GMT https://www.uppmax.uu.se/changelog 2020-01-24T11:40:00Z [bio] subread/2.0.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://subread.sourceforge.net">Subread</a> (high-performance read alignment, quantification and mutation discovery) version 2.0.0 installed on all systems as module subread/2.0.0.</p> Fri, 17 Jan 2020 14:55:00 GMT https://www.uppmax.uu.se/changelog 2020-01-17T14:55:00Z [bio] bambam/1.4 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://sourceforge.net/projects/bambam/">BamBam</a> (numerous tools for analyzing DNA next-generation sequencing data: calling SNPs and indels, identifying large scale deletions, tabulating counts of mapped reads, methylation analysis, and more) version 1.4 is now available as module bambam/1.4 on all systems.</p> Wed, 15 Jan 2020 15:08:00 GMT https://www.uppmax.uu.se/changelog 2020-01-15T15:08:00Z [bio] LDpred/1.0.11 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/bvilhjal/ldpred">LDpred</a> (software package that adjusts GWAS summary statistics for the effects of linkage disequilibrium) version 1.0.11 has been installed as module LDpred/1.0.11 on all systems.</p> Thu, 19 Dec 2019 15:02:00 GMT https://www.uppmax.uu.se/changelog 2019-12-19T15:02:00Z [bio] samtools/1.10, bcftools/1.10 and htslib/1.10 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.htslib.org/">Samtools, BCFtools and HTSlib</a> (extremely useful bioinformatics tools) versions 1.10 have been installed as modules samtools/1.10, bcftools/1.10 and htslib/1.10 on all systems.&nbsp; These have all been compiled with libcurl, AWS S3, GCS and HTSlib plugins enabled.&nbsp; BCFtools has been compiled with Perl filters enabled&nbsp;and GSL support, which adds the +polysomy plugin.</p> Fri, 13 Dec 2019 17:14:00 GMT https://www.uppmax.uu.se/changelog 2019-12-13T17:14:00Z [bio] spaceranger/1.0.0 and spaceranger-data/1.0.0 installed on all systems https://www.uppmax.uu.se/changelog <p>10X Chromium <a href="https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger">Space Ranger</a> (set of analysis pipelines that process Visium spatial RNA-seq output and brightfield microscope images in order to detect tissue, align reads, generate feature-spot matrices, perform clustering and gene expression analysis, and place spots in spatial context on the slide image) version 1.0.0 is now installed as spaceranger/1.0.0 on all systems.&nbsp; Also installed is the data module spaceranger-data/1.0.0, which provides Visium Dual Index sets.&nbsp; Reference data for this module is provided by the cellranger-data/3.0.0 module.</p> Thu, 12 Dec 2019 14:27:00 GMT https://www.uppmax.uu.se/changelog 2019-12-12T14:27:00Z [libs] PLplot/5.15.0 and PLplot/5.15.0-old_wxWidgets installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://plplot.sourceforge.net/">PLplot</a> (a cross-platform software package for creating scientific plots whose (UTF-8) plot symbols and text are limited in practice only by what Unicode-aware system fonts are installed on a user's computer) version 5.15.0 is now installed on all clusters as two modules: PLplot/5.15.0, with default wxWidgets support, and PLplot/5.15.0-old_wxWidgets, which was built with the &nbsp;-DOLD_WXWIDGETS:BOOL=ON option which incorporates an older wxWidgets toolkit driver required by the Gnu Data Language gdl/1.0.0-rc.1 module.</p> Wed, 11 Dec 2019 14:52:00 GMT https://www.uppmax.uu.se/changelog 2019-12-11T14:52:00Z [libs] hdf4/4.2.14-gcc6.3.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://support.hdfgroup.org/products/hdf4/">HDF4</a> (data file format) version 4.2.14 compiled with gcc/6.3.0 is now installed as module hdf4/4.2.14-gcc6.3.0 on all systems.</p> Wed, 11 Dec 2019 14:41:00 GMT https://www.uppmax.uu.se/changelog 2019-12-11T14:41:00Z [libs] pslib/0.4.6 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://pslib.sourceforge.net">pslib</a> (C-library to create PostScript files on the fly, offering many drawing primitives including inclusion of PNG and EPS images and very sophisticated text rendering) version 0.4.6 is now installed on all systems as module pslib/0.4.6.</p> Wed, 11 Dec 2019 14:02:00 GMT https://www.uppmax.uu.se/changelog 2019-12-11T14:02:00Z [libs] wxWidgets/3.1.3-{gtk2,gtk3,qt5} are now installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.wxwidgets.org/">WxWidgets</a>&nbsp;(C++ library that lets developers create applications for Windows, macOS, Linux and other platforms with a single code base) version 3.1.3 is now installed on all systems in three different modules, each supporting a different toolkit.&nbsp; wxWidgets/3.1.3-gtk2 supports the GTK2 toolkit, wxWidgets/3.1.3-gtk3 supports the GTK3 toolkit, and wxWidgets/3.1.3-qt5 supports the Qt5 toolkit.</p> Wed, 11 Dec 2019 13:59:00 GMT https://www.uppmax.uu.se/changelog 2019-12-11T13:59:00Z [comp] patchelf/0.10 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://nixos.org/patchelf.html">Patchelf</a> (small executable patcher) version 0.10 is now installed on all systems as module patchelf/0.10.</p> Wed, 11 Dec 2019 13:56:00 GMT https://www.uppmax.uu.se/changelog 2019-12-11T13:56:00Z [apps] gdl/1.0.0-rc.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/gnudatalanguage/gdl">Gnu Data Language</a> version 1.0.0-rc.1 is now installed on all systems as module gd0/1.0.0-rc.1.</p> Wed, 11 Dec 2019 13:54:00 GMT https://www.uppmax.uu.se/changelog 2019-12-11T13:54:00Z [comp] git-lfs/2.9.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://git-lfs.github.com/">git-lfs</a> (Git Large File Storage (LFS) replaces large files such as audio samples, videos, datasets, and graphics with text pointers inside Git, while storing the file contents on a remote server like GitHub.com or GitHub Enterprise.) version 2.9.1 installed on all systems as module git-lfs/2.9.1.</p> Fri, 06 Dec 2019 13:37:00 GMT https://www.uppmax.uu.se/changelog 2019-12-06T13:37:00Z [comp] git/2.24.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://git-scm.com/">Git</a> (Source control management) version 2.24.0 installed on all systems as module git/2.24.0.</p> Fri, 06 Dec 2019 13:07:00 GMT https://www.uppmax.uu.se/changelog 2019-12-06T13:07:00Z [libs] SHAPELIB/1.5.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://shapelib.maptools.org/">SHAPELIB</a> (library provides the ability to write simple C programs for reading, writing and updating (to a limited extent) ESRI Shapefiles, and the associated attribute file (.dbf)) version 1.5.0 is now installed on all systems as module SHAPELIB/1.5.0.</p> Fri, 06 Dec 2019 09:41:00 GMT https://www.uppmax.uu.se/changelog 2019-12-06T09:41:00Z [libs] Qhull/2019.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://www.qhull.org">Qhull</a> (computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, furthest-site Delaunay triangulation, and furthest-site Voronoi diagram) version 2019.1 installed on all systems as module Qhull/2019.1.</p> Thu, 05 Dec 2019 16:56:00 GMT https://www.uppmax.uu.se/changelog 2019-12-05T16:56:00Z [bio] SignalP/5.0b installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://www.cbs.dtu.dk/services/SignalP/">SignalP</a> (predicts the presence of signal peptides and the location of their cleavage sites in proteins from Archaea, Gram-positive Bacteria, Gram-negative Bacteria and Eukarya) version 5.0b installed on all systems as module SignalP/5.0b.</p> Thu, 05 Dec 2019 15:57:00 GMT https://www.uppmax.uu.se/changelog 2019-12-05T15:57:00Z [bio] cellranger-ATAC/1.2.0 installed on all systems https://www.uppmax.uu.se/changelog <p>10X Genomics' Chromium <a href="https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac">Cell Ranger ATAC</a> (set of analysis pipelines that process Chromium Single Cell ATAC data) version 1.2.0 is now installed on all systems as module cellranger-ATAC/1.2.0.</p> <p>Cell Ranger ATAC reference data is also available in the data module cellranger-ATAC-data/1.2.0.&nbsp; This module is loaded with the cellranger-ATAC/1.2.0 module.</p> Tue, 03 Dec 2019 15:57:00 GMT https://www.uppmax.uu.se/changelog 2019-12-03T15:57:00Z [bio] diamond/0.9.29 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/bbuchfink/diamond">Diamond</a> (sequence aligner for protein and translated DNA searches, designed for high performance analysis of big sequence data) version 0.9.29 installed on all systems as module diamond/0.9.29.</p> Thu, 28 Nov 2019 12:14:00 GMT https://www.uppmax.uu.se/changelog 2019-11-28T12:14:00Z [libs] deal.II/9.1.1-gcc and deal.II/9.1.1-intel installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.dealii.org/">deal.II</a> (open source finite element library) version 9.1.1 is now installed as two modules on all systems: deal.II/9.1.1-gcc, built with GCC 8.2.0 and OpenMPI 3.1.3; and deal.II/9.1.1-intel, build with Intel compilers&nbsp;2019.1.144, Intel MPI&nbsp;2018.4.274, and GCC 8.2.0.</p> <p>These modules are built using EasyBuild with the foss/2019a and the intel/2019a toolchains, respectively.&nbsp; For more information, see 'module help deal.II/9.1.1-gcc and 'module help deal.II/9.1.1-intel'.</p> Wed, 27 Nov 2019 16:06:00 GMT https://www.uppmax.uu.se/changelog 2019-11-27T16:06:00Z [bio] NanoComp/1.9.2 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/wdecoster/nanocomp">NanoComp</a> (compare multiple runs of long read sequencing data and alignments) version 1.9.2 is now installed as module NanoComp/1.9.2 on all systems.</p> Thu, 21 Nov 2019 13:59:00 GMT https://www.uppmax.uu.se/changelog 2019-11-21T13:59:00Z [bio] MultiQC/1.8 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://multiqc.info/">MultiQC</a> (comprehensive log file summariser) version 1.8 is now installed as module MultiQC/1.8 on all systems.</p> Thu, 21 Nov 2019 12:57:00 GMT https://www.uppmax.uu.se/changelog 2019-11-21T12:57:00Z [bio] FastANI/1.2 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/ParBLiSS/FastANI">FastANI</a> (fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI)) version 1.2 installed on all systems as module FastANI/1.2.</p> Wed, 13 Nov 2019 09:43:00 GMT https://www.uppmax.uu.se/changelog 2019-11-13T09:43:00Z [bio] LDpred/1.0.8 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/bvilhjal/ldpred">LDpred</a> (software package that adjusts GWAS summary statistics for the effects of linkage disequilibrium) version 1.0.8 is now installed as module LDpred/1.0.8 on all systems.</p> Tue, 05 Nov 2019 13:22:00 GMT https://www.uppmax.uu.se/changelog 2019-11-05T13:22:00Z [bio] Stacks/2.41 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://catchenlab.life.illinois.edu/stacks/">Stacks</a> (Software pipeline for building loci from short-read sequences)&nbsp;version 2.41 installed on all systems as module Stacks/2.41.</p> Sat, 26 Oct 2019 15:48:00 GMT https://www.uppmax.uu.se/changelog 2019-10-26T15:48:00Z [bio] qctool/2.0.6 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.well.ox.ac.uk/~gav/qctool/#overview">QCTOOL</a>&nbsp;(manipulation and quality control of GWAS datasets and other genome-wide data) version 2.0.6 is installed as module qctool/2.0.6 on all systems.</p> Fri, 25 Oct 2019 20:05:00 GMT https://www.uppmax.uu.se/changelog 2019-10-25T20:05:00Z [bio] Metaxa2/2.2 and Metaxa2/2.1.3 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://microbiology.se/software/metaxa2/">Metaxa2</a> (Improved Identification and Taxonomic Classification of Small and Large Subunit rRNA in Metagenomic Data) version 2.2 is newly installed on all systems as module Metaxa2/2.2, and version 2.1.3, previously available on milou, is now available on all systems as module Metaxa2/2.1.3.</p> Fri, 25 Oct 2019 10:15:00 GMT https://www.uppmax.uu.se/changelog 2019-10-25T10:15:00Z [apps] GOTM/5.3-221-gac7ec88d installed on all ssytems https://www.uppmax.uu.se/changelog <p><a href="https://gotm.net/">GOTM</a> (general ocean turbulence model) version 5.3-221-gac7ec88d is now installed as module GOTM/5.3-221-gac7ec88d on all systems.</p> Fri, 25 Oct 2019 10:13:00 GMT https://www.uppmax.uu.se/changelog 2019-10-25T10:13:00Z [apps] CDO/1.9.5 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://code.mpimet.mpg.de/projects/cdo">CDO</a> (large tool set for working on climate and NWP model data) version 1.9.5 is now installed as module CDO/1.9.5 on all systems.</p> Fri, 25 Oct 2019 10:11:00 GMT https://www.uppmax.uu.se/changelog 2019-10-25T10:11:00Z [bio] usearch/11.0.667 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://www.drive5.com/usearch/download.html">usearch</a> (versatile tool for metagenomics) version 11.0.667 installed on all systems as module usearch/11.0.667.</p> Mon, 21 Oct 2019 15:36:00 GMT https://www.uppmax.uu.se/changelog 2019-10-21T15:36:00Z [bio] vsearch/2.14.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/torognes/vsearch">vsearch</a> (Versatile open source tool for metagenomics) version 2.14.1 installed on all systems as module vsearch/2.14.1.</p> Mon, 21 Oct 2019 15:00:00 GMT https://www.uppmax.uu.se/changelog 2019-10-21T15:00:00Z [bio] bcftools/1.9-develop installed on all systems https://www.uppmax.uu.se/changelog <p>The l<a href="https://github.com/samtools/bcftools">atest development version of BCFTools</a> has been installed as bcftools/1.9-develop on all systems.&nbsp; This also uses the <a href="https://github.com/samtools/htslib">latest development version of HTSlib</a>.&nbsp; This development version provides the +split-vep plugin and perhaps has other features, but its use comes with some risk: some of the tests for the +fill-tags plugin fail, and there may be other bugs as well.&nbsp; Use with these cautions in mind.</p> Thu, 17 Oct 2019 16:09:00 GMT https://www.uppmax.uu.se/changelog 2019-10-17T16:09:00Z [bio] htslib/1.9 installed on all systems https://www.uppmax.uu.se/changelog Thu, 17 Oct 2019 15:27:00 GMT https://www.uppmax.uu.se/changelog 2019-10-17T15:27:00Z [bio] bcftools/1.9 installed on all systems https://www.uppmax.uu.se/changelog Thu, 17 Oct 2019 15:27:00 GMT https://www.uppmax.uu.se/changelog 2019-10-17T15:27:00Z [apps] ALPS/2.3.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://alps.comp-phys.org/mediawiki/index.php/Main_Page">ALPS</a> (Algorithms and Libraries for Physics Simulations) is an open source effort aiming at providing high-end simulation codes for strongly correlated quantum mechanical systems as well as C++ libraries for simplifying the development of such code.&nbsp; Version 2.3.0 has been installed as module ALPS/2.3.0 on all systems.&nbsp; When loading the module the ALPS system will be available to use&nbsp;but not build against; see 'module help ALPS/2.3.0' for instructions on steps to follow so that this module can be built against.</p> Tue, 15 Oct 2019 13:13:00 GMT https://www.uppmax.uu.se/changelog 2019-10-15T13:13:00Z [bio] diamond/0.9.26 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/bbuchfink/diamond">Diamond</a> (Fast blast replacement for protein alignments) version 0.9.26 installed on all systems as module diamond/0.9.26.</p> Tue, 15 Oct 2019 13:11:00 GMT https://www.uppmax.uu.se/changelog 2019-10-15T13:11:00Z [apps] Graphviz version 2.40.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://graphviz.gitlab.io">Graphviz</a> (Graphviz is open source graph visualization software. Graph visualization is a way of representing structural information as diagrams of abstract graphs and networks.) version 2.40.1 installed on all systems as module Graphviz/2.40.1.</p> Thu, 10 Oct 2019 12:22:00 GMT https://www.uppmax.uu.se/changelog 2019-10-10T12:22:00Z [bio] maker/2.31.10 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.yandell-lab.org/software/maker.html">Maker</a> (portable and easily configurable genome annotation pipeline) version 2.31.10 is now installed as module maker/2.31.10 on all systems.&nbsp; This is built with MPI support by default.</p> Wed, 09 Oct 2019 17:16:00 GMT https://www.uppmax.uu.se/changelog 2019-10-09T17:16:00Z [bio] pysam/0.15.3-python3.6.8 and pysam/0.15.3-python3.7.2 now available on all systems https://www.uppmax.uu.se/changelog <p><a href="https://pysam.readthedocs.io/en/latest/">Pysam</a> (Python API for handling SAM and BAM files) version 0.15.3 is now available for two python module versions: pysam/0.15.3-python3.6.8 and pysam/0.15.3-python3.7.2.</p> Tue, 08 Oct 2019 09:05:00 GMT https://www.uppmax.uu.se/changelog 2019-10-08T09:05:00Z [bio] fcGENE version 1.0.7 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://sourceforge.net/projects/fcgene/">fcGENE</a> (Format converting tool for genotype Data (e.g.PLINK-MACH,MACH-PLINK)) version 1.0.7 installed on all systems as module fcGENE/1.0.7.</p> Mon, 07 Oct 2019 07:05:00 GMT https://www.uppmax.uu.se/changelog 2019-10-07T07:05:00Z [bio] kaiju/1.7.2 has bee installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://kaiju.binf.ku.dk/">Kaiju</a> (fast and sensitive taxonomic classification for metagenomics) version 1.7.2 has been installed as module kaiju/1.7.2 on all systems.</p> Sat, 05 Oct 2019 10:54:00 GMT https://www.uppmax.uu.se/changelog 2019-10-05T10:54:00Z Slurm updated to 19.05 https://www.uppmax.uu.se/changelog <p>Slurm received a major update during the October maintenance stop. Check out <a href="/digitalAssets/813/c_813696-l_1-k_slurm-19.05-tisdagsmo-te.pdf">these slides</a> to learn about some of the changes that may impact you!</p> Thu, 03 Oct 2019 09:28:00 GMT https://www.uppmax.uu.se/changelog 2019-10-03T09:28:00Z [bio] BraCeR version 2019_10_03_22e49cb installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/teichlab/bracer">BraCeR</a> (BraCeR - reconstruction of B cell receptor sequences from single-cell RNAseq data) version 2019_10_03_22e49cb installed on all systems as module BraCeR/2019_10_03_22e49cb.<br /> &nbsp;</p> Thu, 03 Oct 2019 09:01:00 GMT https://www.uppmax.uu.se/changelog 2019-10-03T09:01:00Z [bio] blast/2.9.0+ installed on all systems https://www.uppmax.uu.se/changelog <p>UPPMAX-local <a href="https://blast.ncbi.nlm.nih.gov/Blast.cgi">Blast</a>&nbsp;(canonical sequence search tool) version 2.9.0+ is now installed as module blast/2.9.0+ on all Uppmax systems.&nbsp; This is the first blast module version to support the V5 databases now provided by NCBI.&nbsp; Currently available are nr_v5, nt_v5, refseq_protein_v5 and refseq_rna_v5.&nbsp; These&nbsp;databases include taxonomy information and other features.&nbsp; NCBI will discontinue updating the older database versions at the end of September 2019.</p> Tue, 01 Oct 2019 13:43:00 GMT https://www.uppmax.uu.se/changelog 2019-10-01T13:43:00Z [bio] velocyto/0.17.17 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://velocyto.org/velocyto.py/index.html">Velocyto</a> (library for the analysis of&nbsp;RNA velocity) version 0.17.17&nbsp;is now installed as module velocyto/0.17.17&nbsp;on all systems.</p> Mon, 30 Sep 2019 07:49:00 GMT https://www.uppmax.uu.se/changelog 2019-09-30T07:49:00Z [bio] pblat/2.1 and pblat-cluster/1.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/icebert/pblat">pblat</a> (threads-enabled version of the <a href="https://genome.ucsc.edu/FAQ/FAQblat.html">blat</a> aligner) version 2.1 and <a href="https://github.com/icebert/pblat-cluster">pblat-cluster</a> (MPI-enabled version of blat) version 1.0 are now installed on all clusters as pblat/2.1 and pblat-cluster/1.0 , respectively.&nbsp; Each is updated to&nbsp;blat v36x2 (jksrc.v376).</p> Tue, 24 Sep 2019 09:30:00 GMT https://www.uppmax.uu.se/changelog 2019-09-24T09:30:00Z [bio] fasta/36.3.8h and three older versions installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://faculty.virginia.edu/wrpearson/fasta/">FASTA</a> (search protein and DNA sequence databases, and to confirm the statistical significance of a match by comparing the alignment score to a distribution of scores produced by shuffled sequences) version 36.3.8h, together with versions 36.3.6d, 36.3.6f, 36.3.8, are now installed as module fasta/36.3.8h and corresponding modules on all systems.</p> Wed, 18 Sep 2019 14:23:00 GMT https://www.uppmax.uu.se/changelog 2019-09-18T14:23:00Z [apps] R/3.6.1 and R_packages/3.6.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://cran.r-project.org/">R</a> (statistical system) version 3.6.1 and the corresponding <a href="https://www.uppmax.uu.se/support-sv//r_packages-module-guide">R_packages</a>&nbsp;module are now installed on all systems.&nbsp; The R_packages/3.6.1 module contains a total of&nbsp;<span style="font-size:1em">17657 CRAN and BioConductor packages installed, out of 17992 packages available.&nbsp; Of these,&nbsp;</span>14579 CRAN packages are installed, out of 14913 available, and&nbsp;3054 BioConductor-specific packages are installed, out of 3079 available.</p> Wed, 18 Sep 2019 14:12:00 GMT https://www.uppmax.uu.se/changelog 2019-09-18T14:12:00Z [bio] star-fusion/1.7.0 and genome resource libraries installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/STAR-Fusion/STAR-Fusion">STAR-Fusion</a> (fusion transcript detection) version 1.7.0 is now installed as module star-fusion/1.7.0 on all systems.&nbsp; This version requires and loads as a prerequisite the star/2.7.2b module, which contains new features upon which star-fusion/1.7.0 is dependent.&nbsp; Local copies of the <a href="https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB">CTAT Genome Resource Libraries</a> are currently being updated; see 'module help star-fusion/1.7.0' for more information.</p> Wed, 18 Sep 2019 09:53:00 GMT https://www.uppmax.uu.se/changelog 2019-09-18T09:53:00Z [apps] CDO/1.9.7.1 and CDO/1.9.7.1-intel18.3 now installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://code.mpimet.mpg.de/projects/cdo/">CDO</a> (collection of command line Operators to manipulate and analyse climate and NWP model data) version 1.9.7.1 is now installed as modules CDO/1.9.7.1, compiled with and using prerequisites compiled with the system gcc, and CDO/1.8.7.1-intel18.3, compiled with and using prerequisites compiled with the intel/18.3 compiler.</p> Tue, 17 Sep 2019 16:02:00 GMT https://www.uppmax.uu.se/changelog 2019-09-17T16:02:00Z [libs] Magics/3.3.1 and Magics/3.3.1-intel18.3 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://confluence.ecmwf.int/display/MAGP/Magics">Magics</a> (meteorological plotting software) version 3.3.1 is now installed as modules Magics/3.3.1, compiled with the system gcc, and Magics/3.3.1-intel18.3, compiled with the intel/18.3 compiler.</p> Tue, 17 Sep 2019 15:59:00 GMT https://www.uppmax.uu.se/changelog 2019-09-17T15:59:00Z [libs] ecCodes/2.13.1 installed on all systems https://www.uppmax.uu.se/changelog <p>The <a href="https://confluence.ecmwf.int//display/ECC/">ecCodes</a> library (encoding and decoding of meteorological messages in various formats) version 2.13.1 is now installed as module ecCodes/2.13.1 on all systems.</p> Tue, 17 Sep 2019 15:50:00 GMT https://www.uppmax.uu.se/changelog 2019-09-17T15:50:00Z [libs] PROJ.4/4.9.3 and PROJ.4/4.9.3-intel18.3 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://proj.org/">PROJ.4</a> (geographical information library) version 4.9.3 has been installed as module PROJ.4/4.9.3, compiled with system gcc, and PROJ.4/4.9.3-intel18.3, compiled with the intel/18.3 compiler.</p> Tue, 17 Sep 2019 15:45:00 GMT https://www.uppmax.uu.se/changelog 2019-09-17T15:45:00Z [libs] hdf5/1.10.5 and hdf5/1.10.5-intel18.3 installed on all systems https://www.uppmax.uu.se/changelog <p>The&nbsp;<a href="https://www.hdfgroup.org/solutions/hdf5/">HDF5</a>&nbsp;library version 1.10.5 has been installed on all systems as module hdf5/1.10.5, compiled with system gcc, and hdf5/1.10.5-threadsafe-intel18.3, compiled with the threadsafe option and the intel/18.3 compiler.&nbsp; These modules&nbsp;make&nbsp;use of compression provided by szip/2.1.1 and zlib/1.2.11, which are loaded as prerequisites.</p> Tue, 17 Sep 2019 15:42:00 GMT https://www.uppmax.uu.se/changelog 2019-09-17T15:42:00Z [bio] star/2.7.2b installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/alexdobin/STAR">STAR aligner</a> (Spliced Transcripts Alignment to a Reference) version 2.7.2b is now installed as module star/2.7.2b on all systems.</p> Mon, 16 Sep 2019 09:24:00 GMT https://www.uppmax.uu.se/changelog 2019-09-16T09:24:00Z [bio] GEM-Tools/1.7.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://gemtools.github.io/">GEM-Tools</a> (together with the bundled GEM library are a set of very optimized tools for indexing and querying huge genomes and files, and tools to make these easier to use) version 1.7.1 is now installed as module GEM-Tools/1.7.1 on all systems.</p> Tue, 10 Sep 2019 09:25:00 GMT https://www.uppmax.uu.se/changelog 2019-09-10T09:25:00Z [bio] GEM/3.4 and GEM/2.7 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://groups.csail.mit.edu/cgs/gem/">GEM</a>&nbsp;(high resolution peak calling and motif discovery for ChIP-seq and ChIP-exo data) version 3.4 is now installed on all systems, and version 2.7 (previously installed on milou) is also made available on all systems.</p> Tue, 10 Sep 2019 08:29:00 GMT https://www.uppmax.uu.se/changelog 2019-09-10T08:29:00Z [bio] ExaBayes/1.5 and ExaBayes/1.5-mpi installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://cme.h-its.org/exelixis/web/software/exabayes/">ExaBayes</a> (Software package for Bayesian tree inference, particularly suitable for large-scale analyses on computer clusters) version 1.5 is now installed as module ExaBayes/1.5, with single-node multithread support, and ExaBayes/1.5-mpi, with multi-node multithread support.&nbsp; Refer to 'module help ExaBayes' for assistance on using ExaBayes.</p> Mon, 09 Sep 2019 14:48:00 GMT https://www.uppmax.uu.se/changelog 2019-09-09T14:48:00Z [bio] spades/3.13.1 installed on all systems https://www.uppmax.uu.se/changelog <p>The <a href="http://cab.spbu.ru/software/spades/">SPAdes assembler</a> version 3.13.1 is now installed as module spades/3.13.1 on all systems.</p> Thu, 05 Sep 2019 14:23:00 GMT https://www.uppmax.uu.se/changelog 2019-09-05T14:23:00Z [libs] netcdf/4.7.1 and netcdf/4.7.1-intel18.3 installed on all systems https://www.uppmax.uu.se/changelog <p>The <a href="https://www.unidata.ucar.edu/software/netcdf/">NetCDF</a> library version 4.7.1 has been installed as module netcdf/4.7.1, compiled with system gcc, and netcdf/4.7.1-intel18.3, compiled with the intel/18.3 compiler.&nbsp; This makes use of the hdf5/1.10.5 and hdf5/1.10.5-intel18.3 libraries, respectively.</p> Tue, 03 Sep 2019 09:57:00 GMT https://www.uppmax.uu.se/changelog 2019-09-03T09:57:00Z [libs] freetype/2.10.1 installed on all systems https://www.uppmax.uu.se/changelog <p>The <a href="https://www.freetype.org/">FreeType</a> type management library version 2.10.1 is now installed as module freetype/2.10.1 on all systems.</p> Tue, 03 Sep 2019 09:55:00 GMT https://www.uppmax.uu.se/changelog 2019-09-03T09:55:00Z [bio] rtgtools version 3.10.1 installed on all systems https://www.uppmax.uu.se/changelog <p>rtgtools version 3.10.1 installed on all systems,&nbsp;RTG Tools is a subset of <a href="https://github.com/RealTimeGenomics/rtg-core">RTG Core</a> that includes several useful utilities for dealing with VCF files and sequence data. Probably the most interesting is the <code>vcfeval</code> command which performs sophisticated comparison of VCF files.</p> Fri, 30 Aug 2019 09:57:00 GMT https://www.uppmax.uu.se/changelog 2019-08-30T09:57:00Z [bio] ART version 2016-06-05 installed on all systems https://www.uppmax.uu.se/changelog <p>ART (ART is a set of simulation tools to generate synthetic next-generation sequencing reads.) version 2016-06-05 installed on all systems as module ART/2016-06-05.</p> <p>https://www.niehs.nih.gov/research/resources/software/biostatistics/art/</p> Fri, 30 Aug 2019 08:40:00 GMT https://www.uppmax.uu.se/changelog 2019-08-30T08:40:00Z [bio] VerifyBamID2/1.0.6 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://griffan.github.io/VerifyBamID/">VerifyBamID2</a> (robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method) version 1.0.6 is installed as module VerifyBamID2/1.0.5 on all systems.</p> Wed, 28 Aug 2019 15:05:00 GMT https://www.uppmax.uu.se/changelog 2019-08-28T15:05:00Z [bio] verifyBamID/1.1.3 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/statgen/verifyBamID">verifyBamID</a> (verifies whether the reads in particular file match previously known genotypes for an individual (or group of individuals), and checks whether the reads are contaminated as a mixture of two samples) version 1.1.3 is now installed as module verifyBamID/1.1.3 on all systems.</p> Wed, 28 Aug 2019 14:02:00 GMT https://www.uppmax.uu.se/changelog 2019-08-28T14:02:00Z [apps] awscli/1.16.225 installed on all systems https://www.uppmax.uu.se/changelog <p>The latest version of the <a href="https://aws.amazon.com/cli/">Amazon Web Services Command-Line Interface</a> has been installed as module awscli/1.16.225 on all systems.</p> Mon, 26 Aug 2019 11:56:00 GMT https://www.uppmax.uu.se/changelog 2019-08-26T11:56:00Z [bio] blobtools/1.1.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://blobtools.readme.io/docs">Blobtools</a> (modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets) version 1.1.1 is now installed as module blobtools/1.1.1 on all systems.&nbsp; See 'module help blobtools/1.1.1' for advice on building your own taxonomy database.</p> Mon, 26 Aug 2019 11:28:00 GMT https://www.uppmax.uu.se/changelog 2019-08-26T11:28:00Z [apps] circos/0.69-9 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://circos.ca/">Circos</a> (software package that visualizes data in a circular layout) version 0.69-9 is now installed as module circos/0.69-9 on all systems.</p> Fri, 23 Aug 2019 15:15:00 GMT https://www.uppmax.uu.se/changelog 2019-08-23T15:15:00Z [bio] iqtree/1.6.12-omp-mpi installed on all systems https://www.uppmax.uu.se/changelog <p>The latest version of <a href="http://www.iqtree.org/">IQ-TREE</a> (efficient phylogeny estimation) has been installed as module&nbsp;iqtree/1.6.12-omp-mpi on all systems.&nbsp; To use the MPI-enabled versions, it is necessary to load the gcc/8.2.0 and openmpi/3.1.1 modules; see 'module help&nbsp;iqtree/1.6.12-omp-mpi' for more information.</p> Fri, 23 Aug 2019 13:53:00 GMT https://www.uppmax.uu.se/changelog 2019-08-23T13:53:00Z [bio] longranger/2.2.2 fixed https://www.uppmax.uu.se/changelog <p>An error in a module file prevented the longranger/2.2.2 module from working correctly.&nbsp; This is now fixed.</p> Fri, 23 Aug 2019 13:02:00 GMT https://www.uppmax.uu.se/changelog 2019-08-23T13:02:00Z [libs] Various versions of Boost 1.70.0 installed https://www.uppmax.uu.se/changelog <p><a href="https://www.boost.org/">Boost</a> (free peer-reviewed portable C++ source libraries) version 1.70.0 has been provided compiled with different combinations of GCC and Intel compilers, with and without MPI.&nbsp; The name of each module version reflects the compiler(s) used to compile that version but those are <strong>not</strong> loaded when the boost module is loaded; that is left for the user to decide.&nbsp; Now installed as modules on all systems are boost/1.70.0_gcc9.1.0, boost/1.70.0_gcc9.1.0_mpi3.1.3,&nbsp;boost/1.70.0_intel18.3, and boost/1.70.0_intel18.3_mpi3.1.3.</p> Mon, 19 Aug 2019 14:20:00 GMT https://www.uppmax.uu.se/changelog 2019-08-19T14:20:00Z [bio] bgen/1.1.4 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://bitbucket.org/gavinband/bgen">bgen</a> (Reference implementation of the BGEN format) version 1.1.4 installed on all systems as module bgen/1.1.4.</p> Mon, 19 Aug 2019 13:47:00 GMT https://www.uppmax.uu.se/changelog 2019-08-19T13:47:00Z [apps] DOCK version 3.7 installed on all systems https://www.uppmax.uu.se/changelog <p>DOCK version 3.7 installed on all systems as module DOCK/3.7.<br /> http://dock.compbio.ucsf.edu/DOCK_3.7/</p> Tue, 13 Aug 2019 08:53:00 GMT https://www.uppmax.uu.se/changelog 2019-08-13T08:53:00Z [bio] HiCUP/0.7.2 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.bioinformatics.babraham.ac.uk/projects/hicup/">HiCUP</a> (a&nbsp;tool for mapping and performing quality control on Hi-C data) version 0.7.2 installed on all systems as module HiCUP/0.7.2.</p> Thu, 08 Aug 2019 13:01:00 GMT https://www.uppmax.uu.se/changelog 2019-08-08T13:01:00Z [bio] transrate/1.0.1 and transrate/1.0.2 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://hibberdlab.com/transrate/">Transrate</a> (software for transcriptome assembly analysis) versions 1.0.1 and 1.0.2 are now installed as modules transrate/1.0.1 and transrate/1.0.2 on all systems.&nbsp; <a href="https://github.com/blahah/transrate/issues/208">It appears that transrate/1.0.3 has bugs</a>; it is not clear whether this extends to transrate/1.0.2. It is recommended to use transrate/1.0.1.</p> Wed, 07 Aug 2019 14:06:00 GMT https://www.uppmax.uu.se/changelog 2019-08-07T14:06:00Z [bio] HyPhy/2.5.0 and HyPhy/2.5.0-mpi installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://www.hyphy.org/">HyPhy</a>&nbsp;(hypothesis testing using phylogenies) version 2.5.0 is now installed as module HyPhy/2.5.0 (for single-node use, with threads support) and HyPhy/2.5.0-mpi (for multinode use, with MPI support).</p> Wed, 07 Aug 2019 13:24:00 GMT https://www.uppmax.uu.se/changelog 2019-08-07T13:24:00Z [bio] star/2.7.1a installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/alexdobin/STAR/releases/tag/2.7.1a">STAR</a> (spliced RNA-seq aligner) version 2.7.1a is now installed as module star/2.7.1a on all systems.</p> Tue, 06 Aug 2019 14:29:00 GMT https://www.uppmax.uu.se/changelog 2019-08-06T14:29:00Z [bio] FusionCatcher/1.10 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/ndaniel/fusioncatcher">FusionCatcher</a> (finds somatic fusion genes in RNA-seq data) version 1.10 is now installed as module FusionCatcher/1.10 on all systems.&nbsp; See 'module help FusionCatcher/1.10' for more information.</p> Tue, 06 Aug 2019 14:17:00 GMT https://www.uppmax.uu.se/changelog 2019-08-06T14:17:00Z [bio] bowtie/1.2.2 and bowtie/1.2.3 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://bowtie-bio.sourceforge.net/index.shtml">Bowtie</a> (older-tech but still widely used short-read aligner) versions 1.2.2 and 1.2.3 are now installed as modules bowtie/1.2.2 and bowtie/1.2.3 on all systems.</p> Mon, 05 Aug 2019 15:00:00 GMT https://www.uppmax.uu.se/changelog 2019-08-05T15:00:00Z [bio] picard/2.19.2 and picard/2.20.4 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://broadinstitute.github.io/picard/">Picard tools</a> (various tools for manipulating bioinformatics files) versions 2.19.2 and 2.20.4 are now installed as modules picard/2.19.2 and picard/2.20.4, respectively.</p> Mon, 05 Aug 2019 14:35:00 GMT https://www.uppmax.uu.se/changelog 2019-08-05T14:35:00Z [bio] bbmap/38.61b installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://sourceforge.net/projects/bbmap/">BBMap</a> (short-read aligner and other tools) version 38.61b is installed as module bbmap/38.61b on all systems.</p> Mon, 05 Aug 2019 12:43:00 GMT https://www.uppmax.uu.se/changelog 2019-08-05T12:43:00Z [bio] star/2.7.0f installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/alexdobin/STAR">STAR</a> (splice-aware RNA-seq aligner) version 2.7.0f is now installed as module star/2.7.0f on all systems.</p> Mon, 05 Aug 2019 09:42:00 GMT https://www.uppmax.uu.se/changelog 2019-08-05T09:42:00Z [bio] blat/36 available on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/ucscGenomeBrowser/kent">Blat</a> (general-purpose aligner) verison 36 is now available as module blat/36 on all systems.</p> Thu, 01 Aug 2019 13:12:00 GMT https://www.uppmax.uu.se/changelog 2019-08-01T13:12:00Z [bio] older bwa versions now available on all systems https://www.uppmax.uu.se/changelog <p>Four older versions of <a href="https://github.com/lh3/bwa">BWA</a> (read aligner) not available since kalkyl or milou are now available&nbsp;on all systems: bwa/0.5.8a, bwa/0.5.9, bwa/0.6.1, bwa/0.6.2</p> Thu, 01 Aug 2019 13:09:00 GMT https://www.uppmax.uu.se/changelog 2019-08-01T13:09:00Z [bio] SortMeRNA/3.0.3 is now installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/biocore/sortmerna">SortMeRNA</a> (next-generation sequence filtering and alignment tool) version 3.0.3 is now installed as module SortMeRNA/3.0.3 on all systems.&nbsp; Also included are indexed RNA databases, and the auxiliary scripts are now available in the path; see 'module help SortMeRNA/3.0.3' for more information.</p> Thu, 01 Aug 2019 09:28:00 GMT https://www.uppmax.uu.se/changelog 2019-08-01T09:28:00Z [bio] DosageConvertor version 1.0.4 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/Santy-8128/DosageConvertor">DosageConvertor</a> (a C++ tool to convert dosage files (in VCF format) from Minimac3/4 to other formats such as MaCH or PLINK) version 1.0.4 installed on all systems as module DosageConvertor/1.0.4.</p> Fri, 05 Jul 2019 15:34:00 GMT https://www.uppmax.uu.se/changelog 2019-07-05T15:34:00Z [bio] SiBELia/3.0.7 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://bioinf.spbau.ru/sibelia">SiBELia</a> (comparative genomics tool that assists biologists in analysing the genomic variations that correlate with pathogens, or the genomic changes that help microorganisms adapt in different environments) version 3.0.7 is now installed as module SiBELia/3.0.7 on all systems.</p> Fri, 28 Jun 2019 15:09:00 GMT https://www.uppmax.uu.se/changelog 2019-06-28T15:09:00Z [bio] SMARTdenovo/20180219-5cc1356 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/ruanjue/smartdenovo">SMARTdenovo</a> (de novo long-read assembly) through commit 5cc1356 on 19 Feb 2018 is now installed as module&nbsp;SMARTdenovo/20180219-5cc1356 on all systems.</p> Wed, 19 Jun 2019 14:52:00 GMT https://www.uppmax.uu.se/changelog 2019-06-19T14:52:00Z [bio] wtdbg2/2.4 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/ruanjue/wtdbg2">Wtdbg2</a> (<em>de novo</em> sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies) version 2.4 is now installed as module wtdbg2/2.4 on all systems.</p> Tue, 18 Jun 2019 15:53:00 GMT https://www.uppmax.uu.se/changelog 2019-06-18T15:53:00Z [bio] Flye/2.4.2 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/fenderglass/Flye">Flye</a> (de novo assembler for single molecule sequencing reads) version 2.4.2 is now installed as module Flye/2.4.2 on all systems.</p> Tue, 18 Jun 2019 14:12:00 GMT https://www.uppmax.uu.se/changelog 2019-06-18T14:12:00Z [bio] Filtlong/0.2.0-20190515-13504b7 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/rrwick/Filtlong">Filtlong</a> (tool for filtering long reads by quality) version 0.2.0 through commit&nbsp;13504b7 on 15 May 2019 is now installed as module Filtlong/0.2.0-20190515-13504b7 on all systems.</p> Tue, 18 Jun 2019 10:41:00 GMT https://www.uppmax.uu.se/changelog 2019-06-18T10:41:00Z [bio] Porechop/0.2.4 has been installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/rrwick/Porechop">Porechop</a> (tool for finding and removing adapters from&nbsp;<a href="https://nanoporetech.com/">Oxford Nanopore</a>&nbsp;reads) is now installed as module Porechop/0.2.4 on all systems.</p> Tue, 18 Jun 2019 10:15:00 GMT https://www.uppmax.uu.se/changelog 2019-06-18T10:15:00Z [bio] sratools/2.9.6-1 installed on all systems https://www.uppmax.uu.se/changelog <p>The <a href="https://ncbi.github.io/sra-tools/">SRA Toolkit</a> (tools for interacting with NCBI's Short Read Archive) version 2.9.6 has been installed as module sratools/2.9.6-1 on all systems.</p> Tue, 18 Jun 2019 10:13:00 GMT https://www.uppmax.uu.se/changelog 2019-06-18T10:13:00Z [bio] canu/1.8 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://canu.readthedocs.io/en/latest/">Canu</a> (single-molecule assembly, a fork of the original Celera Assembler) version 1.8 is now installed as module canu/1.8 on all systems.</p> Mon, 17 Jun 2019 11:04:00 GMT https://www.uppmax.uu.se/changelog 2019-06-17T11:04:00Z [apps] gnuplot/5.2.7 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://www.gnuplot.info/">Gnuplot</a> (general purpose plotting tool) version 5.2.7 is now installed as module gnuplot/5.2.7 on all systems.</p> Mon, 17 Jun 2019 10:39:00 GMT https://www.uppmax.uu.se/changelog 2019-06-17T10:39:00Z [bio] BioPerl/1.7.2_Perl5.26.2 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://bioperl.org/">BioPerl</a> (Perl toolkit for working with bioinformatic data) version 1.7.2 for perl version 5.26.2 is now installed as module BioPerl/1.7.2_Perl5.26.2 on all systems.</p> Mon, 17 Jun 2019 07:40:00 GMT https://www.uppmax.uu.se/changelog 2019-06-17T07:40:00Z [bio] PhyML/3.3.20190321 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/stephaneguindon/phyml">PhyML</a> (Phylogenetic estimation using (Maximum) Likelihood) version 3.3.20190321 has been installed as module PhyML/3.3.20190321 on all systems.&nbsp; The tools&nbsp;phyml, phyrex and phytime are available.</p> Fri, 14 Jun 2019 13:07:00 GMT https://www.uppmax.uu.se/changelog 2019-06-14T13:07:00Z [bio] several bioinformatics modules enabled on all systems https://www.uppmax.uu.se/changelog <p>Several bioinformatics modules that were previously available on Milou or on a subset of current systems are now available on all systems: rdp-classifier/2.2, rdp-classifier/2.4, Roary/3.6.2, QuorUM/1.0.0, RDXplorer/3.2.&nbsp; If you require any&nbsp;other modules not currently available on active systems that were previously available on Milou, please let us know.</p> Thu, 13 Jun 2019 09:33:00 GMT https://www.uppmax.uu.se/changelog 2019-06-13T09:33:00Z [bio] RegScan/0.5 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.geenivaramu.ee/en/tools/regscan">RegScan</a> (fast association analysis between allele frequencies and continuous traits. It uses linear regression to estimate marker effects on continuous traits) version 0.5 is now installed as module RegScan/0.5 on all systems.&nbsp; Please give it a couple of days to propogate to all compute nodes, as there is a system library that needs to be installed for it to work everywhere.</p> Thu, 13 Jun 2019 09:12:00 GMT https://www.uppmax.uu.se/changelog 2019-06-13T09:12:00Z [comp] perl6/rakudo-star-2019.03 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://perl6.org/">Perl 6</a> (advanced scripting language) version Rakudo Star 2019.03 is now installed as module&nbsp;perl6/rakudo-star-2019.03 on all systems.</p> Sat, 08 Jun 2019 14:01:00 GMT https://www.uppmax.uu.se/changelog 2019-06-08T14:01:00Z [comp] julia/1.1.1 installed on all systems https://www.uppmax.uu.se/changelog <p>The <a href="https://julialang.org/">Julia programming language</a> version 1.1.1 is now installed as module julia/1.1.1 on all systems.</p> Sat, 08 Jun 2019 13:51:00 GMT https://www.uppmax.uu.se/changelog 2019-06-08T13:51:00Z [bio] SMRT/7.0.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.pacb.com">SMRT Link</a>&nbsp;(analysis software for PacBio long-read technology) version 7.0.1 has been installed on all systems as module SMRT/7.0.1.</p> Fri, 07 Jun 2019 14:19:00 GMT https://www.uppmax.uu.se/changelog 2019-06-07T14:19:00Z [comp] git/2.21.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://git-scm.com/">Git</a> (free and open source distributed version control system) version 2.21.0 is now installed as module git/2.21.0 on all systems.</p> Tue, 04 Jun 2019 08:38:00 GMT https://www.uppmax.uu.se/changelog 2019-06-04T08:38:00Z [bio] bowtie2/2.3.5.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://bowtie-bio.sourceforge.net/bowtie2/index.shtml">Bowtie2</a> (ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences) version 2.3.5.1 has been installed as module bowtie2/2.3.5.1 on all systems.</p> Mon, 03 Jun 2019 12:46:00 GMT https://www.uppmax.uu.se/changelog 2019-06-03T12:46:00Z [bio] bismark/0.22.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.bioinformatics.babraham.ac.uk/projects/bismark">Bismark</a> ((tool to map bisulfite converted sequence reads and determine cytosine methylation states) version 0.22.1 installed on all systems as module bismark/0.22.1 on all systems.</p> Mon, 03 Jun 2019 12:45:00 GMT https://www.uppmax.uu.se/changelog 2019-06-03T12:45:00Z [bio] Chromium Long Ranger version 2.2.2 is now installed as module longranger/2.2.2 on all systems. https://www.uppmax.uu.se/changelog <p><a href="https://support.10xgenomics.com/genome-exome/software/pipelines/latest/what-is-long-ranger">Chromium Long Ranger</a> (set of analysis pipelines that processes Chromium sequencing output to align reads and call and phase SNPs, indels, and structural variants) version 2.2.2 is now installed on all systems as module longranger/2.2.2.</p> Wed, 29 May 2019 12:41:00 GMT https://www.uppmax.uu.se/changelog 2019-05-29T12:41:00Z [bio] RAxML-NG/0.9.0 and RAxML-NG/0.9.0-mpi installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/amkozlov/raxml-ng/wiki">RAxML-NG</a> (phylogenetic tree inference tool which uses maximum-likelihood optimality criterion) version 0.9.0 has been installed as module RAxML-NG/0.9.0 (single-node runs) and MPI-enabled as module RAxML-NG/0.9.0-mpi, which supports running on multiple nodes.</p> Wed, 29 May 2019 10:06:00 GMT https://www.uppmax.uu.se/changelog 2019-05-29T10:06:00Z [bio] Yleaf/2.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://cluster15.erasmusmc.nl/fmb/Yleaf_v2/index.html">Yleaf</a> (Detection of Y-Haplogroups in Human genome DNA) version 2.0 installed on all systems as module Yleaf/2.0.&nbsp; Indices for both hg19 and hg38 are available.</p> Tue, 28 May 2019 13:59:00 GMT https://www.uppmax.uu.se/changelog 2019-05-28T13:59:00Z [bio] medaka version 0.7.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/nanoporetech/medaka">medaka</a> (A tool to create a consensus sequence from nanopore sequencing data) version 0.7.1 installed on all systems as module medaka/0.7.1.<br /> &nbsp;</p> <p></p> Tue, 28 May 2019 08:22:00 GMT https://www.uppmax.uu.se/changelog 2019-05-28T08:22:00Z [bio] oncotator version 1.9.9.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/broadinstitute/oncotator">Oncotator</a> (A tool for annotating human genomic point mutations and indels with data relevant to cancer researchers.) version 1.9.9.0 installed on all systems as module oncotator/1.9.9.0.</p> Mon, 27 May 2019 13:00:00 GMT https://www.uppmax.uu.se/changelog 2019-05-27T13:00:00Z [bio] Kraken2/2.0.8-beta installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://ccb.jhu.edu/software/kraken2/">Kraken2</a> (second version of the Kraken taxonomic sequence classification system.) version 2.0.8-beta installed on all systems as module Kraken2/2.0.8-beta.</p> Mon, 27 May 2019 09:47:00 GMT https://www.uppmax.uu.se/changelog 2019-05-27T09:47:00Z [bio] psmc/0.6.5-r67-e5f7df5 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/lh3/psmc">PSMC</a> (Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model) version 0.6.5-r67-e5f7df5 (version 0.6.5-r67 with additional changes, see website) installed on all systems as module psmc/0.6.5-r67-e5f7df5.</p> Thu, 23 May 2019 13:34:00 GMT https://www.uppmax.uu.se/changelog 2019-05-23T13:34:00Z [bio] GEMMA version 0.98.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://www.xzlab.org/software.html">GEMMA</a> (Software toolkit for fast application of linear mixed models (LMMs) and related models to genome-wide association studies (GWAS) and other large-scale data sets.) version 0.98.1 installed on all systems as module GEMMA/0.98.1.</p> Thu, 23 May 2019 10:30:00 GMT https://www.uppmax.uu.se/changelog 2019-05-23T10:30:00Z [bio] kallisto/0.45.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://pachterlab.github.io/kallisto/">Kallisto</a> (quantifying abundances of transcripts from bulk and single-cell RNA-Seq data) version 0.45.1 is now installed as module kallisto/0.45.1 on all systems.</p> Thu, 16 May 2019 10:35:00 GMT https://www.uppmax.uu.se/changelog 2019-05-16T10:35:00Z [bio] exonerate/2.4.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate">Exonerate</a> (protein alignment and utilities) version 2.4.0 is now installed as module exonerate/2.4.0 on all systems.</p> Tue, 14 May 2019 16:25:00 GMT https://www.uppmax.uu.se/changelog 2019-05-14T16:25:00Z [apps] R/3.6.0 and R_packages/3.6.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.r-project.org/">R</a> (statistical language and environment) version 3.6.0 &quot;Planting of a Tree&quot; is now installed as module R/3.6.0 on all systems.&nbsp; The <a href="https://www.uppmax.uu.se/support-sv//r_packages-module-guide">R_packages/3.6.0</a> module has also been updated and now contains&nbsp;16800 CRAN and BioConductor packages.</p> Tue, 14 May 2019 13:27:00 GMT https://www.uppmax.uu.se/changelog 2019-05-14T13:27:00Z [bio] DeepVariant version 0.8.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/google/deepvariant">DeepVariant </a>(An analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.) version 0.8.0 installed on all systems as module DeepVariant/0.8.0.</p> Mon, 13 May 2019 12:34:00 GMT https://www.uppmax.uu.se/changelog 2019-05-13T12:34:00Z [bio] diamond/0.9.24 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://www.diamondsearch.org/index.php">Diamond</a> (accelerated BLAST compatible local sequence aligner) version 0.9.24 is now available as module diamond/0.9.24 on all systems.</p> Mon, 13 May 2019 12:27:00 GMT https://www.uppmax.uu.se/changelog 2019-05-13T12:27:00Z [bio] snakemake version 5.4.5 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://snakemake.readthedocs.io/en/stable/">snakemake</a> version 5.4.5 installed on all systems as module snakemake/5.4.5.</p> Mon, 06 May 2019 12:12:00 GMT https://www.uppmax.uu.se/changelog 2019-05-06T12:12:00Z [bio] TrimGalore/0.6.1 now installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/">Trim Galore!</a> (wrapper tool around Cutadapt and FastQC&nbsp;to consistently apply quality and adapter trimming to FastQ files) version 0.6.1 is now installed as module TrimGalore/0.6.1 on all systems.</p> Fri, 03 May 2019 09:29:00 GMT https://www.uppmax.uu.se/changelog 2019-05-03T09:29:00Z [bio] FastQC/0.11.8 now installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/">FastQC</a> (sequence quality tools) version 0.11.8 is now installed as module FastQC/0.11.8 on all systems.</p> Fri, 03 May 2019 09:28:00 GMT https://www.uppmax.uu.se/changelog 2019-05-03T09:28:00Z [bio] cutadapt/2.3 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://cutadapt.readthedocs.io/en/stable/">Cutadapt</a> (flexible adapter trimming) version 2.3 is now installed as module cutadapt/2.3 on all systems.</p> Fri, 03 May 2019 09:26:00 GMT https://www.uppmax.uu.se/changelog 2019-05-03T09:26:00Z [bio] Redundans/0.14a-de_novo-42e8edf-20190314 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/lpryszcz/redundans/tree/de_novo">Redundans</a> (pipeline that assists an assembly of heterozygous/polymorphic genomes, including de novo assembly)&nbsp;version 0.14a, branch de_novo, as of the latest commit 42e8edf on 2019-03-14, has been installed as module Redundans/0.14a-de_novo-42e8edf-20190314&nbsp;on all systems.&nbsp; <em><strong>This is a development project and may contain bugs</strong></em>, use Redundans/0.14a-d11d32b-20190313 unless you know what you are doing.&nbsp; See 'module help&nbsp;Redundans/0.14a-de_novo-42e8edf-20190314' for more information.</p> Thu, 02 May 2019 15:18:00 GMT https://www.uppmax.uu.se/changelog 2019-05-02T15:18:00Z [bio] Redundans/0.14a-d11d32b-20190313 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/lpryszcz/redundans">Redundans</a>&nbsp;(pipeline that assists an assembly of heterozygous/polymorphic genomes) version 0.14a and following commits up to d11d32b on 2019-03-13, is now installed as module&nbsp;Redundans/0.14a-d11d32b-20190313 on all systems.</p> Thu, 02 May 2019 15:09:00 GMT https://www.uppmax.uu.se/changelog 2019-05-02T15:09:00Z [bio] Platanus-allee/2.0.2 now installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://platanus.bio.titech.ac.jp/platanus2">Platanus-allee</a> (assembler that attempts to assemble separate homologous chromosomes in highly heterozygous species) version 2.0.2 is now installed as module Platanus-allee/2.0.2 on all systems.</p> Thu, 02 May 2019 15:07:00 GMT https://www.uppmax.uu.se/changelog 2019-05-02T15:07:00Z [bio] Platanus/1.2.4 now installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://platanus.bio.titech.ac.jp/platanus-assembler">Platanus</a> (high-throughput assembler that can handle highly heterozygous genomes) version 1.2.4 is now installed as module Platanus/1.2.4 on all systems.&nbsp; The version 1.2.1 previously available on milou is also now installed for all current clusters.</p> Thu, 02 May 2019 11:00:00 GMT https://www.uppmax.uu.se/changelog 2019-05-02T11:00:00Z [bio] minimap2/2.16 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/lh3/minimap2">Minimap2</a> (versatile pairwise aligner) version 2.16 is now installed as module minimap2/2.16 on all systems.</p> Thu, 02 May 2019 10:57:00 GMT https://www.uppmax.uu.se/changelog 2019-05-02T10:57:00Z [bio] Stargazer version 1.0.4 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://stargazer.gs.washington.edu/stargazerweb/index.html">Stargazer</a> (a bioinformatics tool for calling star alleles in various polymorphic pharmacogenes from next-generation sequencing (NGS) data.) version 1.0.4 installed on all systems as module Stargazer/1.0.4.</p> Tue, 23 Apr 2019 13:31:00 GMT https://www.uppmax.uu.se/changelog 2019-04-23T13:31:00Z [bio] LTR_Finder/1.0.7 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/xzhub/LTR_Finder">LTR_Finder</a> (efficient program for finding full-length LTR retrotranspsons in genome sequences) version 1.0.7 is available as module LTR_Finder/1.0.7 on all systems.&nbsp; GtRNAdb databases are available, see 'module help LTR_Finder/1.0.7' for more information.&nbsp; When on milou, this module was named 'ltr-finder'.</p> Mon, 15 Apr 2019 12:47:00 GMT https://www.uppmax.uu.se/changelog 2019-04-15T12:47:00Z [apps] gromacs 2019.1 with threads https://www.uppmax.uu.se/changelog <p>Gromacs versions 2019.1 and 2018.6 compiled with -DGMX_THREAD_MPI=ON -DGMX_OPENMP=ON are availabe on Rackham.</p> <ul> <li>gromacs/2019.1.th</li> <li>gromacs/2018.6.th</li> </ul> Sat, 13 Apr 2019 13:24:00 GMT https://www.uppmax.uu.se/changelog 2019-04-13T13:24:00Z [bio] GATK/4.1.0.0 and GATK/4.1.1.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://software.broadinstitute.org/gatk/">GATK</a> (variant calling and more) versions 4.1.0.0 and 4.1.1.0 are now installed as modules GATK/4.1.0.0 and GATK/4.1.1.0 on all systems.&nbsp; The&nbsp;<strong>gatk</strong>&nbsp;wrapper available for each makes it easy to run each; see 'module help GATK/4.1.1.0' for more information.</p> Fri, 12 Apr 2019 15:57:00 GMT https://www.uppmax.uu.se/changelog 2019-04-12T15:57:00Z [apps] p7zip/16.02 module repaired https://www.uppmax.uu.se/changelog <p>The p7zip/16.02 module has been repaired, by adding additional executables 7z and 7zr.</p> Fri, 12 Apr 2019 15:56:00 GMT https://www.uppmax.uu.se/changelog 2019-04-12T15:56:00Z [apps] Octave 5.1.0 installed on all systems https://www.uppmax.uu.se/changelog <p>Version 5.1.0 of GNU&nbsp;Octave, a Matlab-compatible&nbsp;programming&nbsp;language for scientific computing, &nbsp;is now available on all systems as module octave/5.1.0.</p> Fri, 12 Apr 2019 13:31:00 GMT https://www.uppmax.uu.se/changelog 2019-04-12T13:31:00Z [bio] umi_tools/1.0.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/CGATOxford/UMI-tools">UMI-tools</a> (tools for dealing with Unique Molecular Identifiers) version&nbsp;1.0.0 was published as module umi_tools/1.0.0.</p> Wed, 03 Apr 2019 12:34:00 GMT https://www.uppmax.uu.se/changelog 2019-04-03T12:34:00Z [bio] star-fusion/1.5.0 and genome resource libraries installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/STAR-Fusion/STAR-Fusion/wiki">STAR-fusion</a> (use the&nbsp;<a href="https://github.com/alexdobin/STAR">STAR</a>&nbsp;aligner to identify candidate fusion transcripts supported by Illumina reads) version 1.5.0 is now installed as module star-fusion/1.5.0 on all systems.&nbsp; Also installed and newly available are the genome resource libraries both for version 1.5.0 and earlier versions of star-fusion.&nbsp; See 'module help star-fusion/1.5.0' for more information.</p> Wed, 03 Apr 2019 11:14:00 GMT https://www.uppmax.uu.se/changelog 2019-04-03T11:14:00Z [bio] prinseq/0.20.4 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://prinseq.sourceforge.net/">PRINSEQ</a> (sequence data quality control and preprocessing) version 0.20.4 is installed as module prinseq/0.24.1 on all systems.</p> Tue, 02 Apr 2019 15:52:00 GMT https://www.uppmax.uu.se/changelog 2019-04-02T15:52:00Z [apps] OpenFOAM v4.1 installed on Rackham​ https://www.uppmax.uu.se/changelog <p>OpenFOAM 4.1 is now installed on Rackham.</p> <p><strong>module load OpenFOAM/4.1</strong></p> <p><strong>source &#36;FOAM_BASHRC</strong></p> <p>Should you wish to use it together with the waves2Foam tool:</p> <p><strong>module load OpenFOAM/4.1-waves2Foam</strong></p> <p><strong>source &#36;FOAM_BASHRC</strong></p> <p>Please unload all modules (except for the&nbsp;<em>uppmax</em>&nbsp;one) prior to loading OpenFOAM.</p> Tue, 02 Apr 2019 09:21:00 GMT https://www.uppmax.uu.se/changelog 2019-04-02T09:21:00Z [apps] gromacs/2019.1 installed on Rackham https://www.uppmax.uu.se/changelog <p>Gromacs versions 2019.1,&nbsp;2018.6, and 2016.6 are available as modules on Rackham:&nbsp;</p> <ul> <li>gromacs/2019.1</li> <li>gromacs/2018.6</li> <li>gromacs/2016.6</li> </ul> Wed, 27 Mar 2019 13:50:00 GMT https://www.uppmax.uu.se/changelog 2019-03-27T13:50:00Z [libs] cairo/1.17.2 installed on all systems https://www.uppmax.uu.se/changelog <p>The <a href="https://www.cairographics.org/">cairo</a>&nbsp;libraries (2D graphics plotting) version 1.17.2 are now installed as module cairo/1.17.2 on all systems.</p> Tue, 26 Mar 2019 15:49:00 GMT https://www.uppmax.uu.se/changelog 2019-03-26T15:49:00Z [apps] vim/8.1-1053 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.vim.org/">VIM</a> (text editor and more) version 8.1-1053 is now installed as module vim/8.1-1053 on all systems.&nbsp; Included is scripting support for python/2.7.15, python3/3.7.2, ruby/2.6.2, perl, and tcl.</p> Tue, 26 Mar 2019 15:47:00 GMT https://www.uppmax.uu.se/changelog 2019-03-26T15:47:00Z [comp] ruby/2.6.2 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.ruby-lang.org/en/">Ruby</a> (programming language) version 2.6.2 is now installed as ruby/2.6.2 on all systems.&nbsp; Both shared and static versions of libruby are also provided.</p> Tue, 26 Mar 2019 15:42:00 GMT https://www.uppmax.uu.se/changelog 2019-03-26T15:42:00Z [bio] star/2.7.0e installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/alexdobin/STAR">STAR</a> (Spliced Transcripts Alignment to a Reference) version 2.7.0e is now installed as module star/2.7.0e on all systems.&nbsp; The 2.7.0 released include support for STARsolo, single-cell alignments that are said to be ~10x faster than CellRanger.</p> Mon, 25 Mar 2019 14:59:00 GMT https://www.uppmax.uu.se/changelog 2019-03-25T14:59:00Z [bio] phast/1.5 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://compgen.cshl.edu/phast/">Phast</a> (phylogenetic analysis with space/time models) version 1.5 is now installed as module phast/1.5 on all systems.</p> Mon, 25 Mar 2019 11:53:00 GMT https://www.uppmax.uu.se/changelog 2019-03-25T11:53:00Z [build] maven/3.6.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://maven.apache.org/index.html">Apache Maven</a> (software project management and comprehension tool) version 3.6.0 has been installed as module maven/3.6.0 as part of build-tools on all systems.</p> Thu, 21 Mar 2019 15:43:00 GMT https://www.uppmax.uu.se/changelog 2019-03-21T15:43:00Z [build] automake/1.16.1 installed on all systems https://www.uppmax.uu.se/changelog <p>Gnu <a href="https://www.gnu.org/software/automake/">automake</a> (build configuration) version 1.16.1 is installed as module automake/1.16.1 on all systems.</p> Tue, 19 Mar 2019 16:15:00 GMT https://www.uppmax.uu.se/changelog 2019-03-19T16:15:00Z [apps] RStudio/1.1.463 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.rstudio.com/">RStudio</a> (integrated development environment for R statistical language) version 1.1.463 is now installed as module RStudio/1.1.463 on all systems.</p> Tue, 19 Mar 2019 15:25:00 GMT https://www.uppmax.uu.se/changelog 2019-03-19T15:25:00Z [bio] SNPTEST/2.5.5 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://mathgen.stats.ox.ac.uk/genetics_software/snptest/snptest.html">SNPTEST</a> (analysis of single SNP association in genome-wide studies) version 2.5.5 has been installed as module SNPTEST/2.5.5 on all systems.</p> Tue, 19 Mar 2019 15:13:00 GMT https://www.uppmax.uu.se/changelog 2019-03-19T15:13:00Z [bio] qctool/2.0.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.well.ox.ac.uk/~gav/qctool_v2/">QCTOOL</a> (command-line utility program for manipulation and quality control of gwas datasets and other genome-wide data) version 2.0.1 is now installed as module qctool/2.0.1 on all systems.</p> Tue, 19 Mar 2019 15:12:00 GMT https://www.uppmax.uu.se/changelog 2019-03-19T15:12:00Z [bio] fineSTRUCTURE/4.0.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://people.maths.bris.ac.uk/~madjl/finestructure/finestructure.html">FineSTRUCTURE</a>&nbsp;(fast and powerful algorithm for identifying population structure using dense sequencing data) version 4.0.1 is now installed as module fineSTRUCTURE/4.0.1 on all systems.&nbsp; See 'module help fineSTRUCTURE/4.0.1' for more information.</p> Mon, 18 Mar 2019 15:35:00 GMT https://www.uppmax.uu.se/changelog 2019-03-18T15:35:00Z [comp] python/3.7.2 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.python.org/">Python</a>&nbsp;version 3.7.2 is now installed as module python/3.7.2&nbsp;on all systems.&nbsp; Several packages are included with this installation, including up-to-date versions of pip, setuptools, wheel, Cython, numpy, scipy, matplotlib, PyYAML, pandas, h5py, twisted, requests, nltk, pillow, pygments, ipython, jupyter, virtualenv, gitpython, and graphviz.</p> Mon, 18 Mar 2019 13:43:00 GMT https://www.uppmax.uu.se/changelog 2019-03-18T13:43:00Z [bio] iqtree/1.6.10-omp-mpi now installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://www.iqtree.org/">IQ-TREE</a> (efficient software for phylogenomic inference) version 1.6.10 is now installed as module iqtree/1.6.10-omp-mpi.&nbsp; Several different executables with different multithreading capabilities are available; see 'module help iqtree/1.6.10-omp-mpi' for more information.</p> Sat, 16 Mar 2019 13:48:00 GMT https://www.uppmax.uu.se/changelog 2019-03-16T13:48:00Z [bio] eggNOG-mapper/1.0.3 and EggNOG 4.5.1 databases installed https://www.uppmax.uu.se/changelog <p><a href="https://github.com/eggnogdb/eggnog-mapper">EggNOG mapper </a>(fast genome-wide functional annotation through orthology assignment) version 1.0.3 is now installed as module eggNOG-mapper/1.0.3.&nbsp; The <a href="http://eggnogdb.embl.de/#/app/downloads">EggNOG databases</a> version 4.5.1 are also installed for local use; see 'module help eggNOG-mapper/1.0.3' for more information.</p> Sat, 16 Mar 2019 13:34:00 GMT https://www.uppmax.uu.se/changelog 2019-03-16T13:34:00Z [bio] SURVIVOR 1.0.3 installed on all systems https://www.uppmax.uu.se/changelog <p>SURVIVOR (Tools for Structural Variations in the VCF format) version 1.0.3,</p> <p>is a tool set for simulating/evaluating SVs, merging and comparing SVs within and among samples, and includes various methods to reformat or summarize SVs, is now installed on all systems as module SURVIVOR/1.0.3.</p> <pre> </pre> <pre> </pre> Fri, 15 Mar 2019 12:45:00 GMT https://www.uppmax.uu.se/changelog 2019-03-15T12:45:00Z [comp] python/3.6.8 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.python.org/">Python</a> version 3.6.8 (last bugfix release of python3.6) is now installed as module python/3.6.8 on all systems.&nbsp; Several packages are included with this installation, including up-to-date versions of pip, setuptools, wheel, Cython, numpy, scipy, matplotlib, PyYAML, pandas, h5py, twisted, requests, nltk, pillow, pygments, ipython, jupyter, virtualenv, gitpython, and graphviz.</p> Thu, 14 Mar 2019 15:58:00 GMT https://www.uppmax.uu.se/changelog 2019-03-14T15:58:00Z [bio] phyutility/2.7.3 is now installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/blackrim/phyutility">Phyutility</a> (simple analyses and modifications of trees and data matrices on the command line) version 2.7.3 is now installed as phyutility/2.7.3 on all systems.</p> Thu, 14 Mar 2019 15:36:00 GMT https://www.uppmax.uu.se/changelog 2019-03-14T15:36:00Z [bio] SLiM/3.2.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://messerlab.org/slim/">SLiM</a> (evolutionary simulation framework that combines a powerful engine for population genetic simulations with the capability of modeling arbitrarily complex evolutionary scenarios) version 3.2.1 is now installed as module SLiM/3.2.1 as part of bioinfo-tools on all systems.</p> Wed, 13 Mar 2019 11:37:00 GMT https://www.uppmax.uu.se/changelog 2019-03-13T11:37:00Z [bio] blasr/5.3.2 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/PacificBiosciences/blasr/wiki">Blasr</a> (PacBio's own long read aligner) version 5.3.2 is now installed as module blasr/5.3.2 on all systems.</p> Mon, 11 Mar 2019 12:52:00 GMT https://www.uppmax.uu.se/changelog 2019-03-11T12:52:00Z [bio] cutadapt/2.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://cutadapt.readthedocs.io/en/stable/index.html">Cutadapt</a> (finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from high-throughput sequencing reads) version 2.0 is now installed as module cutadapt/2.0 on all systems.</p> Mon, 11 Mar 2019 10:44:00 GMT https://www.uppmax.uu.se/changelog 2019-03-11T10:44:00Z [bio] RGT version 0.11.6 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.regulatory-genomics.org/">RGT</a> (A python library and set of tools&nbsp;&nbsp;for the integrative analysis of &nbsp;high throughput regulatory genomics data) version 0.11.6 installed on all systems as module RGT/0.11.6</p> Fri, 08 Mar 2019 12:40:00 GMT https://www.uppmax.uu.se/changelog 2019-03-08T12:40:00Z [build] meson/0.49.2 installed https://www.uppmax.uu.se/changelog <p>The <a href="https://mesonbuild.com/">meson</a> build system version 0.49.2 is now installed as module meson/0.49.2 as part of the build-tools subgroup of modules.</p> Wed, 06 Mar 2019 13:50:00 GMT https://www.uppmax.uu.se/changelog 2019-03-06T13:50:00Z [build] ninja/1.9.0 installed on all systems https://www.uppmax.uu.se/changelog <p>The <a href="https://ninja-build.org/">Ninja</a> build system version 1.9.0 has been installed as module ninja/1.9.0 as part of the build-tools subgroup of modules on all systems.</p> Wed, 06 Mar 2019 12:02:00 GMT https://www.uppmax.uu.se/changelog 2019-03-06T12:02:00Z [bio] LoRDEC/0.9 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://gite.lirmm.fr/lordec/lordec-releases/wikis/home">LoRDEC</a> (correcting sequencing errors in long reads such as PacBio and Oxford Nanopore using highly accurate short reads such as Illumina) version 0.9 is now installed as module LoRDEC/0.9 on all systems.</p> Tue, 05 Mar 2019 16:22:00 GMT https://www.uppmax.uu.se/changelog 2019-03-05T16:22:00Z [bio] nibabel version 2.3.3 installed on all systems https://www.uppmax.uu.se/changelog <p></p> <p><a href="https://github.com/nipy/nibabel">Nibabel</a> version 2.3.3 installed on all systems as module nibabel/2.3.3.</p> <p></p> Tue, 05 Mar 2019 15:24:00 GMT https://www.uppmax.uu.se/changelog 2019-03-05T15:24:00Z [bio] new GATK data bundle installed https://www.uppmax.uu.se/changelog <p>An updated GATK resource bundle from Broad Institute has been installed at&nbsp;/sw/data/uppnex/GATK/.</p> Tue, 05 Mar 2019 10:28:00 GMT https://www.uppmax.uu.se/changelog 2019-03-05T10:28:00Z [bio] biopython/1.73 (python/2.7.15) and biopython/1.73 (python/3.6.0) installed https://www.uppmax.uu.se/changelog <p><a href="https://biopython.org/">BioPython</a> 1.73 has been installed on all systems.&nbsp; The module biopython/1.73 is installed with and uses python/2.7.15, and biopython/1.73-py3 is installed with and uses python/3.6.0.</p> Tue, 05 Mar 2019 10:06:00 GMT https://www.uppmax.uu.se/changelog 2019-03-05T10:06:00Z [bio] CheckM/1.0.12 installed and data directory installed https://www.uppmax.uu.se/changelog <p><a href="https://github.com/Ecogenomics/CheckM/wiki">CheckM</a> (tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes) 1.0.12 is now installed as CheckM/1.0.12 on all systems.&nbsp; Also installed and configured are the CheckM data files.</p> Tue, 05 Mar 2019 09:17:00 GMT https://www.uppmax.uu.se/changelog 2019-03-05T09:17:00Z [bio] Drosophila melanogaster genomes installed for ngsplot https://www.uppmax.uu.se/changelog <p>[bio] Drosophila melanogaster genomes (dm3, dm6)&nbsp;installed for ngsplot.</p> Fri, 01 Mar 2019 08:44:00 GMT https://www.uppmax.uu.se/changelog 2019-03-01T08:44:00Z |apps] Mathematica 11.2 installed https://www.uppmax.uu.se/changelog <p>The Wolfram Mathematica program has been installed on Rackham and Snowy as module mathematica/11.2. We have no generally available license for this software, please turn to your local license responsible and ask for network licenses.</p> Fri, 01 Mar 2019 08:40:00 GMT https://www.uppmax.uu.se/changelog 2019-03-01T08:40:00Z [apps] R/3.5.2 and R_packages/3.5.2 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.r-project.org/">R</a> (statistical analysis system) version 3.5.2 and the corresponding omnibus module containing R packages, R_packages/3.5.2, are now installed on all systems.&nbsp; R_packages/3.5.2 contains&nbsp;13355 CRAN packages installed, out of 13683 available, and&nbsp;2933 BioConductor-specific packages installed, out of 2959 available.&nbsp;</p> Fri, 08 Feb 2019 16:46:00 GMT https://www.uppmax.uu.se/changelog 2019-02-08T16:46:00Z [bio] annovar/2018.04.16 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://annovar.openbioinformatics.org/en/latest/">ANNOVAR</a> (variant annotation) version 2018.04.06 has been installed as module annovar/2018.04.16 on all systems.</p> Tue, 05 Feb 2019 08:34:00 GMT https://www.uppmax.uu.se/changelog 2019-02-05T08:34:00Z [bio] PILER-64/1.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/eernst/piler-64">PILER-64</a> (identification and classification of genomic repeats) version 1.0 is now installed as module PILER-64/1.0 on all systems.&nbsp; This is a 64-bit large-memory version of the original PILER (http://www.drive5.com/piler/piler_userguide.html), and thus suitable for finding repeats in large, complex genomes.</p> Mon, 28 Jan 2019 16:48:00 GMT https://www.uppmax.uu.se/changelog 2019-01-28T16:48:00Z [bio] trf/4.09 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://tandem.bu.edu/trf/trf.html">TRF</a> (tandem repeats finder) version 4.09 is installed as module trf/4.09 on all systems.&nbsp; The legacy version trf/4.07b is now also available on all systems.</p> Mon, 28 Jan 2019 16:46:00 GMT https://www.uppmax.uu.se/changelog 2019-01-28T16:46:00Z [bio] RepeatModeler/1.0.11 installed https://www.uppmax.uu.se/changelog <p><a href="http://www.repeatmasker.org/RepeatModeler/">RepeatModeler</a> (de-novo repeat family identification and modeling package)1.0.11 is now installed as module RepeatModeler/1.0.11 on all systems.&nbsp; Several auxiliary programs are provided; see 'module help RepeatModeler/1.0.11' for more details.</p> Fri, 25 Jan 2019 17:38:00 GMT https://www.uppmax.uu.se/changelog 2019-01-25T17:38:00Z [bio] RepeatMasker/4.0.8 installed https://www.uppmax.uu.se/changelog <p><a href="http://www.repeatmasker.org/">RepeatMasker</a> version 4.0.8 (screen DNA sequences for interspersed repeats and low complexity DNA sequences) has been installed as module RepeatMasker/4.0.8 on all systems.&nbsp; This includes RMBlastn 2.6.0+, hmmer, cross_match, trf, nseg, as well as RepBase RepeatMasker edition 20181026, Dfam 2.0 and Dfam_consensus 20171107.</p> Thu, 24 Jan 2019 15:17:00 GMT https://www.uppmax.uu.se/changelog 2019-01-24T15:17:00Z [bio] ANTs/2.3.1 installed https://www.uppmax.uu.se/changelog <p><a href="https://github.com/ANTsX/ANTs">ANTs</a> (Advanced Normalization Tools for biomedical images) version 2.3.1 is now installed as module ANTs/2.3.1 on all clusters.</p> Mon, 14 Jan 2019 14:28:00 GMT https://www.uppmax.uu.se/changelog 2019-01-14T14:28:00Z [build] cmake/3.13.2 installed https://www.uppmax.uu.se/changelog <p><a href="https://cmake.org">CMake</a> (build configuration and automation tool) version 3.13.2 is now installed as cmake/3.13.2 on Uppmax clusters.</p> Mon, 14 Jan 2019 14:18:00 GMT https://www.uppmax.uu.se/changelog 2019-01-14T14:18:00Z [bio] Stacks/2.2 installed https://www.uppmax.uu.se/changelog <p><a href="http://catchenlab.life.illinois.edu/stacks/">Stacks</a> 2.2 (software pipeline for building loci from short-read sequences such as RAD-Seq) is installed as module Stacks/2.2 on all systems.</p> Tue, 08 Jan 2019 15:27:00 GMT https://www.uppmax.uu.se/changelog 2019-01-08T15:27:00Z [bio] MultiQC/1.7 installed https://www.uppmax.uu.se/changelog <p><a href="https://multiqc.info/">MultiQC</a> version 1.7 (results aggregator for bioinformatic analyses) is now installed as module MultiQC/1.7 on all systems.</p> Tue, 08 Jan 2019 14:35:00 GMT https://www.uppmax.uu.se/changelog 2019-01-08T14:35:00Z [bio] cellranger/3.0.1 installed together with Cell Ranger data 3.0.0 https://www.uppmax.uu.se/changelog <p><a href="https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome">10X Chromium Cell Ranger</a> version 3.0.1 (single-cell RNA-Seq; works with the latest 10X chemistry) is now installed as module cellranger/3.0.1 on all systems.</p> <p>The latest version of Cell Ranger data (3.0.0) is also installed.&nbsp; See 'module help cellranger/3.0.1' for more information.</p> Tue, 08 Jan 2019 13:31:00 GMT https://www.uppmax.uu.se/changelog 2019-01-08T13:31:00Z [bio] gmap-gsnap/2018-07-04 installed https://www.uppmax.uu.se/changelog <p><a href="http://research-pub.gene.com/gmap/">GMAP-GSNAP</a> version 2018-07-04 (alignment of transcripts and short reads) is isntalled as gmap-gsnap/2018-07-04 on all Uppmax systems.&nbsp;</p> Mon, 07 Jan 2019 13:34:00 GMT https://www.uppmax.uu.se/changelog 2019-01-07T13:34:00Z [bio] rrbgen 0.0.6 and STITCH 1.5.4 installed to R_packages/3.5.0 https://www.uppmax.uu.se/changelog <p>The R packages <a href="https://github.com/rwdavies/rrbgen">rrbgen</a> version 0.0.6 (read and write BGEN SNP files) and <a href="https://github.com/rwdavies/STITCH">STITCH</a> version 1.5.4 (haplotype imputation) have been installed as part of the existing R_packages/3.5.0 module, and will be included in future versions of the R_packages module.</p> Mon, 07 Jan 2019 13:25:00 GMT https://www.uppmax.uu.se/changelog 2019-01-07T13:25:00Z [bio] bowtie2/2.3.4.3 installed on all systems https://www.uppmax.uu.se/changelog <p>Bowtie2 (short read aligner) version 2.3.4.3 has been installed as module bowtie2/2.3.4.3 on all systems.</p> Thu, 13 Dec 2018 09:35:00 GMT https://www.uppmax.uu.se/changelog 2018-12-13T09:35:00Z [bio] chipster module fixed https://www.uppmax.uu.se/changelog <p>The URL used by the chipster/webstart module has been updated to use https.&nbsp; The use of chipster via this module still requires an account at&nbsp;https://chipster.csc.fi/, and it will request account credentials when started.</p> Mon, 10 Dec 2018 13:25:00 GMT https://www.uppmax.uu.se/changelog 2018-12-10T13:25:00Z [bio] HiCExplorer version 2.2-beta installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/deeptools/HiCExplorer">HiCExplorer</a> (a set of tools to process, normalize and visualize Hi-C data) version 2.2-beta installed as module HiCExporer/2.2-beta on all systems.</p> Wed, 28 Nov 2018 14:48:00 GMT https://www.uppmax.uu.se/changelog 2018-11-28T14:48:00Z [bio] TIDDIT version 2.3.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/SciLifeLab/TIDDIT">TIDDIT</a> (Tool to identify chromosomal rearrangements using Mate Pair or Paired End sequencing data.) version 2.3.0 was installed as module TIDDIT/2.3.0 on all systems</p> Wed, 28 Nov 2018 10:15:00 GMT https://www.uppmax.uu.se/changelog 2018-11-28T10:15:00Z [bio] Minimac4 version 1.0.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/statgen/Minimac4">Minimac4</a> (an efficient implementation of the genotype imputation algorithms in minimac/mininac2/minimac3) version 1.0.0 installed as module Minimac4/1.0.0 on all systems</p> Wed, 28 Nov 2018 09:45:00 GMT https://www.uppmax.uu.se/changelog 2018-11-28T09:45:00Z [bio] tigment/1.1.2 now installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://bcgsc.github.io/tigmint/">Tigmint</a> (assembly correction via linked reads) version 1.1.2 is now installed as module tigmint/1.1.2 on all Uppmax systems.</p> Mon, 26 Nov 2018 14:06:00 GMT https://www.uppmax.uu.se/changelog 2018-11-26T14:06:00Z [bio] MUMmer/4.0.0beta2 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/mummer4/mummer">MUMmer4</a> version 4.0.0beta2 is now installed as MUMmer/4.0.0beta2 on all systems.</p> Mon, 26 Nov 2018 13:41:00 GMT https://www.uppmax.uu.se/changelog 2018-11-26T13:41:00Z [bio] qiime2 version 2018.11.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://qiime2.org">Qiime2</a> (next-generation microbiome bioinformatics platform) version 2018.11.0 installed as module qiime2/2018.11.0 on all systems</p> Thu, 22 Nov 2018 18:14:00 GMT https://www.uppmax.uu.se/changelog 2018-11-22T18:14:00Z [bio] MaxBin version 2.2.5 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html">MaxBin</a> (clustering metagenomic contigs into different bins, each consists of contigs from one species) version 2.2.5 was install as module MaxBin/2.2.5 on all systems.</p> Thu, 22 Nov 2018 11:47:00 GMT https://www.uppmax.uu.se/changelog 2018-11-22T11:47:00Z [bio] CONCOCT version 0.5.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/BinPro/CONCOCT">CONCOCT</a> (program for unsupervised binning of metagenomic contigs) development version 0.5.0 installed as module CONCOCT/0.5.0 on all systems</p> Tue, 20 Nov 2018 12:56:00 GMT https://www.uppmax.uu.se/changelog 2018-11-20T12:56:00Z [bio] albacore build 4aee41d installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/dvera/albacore">albacore</a> (data processing pipeline that provides the Oxford Nanopore basecalling algorithms, and several post-processing steps.) build 4aee41d installed as module albacore/4aee41d on all systems.</p> Mon, 19 Nov 2018 14:10:00 GMT https://www.uppmax.uu.se/changelog 2018-11-19T14:10:00Z [bio] LASER/2.04 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://csg.sph.umich.edu/chaolong/LASER/">LASER</a> (estimate individual ancestry for sequencing reads) 2.04 is now installed as module LASER/2.04 on all systems.&nbsp; The earlier versions LASER/2.01 and LASER/2.02 were also provided for all systems.</p> Tue, 13 Nov 2018 12:51:00 GMT https://www.uppmax.uu.se/changelog 2018-11-13T12:51:00Z [bio] RAxML-NG/0.7.0b and RAxML-NG/0.7.0b-mpi now installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/amkozlov/raxml-ng">RAxML-NG</a> (next-generation phylogenetic inference) version 0.7.0 Beta has been installed without and with MPI support, as module versions RAxML-NG/0.7.0b and RAxML-NG/0.7.0b-mpi, respectively.</p> Thu, 08 Nov 2018 16:25:00 GMT https://www.uppmax.uu.se/changelog 2018-11-08T16:25:00Z [bio] MACS/2.1.2 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/taoliu/MACS">MACS</a> (tool for identifying transcript factor binding sites) version 2.1.2 was installed as module MACS/2.1.2 on all systems</p> Thu, 08 Nov 2018 14:07:00 GMT https://www.uppmax.uu.se/changelog 2018-11-08T14:07:00Z [bio] hichipper/0.7.3 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/aryeelab/hichipper">hichipper</a> (data processing and quality control pipeline for HiChIP data) version 0.7.3 was installed as module hichipper/0.7.3 on all systems</p> Thu, 08 Nov 2018 12:35:00 GMT https://www.uppmax.uu.se/changelog 2018-11-08T12:35:00Z [bio] OrthoMCL/2.0.9 now creates goodProteins.fasta database with -parse_seqids option https://www.uppmax.uu.se/changelog <p>OrthoMCL/2.0.9 now creates its goodProteins.fasta Blast database of orthologs with the -parse_seqids option, so that blastdbcmd queries against this database can extract specific sequences.</p> Thu, 08 Nov 2018 09:23:00 GMT https://www.uppmax.uu.se/changelog 2018-11-08T09:23:00Z [bio] pyGenomeTracks/2.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/deeptools/pyGenomeTracks">pyGenomeTracks</a> (visualisation tools for genome tracks) 2.1 is now installed as module pyGenomeTrakcs/2.1 on all systems.</p> Tue, 06 Nov 2018 09:54:00 GMT https://www.uppmax.uu.se/changelog 2018-11-06T09:54:00Z [bio] HiC-Pro/2.11.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/nservant/HiC-Pro">HiC-Pro</a> (An optimized and flexible pipeline for Hi-C data processing) version 2.11.1 was installed as module HiC-Pro/2.11.1 on all systems</p> Fri, 26 Oct 2018 13:51:00 GMT https://www.uppmax.uu.se/changelog 2018-10-26T13:51:00Z [bio] Kourami/0.9.6 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/Kingsford-Group/kourami">Kourami </a>(A graph-guided assembler for HLA haplotypes covering typing exons (exons 2 and 3 for Class I and exon 3 for Class II) using high-coverage whole genome sequencing data) version 0.9.6 was installed on all systems.</p> Wed, 24 Oct 2018 14:37:00 GMT https://www.uppmax.uu.se/changelog 2018-10-24T14:37:00Z [bio] MIP/6.0.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/Clinical-Genomics/MIP">MIP</a> (Mutation Identification Pipeline) version 6.0.0 was installed as module mip/6.0.0 on all systems</p> Wed, 24 Oct 2018 12:37:00 GMT https://www.uppmax.uu.se/changelog 2018-10-24T12:37:00Z [bio] Stampy/1.0.32 installed on all systems https://www.uppmax.uu.se/changelog <p>The <a href="http://www.well.ox.ac.uk/project-stampy">Stampy</a> short read aligner version 1.0.32 is now installed as module Stampy/1.0.32 on all systems.</p> Mon, 22 Oct 2018 15:25:00 GMT https://www.uppmax.uu.se/changelog 2018-10-22T15:25:00Z [bio] Mothur/1.41.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.mothur.org/">Mothur</a> (open-source, expandable software to fill the bioinformatics needs of the microbial ecology community) version 1.41.0 is now installed as module Mothur/1.41.0 on all systems.</p> Tue, 09 Oct 2018 09:58:00 GMT https://www.uppmax.uu.se/changelog 2018-10-09T09:58:00Z [bio] Kraken2/2.0.7-beta-bc14b13 installed on all systems https://www.uppmax.uu.se/changelog <p>The <a href="http://ccb.jhu.edu/software/kraken/MANUAL.html">Kraken2</a> sequence classificiation system version&nbsp;2.0.7-beta as of the commit tagged bc14b13 has been installed as Kraken2/2.0.7-beta-bc14b13 on all systems.&nbsp; The default database, as well as the special greengenes, rdp and silva databases have been built and will be rebuilt monthly.&nbsp; See 'module help Kraken2/2.0.7-beta-bc14b13' for more.</p> Wed, 26 Sep 2018 12:24:00 GMT https://www.uppmax.uu.se/changelog 2018-09-26T12:24:00Z [parallel] gnuparallel/20180822 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://savannah.gnu.org/projects/parallel/">Gnu Parallel</a> version 20180822 has been installed on all systems as module gnuparallel/20180822.</p> Thu, 20 Sep 2018 12:58:00 GMT https://www.uppmax.uu.se/changelog 2018-09-20T12:58:00Z [bio] InterProScan/5.30-69.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.ebi.ac.uk/interpro/interproscan.html">InterProScan</a> (scans protein and nucleic acid sequences against InterPro protein signatures, which are predictive models provided by several different databases&nbsp;that make up the InterPro consortium) version 5.30-69.0 is now installed as module InterProScan/5.30-69.0 on all Uppmax systems.</p> <p>This installation includes support for Panther database 12.0, and the additional analysis tools&nbsp;Phobius/1.01,&nbsp;SignalP/4.1f, and&nbsp;tmhmm/2.0c.</p> Thu, 06 Sep 2018 15:29:00 GMT https://www.uppmax.uu.se/changelog 2018-09-06T15:29:00Z [bio] Phobius/1.01 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://phobius.sbc.su.se/data.html">Phobius</a> (combined transmembrane topology and signal peptide predictor) 1.01 has been installed as module Phobius/1.01 on all Uppmax systems.&nbsp; The 64-bit executable is used for the subsidiary tool decodeanhmm.&nbsp;</p> Thu, 06 Sep 2018 15:04:00 GMT https://www.uppmax.uu.se/changelog 2018-09-06T15:04:00Z [bio] umi_tools/0.5.3 and umi_tools/0.5.4 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/CGATOxford/UMI-tools">UMI-tools</a> (tools for handling Unique Molecular Identifiers in NGS data sets) versions 0.5.3 and 0.5.4 are now installed as modules umi_tools/0.5.3 and umi_tools/0.5.4 on all systems.</p> Fri, 17 Aug 2018 08:13:00 GMT https://www.uppmax.uu.se/changelog 2018-08-17T08:13:00Z [bio] samstat/1.5.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://samstat.sourceforge.net/">Samstat</a> (sequence statistics) has been installed as module samstat/1.5.1 on all systems.&nbsp; This module requires samtools, and the samtools/1.8 module will be loaded if another module version of samtools is not already loaded.</p> Thu, 16 Aug 2018 12:44:00 GMT https://www.uppmax.uu.se/changelog 2018-08-16T12:44:00Z [bio] Mothur 1.40.5 installed on all systems https://www.uppmax.uu.se/changelog <p>Mothur, a bioinformatics package developed by and&nbsp;for the microbial ecology community, has been installed on Rackham, Bianca, and Irma. Versions up to 1.38.1 were previously installed on Milou. Load the module with &quot;module load Mothur/1.40.5&quot;.</p> Thu, 16 Aug 2018 08:02:00 GMT https://www.uppmax.uu.se/changelog 2018-08-16T08:02:00Z [bio] GenomeThreader/1.7.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://genomethreader.org/">GenomeThreader</a> (robust de novo gene discovery) version 1.7.0 is now installed as module GenomeThreader/1.7.0 on all systems.</p> Mon, 13 Aug 2018 12:28:00 GMT https://www.uppmax.uu.se/changelog 2018-08-13T12:28:00Z [bio] clustalo/1.2.4 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.ebi.ac.uk/seqdb/confluence/display/THD/Clustal+Omega">Clustal Omega</a> (large multiple sequence alignments) version 1.2.4 has been installed as module clustalo/1.2.4 on all systems.</p> Mon, 06 Aug 2018 12:33:00 GMT https://www.uppmax.uu.se/changelog 2018-08-06T12:33:00Z [bio] MAFFT/7.407 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://mafft.cbrc.jp/alignment/software/">MAFFT</a> multiple sequence alignment version 7.407 is now installed on all systems as module MAFFT/7.407.&nbsp; This includes MAFFT extensions.</p> Mon, 06 Aug 2018 12:32:00 GMT https://www.uppmax.uu.se/changelog 2018-08-06T12:32:00Z [apps] R_packages/3.5.0 updated https://www.uppmax.uu.se/changelog <p>The R_packages omnibus module containing R packages has been updated with modules R2jags, rjags, units, and others.&nbsp; R_packages/3.5.0 contains&nbsp;11746 CRAN packages, out of&nbsp;12772 available, and 14544 BioConductor packages, out of&nbsp;15615 available. See the <a href="https://www.uppmax.uu.se/support/user-guides/r_packages-module-guide/">R_packages module guide</a> for a complete list of available R packages.</p> Thu, 26 Jul 2018 16:40:00 GMT https://www.uppmax.uu.se/changelog 2018-07-26T16:40:00Z [apps] JAGS/4.3.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://mcmc-jags.sourceforge.net/">JAGS</a> (Just Another Gibbs Sampler) version 4.3.0 is now installed as module JAGS/4.3.0 on all systems.</p> Thu, 26 Jul 2018 14:49:00 GMT https://www.uppmax.uu.se/changelog 2018-07-26T14:49:00Z [libs] UDUNITS/2.2.26 installed on all systems https://www.uppmax.uu.se/changelog <p>The <a href="https://www.unidata.ucar.edu/software/udunits/">UDUNITS</a> library (arithmetic manipulation of units and for conversion of numeric values between compatible units) version 2.2.26 is now installed as module UDUNITS/2.2.26 on all systems.&nbsp; This module should be loaded before loading the package 'units' from R_packages/3.5.0.</p> Thu, 26 Jul 2018 13:39:00 GMT https://www.uppmax.uu.se/changelog 2018-07-26T13:39:00Z [bio] Centrifuge/1.0.4-beta installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://ccb.jhu.edu/software/centrifuge/">Centrifuge</a> (classifier for metagenomic sequences) has been installed as Centrifuge/1.0.4-beta on all systems.&nbsp; The indices&nbsp;p_compressed p_compressed+h+v p+h+v p+v v are prebuilt and available in &#36;CENTRIFUGE_DB, set to the appropriate location when the module is loaded.</p> Tue, 24 Jul 2018 11:53:00 GMT https://www.uppmax.uu.se/changelog 2018-07-24T11:53:00Z [bio] deepTools/3.1.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://deeptools.readthedocs.io/">deepTools</a> (tools for exploring deep sequencing data) version 3.1.0 is now installed as module deepTools/3.1.0 on all systems.</p> Thu, 19 Jul 2018 12:45:00 GMT https://www.uppmax.uu.se/changelog 2018-07-19T12:45:00Z [bio] GATK/3.8-0 now includes gatk wrapper script https://www.uppmax.uu.se/changelog <p>The GATK/3.8-0 module now includes the&nbsp;<strong>gatk</strong>&nbsp;wrapper script modified from <a href="https://github.com/bioconda/bioconda-recipes/tree/master/recipes/gatk">Bioconda</a>, so that GATK can be run from the command line using&nbsp;<strong>gatk ...</strong>&nbsp;or&nbsp;<strong>GenomeAnalysisTK ...</strong>&nbsp;directly.</p> Thu, 19 Jul 2018 11:29:00 GMT https://www.uppmax.uu.se/changelog 2018-07-19T11:29:00Z [bio] sratools/2.9.1-1 installed on all systems https://www.uppmax.uu.se/changelog <p>The <a href="https://github.com/ncbi/sra-tools/wiki">SRA Toolkit</a> (interaction with NCBI's SRA databases) version 2.9.1-1 is now installed as module sratools/2.9.1-1 on all Uppmax systems.&nbsp; This includes the fasterq-dump tool to speed the download of FastQ files from SRA.</p> Wed, 18 Jul 2018 09:25:00 GMT https://www.uppmax.uu.se/changelog 2018-07-18T09:25:00Z [bio] CIRCexplorer/1.1.10 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/YangLab/CIRCexplorer">CIRCexplorer</a> (CIRCexplorer is a combined strategy to identify junction reads from back spliced exons and intron lariats.) version 1.1.10 is now installed as module CIRCexplorer/1.1.10 on all systems.</p> Wed, 11 Jul 2018 15:32:00 GMT https://www.uppmax.uu.se/changelog 2018-07-11T15:32:00Z [bio] rvtests/2.0.6 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/zhanxw/rvtests">rvtests</a> (a flexible software package for genetic association analysis for sequence datasets) version 2.0.6 is installed as module rvtests/2.0.6 on all systems.</p> Tue, 10 Jul 2018 12:56:00 GMT https://www.uppmax.uu.se/changelog 2018-07-10T12:56:00Z [bio] PLINK/2 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://https://www.cog-genomics.org/plink/2.0/">PLINK</a> (A comprehensive update to the PLINK association analysis toolset. Beta testing of the first new version (1.90), focused on speed and memory efficiency improvements, is finishing up. Future development will revolve around critical extensions to the core file format (multiallelic variants, dosage, phase). version 2.00-c1defe4 installed on all systems as module plink/2.00-c1defe4</p> Mon, 09 Jul 2018 14:34:00 GMT https://www.uppmax.uu.se/changelog 2018-07-09T14:34:00Z [bio] KrakenHLL/0.4.9 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/fbreitwieser/krakenhll">KrakenHLL</a> (taxonomic sequence classification system with unique k-mer counting) version 0.4.9 has been installed as module KrakenHLL/0.4.9 on all systems.</p> Fri, 06 Jul 2018 15:33:00 GMT https://www.uppmax.uu.se/changelog 2018-07-06T15:33:00Z [bio] blobtools/1.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/DRL/blobtools">Blobtools</a> (A modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets) version 1.0 is now installed as module&nbsp;blobtools/1.0 on all UPPMAX systems.</p> Fri, 06 Jul 2018 14:43:00 GMT https://www.uppmax.uu.se/changelog 2018-07-06T14:43:00Z [bio] malder/1.0 available for rackham, bianca, irma https://www.uppmax.uu.se/changelog <p><a href="https://github.com/joepickrell/malder">MALDER</a> (admixture estimation) version 1.0 is now available as module malder/1.0 on all UPPMAX systems.&nbsp; It was previously available only on milou.</p> Thu, 28 Jun 2018 11:00:00 GMT https://www.uppmax.uu.se/changelog 2018-06-28T11:00:00Z [bio] bbmap/38.08 installed https://www.uppmax.uu.se/changelog <p><a href="https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/bbmap-guide/">BBMap</a> package version 38.08 is now installed as module bbmap/38.08 on all UPPMAX systems.</p> Thu, 28 Jun 2018 10:37:00 GMT https://www.uppmax.uu.se/changelog 2018-06-28T10:37:00Z [apps] siesta/4.1-b3 installed https://www.uppmax.uu.se/changelog <p>Siesta 4.1-b3</p> Wed, 27 Jun 2018 14:20:00 GMT https://www.uppmax.uu.se/changelog 2018-06-27T14:20:00Z [bio] LDhelmet/1.10 installed https://www.uppmax.uu.se/changelog <p><a href="https://sourceforge.net/projects/ldhelmet/">LDhelmet</a> (statistical inference for fine-scale variable recombination rate estimation) version 1.10 is now installed as module LDhelmet/1.10 on all UPPMAX clusters.</p> Tue, 26 Jun 2018 13:37:00 GMT https://www.uppmax.uu.se/changelog 2018-06-26T13:37:00Z [apps] siesta/4.0.1 installed https://www.uppmax.uu.se/changelog <p>Siesta 4.0.1</p> Tue, 26 Jun 2018 08:21:00 GMT https://www.uppmax.uu.se/changelog 2018-06-26T08:21:00Z [comp] intel/18.3 installed https://www.uppmax.uu.se/changelog <p>Intel&nbsp;Parallel Studio XE Cluster Edition upgrade 3 have been installed.<br /> intel/18.3<br /> intelmpi/18.3<br /> advisor/18.3<br /> intelamplifier/18.3<br /> inspector/18.3.0<br /> itac/18.3<br /> have been installed.</p> Thu, 21 Jun 2018 11:22:00 GMT https://www.uppmax.uu.se/changelog 2018-06-21T11:22:00Z [bio] iqtree/1.6.5-omp-mpi installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://www.iqtree.org/">IQ-Tree</a> (phylogenetic tree construction) version 1.6.5 is now installed as module iqtree/1.6.5-omp-mpi on all systems.&nbsp; Different executables provide single-core, multi-core single-node, MPI, and hybrid MPI solutions.&nbsp; See 'module help iqtree/1.6.5-omp-mpi' for more information.</p> Fri, 01 Jun 2018 10:55:00 GMT https://www.uppmax.uu.se/changelog 2018-06-01T10:55:00Z [bio] cutadapt/1.16 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://cutadapt.readthedocs.io/en/stable/index.html">Cutadapt</a> (read trimming) version 1.16 has been installed as module cutadapt/1.16 on all UPPMAX systems. &nbsp;This version uses a python 3 virtual environment and supports threading.</p> Mon, 28 May 2018 13:30:00 GMT https://www.uppmax.uu.se/changelog 2018-05-28T13:30:00Z [bio] vep/92 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://www.ensembl.org/info/docs/tools/vep/index.html">Ensembl Variant Effect Predictor</a> version 92.3 is now installed as module vep/92 on all systems. Cache files, fasta files and plugins are also installed. See the module help for information.</p> Thu, 24 May 2018 14:13:00 GMT https://www.uppmax.uu.se/changelog 2018-05-24T14:13:00Z [bio] snpEff/4.3t installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://snpeff.sourceforge.net/">SnpEff</a> (variant annotation) version 4.3t is installed as module snpEff/4.3t on all systems. &nbsp;This installation also includes the databases&nbsp;CanFam3.1.75,&nbsp;CanFam3.1.86,&nbsp;GRCh37.75,&nbsp;GRCh37.p13.RefSeq,&nbsp;GRCh38.86,&nbsp;GRCh38.p7.RefSeq.</p> Thu, 24 May 2018 13:36:00 GMT https://www.uppmax.uu.se/changelog 2018-05-24T13:36:00Z [bio] KAT/2.4.2 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://kat.readthedocs.io/en/latest/">KAT</a> (Kmer Analysis Toolkit) 2.4.2 is now installed as module KAT/2.4.2 on all systems.</p> Wed, 23 May 2018 11:10:00 GMT https://www.uppmax.uu.se/changelog 2018-05-23T11:10:00Z [bio] PBSuite/15.8.24 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://sourceforge.net/p/pb-jelly/wiki/Home/">PBSuite</a> (PacBio assembler) version 15.8.24 is now installed as module PBSuite/15.8.24 on all systems.&nbsp; It was previously installed only on milou.</p> Tue, 22 May 2018 22:39:00 GMT https://www.uppmax.uu.se/changelog 2018-05-22T22:39:00Z [bio] blast/2.7.1+ installed on all systems https://www.uppmax.uu.se/changelog <p>Blast+ (sequence search) version 2.7.1+ has been installed as module blast/2.7.1+ on all systems.</p> Tue, 22 May 2018 22:36:00 GMT https://www.uppmax.uu.se/changelog 2018-05-22T22:36:00Z [apps] R_packages/3.5.0 installed on all systems https://www.uppmax.uu.se/changelog <p>The <a href="http://www.uppmax.uu.se/support/user-guides/r_packages-module-guide/">R_packages</a> omnibus package 3.5.0 is now installed on all systems as packages R_packages/3.5.0.&nbsp; This package includes&nbsp;11937 <a href="https://ftp.acc.umu.se/mirror/CRAN/">CRAN</a> packages installed, out of&nbsp;12571 available, and 14735 <a href="http://bioconductor.org/packages/release/BiocViews.html#___Software">BioConductor</a> packages installed, out of&nbsp;15411 available.</p> Sun, 20 May 2018 14:51:00 GMT https://www.uppmax.uu.se/changelog 2018-05-20T14:51:00Z [apps] R/3.5.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.r-project.org/">R</a> (statistical system) version 3.5.0 is now installed as module R/3.5.0 on all systems.</p> Sun, 20 May 2018 14:50:00 GMT https://www.uppmax.uu.se/changelog 2018-05-20T14:50:00Z [bio] Installed htslib version 1.8 on bianca, irma and rackham https://www.uppmax.uu.se/changelog <p>New version of <a href="https://github.com/samtools/htslib">htslib</a> (1.8) installed as module htslib/1.8</p> Fri, 18 May 2018 09:45:00 GMT https://www.uppmax.uu.se/changelog 2018-05-18T09:45:00Z [bio] satsuma2/2016-12-07 installed on all systems https://www.uppmax.uu.se/changelog <p>Satsuma2 (whole genome alignment) version 2016-12-07 is now available on all Uppmax systems.&nbsp; It was previously available only on milou.</p> Fri, 18 May 2018 08:54:00 GMT https://www.uppmax.uu.se/changelog 2018-05-18T08:54:00Z [bio] Kraken/1.1-352e780 has been installed on all systems https://www.uppmax.uu.se/changelog <p>Kraken (metagenomic assignment) version 1.1-352e780 has been installed on all systems.&nbsp; This is Kraken 1.1 plus a bugfix for the new paired-reads output mode.</p> Thu, 17 May 2018 10:46:00 GMT https://www.uppmax.uu.se/changelog 2018-05-17T10:46:00Z [apps] rspt/2018-03-31_rackham_intel_mkl installed on Rackham https://www.uppmax.uu.se/changelog <p>RSPt version released March 31st, 2018 is installed on Rackham.</p> Mon, 14 May 2018 13:58:00 GMT https://www.uppmax.uu.se/changelog 2018-05-14T13:58:00Z [parallel] openmpi/3.1.0 https://www.uppmax.uu.se/changelog <p>openmpi 3.1.0 is now installed on Irma, Milou and Rackham.</p> Wed, 09 May 2018 10:22:00 GMT https://www.uppmax.uu.se/changelog 2018-05-09T10:22:00Z [comp] gcc/8.1.0 installed https://www.uppmax.uu.se/changelog <p>gcc 8.1.0 is now installed on Bianca, Irma, Milou and Rackham</p> Wed, 09 May 2018 10:21:00 GMT https://www.uppmax.uu.se/changelog 2018-05-09T10:21:00Z [apps] amber/ambertools18_intel_python2 installed on Rackham https://www.uppmax.uu.se/changelog <p>AmberTools18 (released on April 17, 2018) is installed as a module on Rackham.</p> Tue, 08 May 2018 09:26:00 GMT https://www.uppmax.uu.se/changelog 2018-05-08T09:26:00Z [bio] cd-hit/4.6.8-2017-1208 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/weizhongli/cdhit">CD-HIT</a>&nbsp;(sequence clustering) version&nbsp;4.6.8-2017-1208 has been installed as&nbsp;module cd-hit/4.6.8-2017-1208 on all systems.</p> Thu, 03 May 2018 13:50:00 GMT https://www.uppmax.uu.se/changelog 2018-05-03T13:50:00Z [bio] FastTree/2.1.10 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://www.microbesonline.org/fasttree/">FastTree</a> (fast phylogenetic tree inference) version 2.1.10 has been installed as module FastTree/2.1.10 on all systems. &nbsp;Three executables are available, including single- and multi-threaded versions; see 'module help FastTree/2.1.10' for more information.</p> Thu, 03 May 2018 13:13:00 GMT https://www.uppmax.uu.se/changelog 2018-05-03T13:13:00Z [bio] eigensoft/7.2.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/DReichLab/EIG">Eigensoft</a> 7.2.1 (with the fix restoring the ploteig tool) is now installed as module eigensoft/7.2.1 on all systems.</p> Thu, 26 Apr 2018 13:38:00 GMT https://www.uppmax.uu.se/changelog 2018-04-26T13:38:00Z [bio] AdmixTools/5.0-20171024 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/DReichLab/AdmixTools">AdmixTools</a> version 5.0 with the latest commit as of 2017 Oct 24, which includes the&nbsp;qpDpart and rolloffp tools, is now installed as module&nbsp;&nbsp;AdmixTools/5.0-20171024 on all systems.&nbsp; Also installed on all systems are AdmixTools/20160803 and AdmixTools/5.0-20170312, previously available only on milou.</p> Wed, 25 Apr 2018 09:52:00 GMT https://www.uppmax.uu.se/changelog 2018-04-25T09:52:00Z [bio] BUSCO/3.0.2b installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://busco.ezlab.org/">BUSCO</a> (Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs) version 3.0.2b is now installed on all systems as module BUSCO/3.0.2b.</p> Mon, 23 Apr 2018 12:18:00 GMT https://www.uppmax.uu.se/changelog 2018-04-23T12:18:00Z [comp] ruby/2.5.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.ruby-lang.org/en/">Ruby</a> 2.5.0 is now installed as module ruby/2.5.0 on all systems.</p> Wed, 18 Apr 2018 15:23:00 GMT https://www.uppmax.uu.se/changelog 2018-04-18T15:23:00Z [bio] ANGSD/0.921 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://www.popgen.dk/angsd/index.php/ANGSD">ANGSD</a>&nbsp;(program for analysing next generation sequencing data) 0.921 is now installed as module ANGSD/0.921 on all systems.</p> Wed, 18 Apr 2018 15:21:00 GMT https://www.uppmax.uu.se/changelog 2018-04-18T15:21:00Z [bio] bamtools/2.5.1 installed on all systems https://www.uppmax.uu.se/changelog <p>bamtools (BAM file manipulation and API) 2.5.1 is now installed as bamtools/2.5.1 on all systems.&nbsp; Both static and shared libraries are provided.</p> Tue, 10 Apr 2018 14:37:00 GMT https://www.uppmax.uu.se/changelog 2018-04-10T14:37:00Z [bio] fastPHASE/1.4.8 and fastPHASE/1.4.0 available on all systems https://www.uppmax.uu.se/changelog <p><a href="http://scheet.org/software.html">fastPHASE</a> (estimate missing genotypes and unobserved haplotypes) 1.4.8 is now installed on all systems as fastPHASE/1.4.8, and fastPHASE/1.4.0 is now available on all systems.&nbsp; It was previously available only on milou.</p> Thu, 05 Apr 2018 15:05:00 GMT https://www.uppmax.uu.se/changelog 2018-04-05T15:05:00Z [bio] gubbins/2.3.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://sanger-pathogens.github.io/gubbins/">Gubbins</a> (rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences) version 2.3.1 is now installed as module gubbins/2.3.1 on all systems.</p> Thu, 05 Apr 2018 13:48:00 GMT https://www.uppmax.uu.se/changelog 2018-04-05T13:48:00Z [bio] OrthoMCL/2.0.9 now available on all systems https://www.uppmax.uu.se/changelog <p>OrthoMCL (ortholog identification) version 2.0.9 is now installed as module OrthoMCL/2.0.9 on all systems.&nbsp; This was previously available only on milou.&nbsp; See 'module help OrthoMCL/2.0.9' for Uppmax-specific advice.</p> Thu, 05 Apr 2018 13:46:00 GMT https://www.uppmax.uu.se/changelog 2018-04-05T13:46:00Z [apps] Matlab R2018a installed https://www.uppmax.uu.se/changelog <p>Matlab R2018a is installed as matlab/R2018a on all systems.</p> Thu, 29 Mar 2018 06:57:00 GMT https://www.uppmax.uu.se/changelog 2018-03-29T06:57:00Z [comp] intel/18.2 installed https://www.uppmax.uu.se/changelog <p>ntel&nbsp;Parallel Studio XE Cluster Edition 2018 update 2 has been installed on Rackham, Irma and Milou.</p> Thu, 29 Mar 2018 06:55:00 GMT https://www.uppmax.uu.se/changelog 2018-03-29T06:55:00Z [comp] pgi/18.3 installed https://www.uppmax.uu.se/changelog <p>pgi/18.3 is&nbsp;installed on Rackham and Milou</p> Thu, 29 Mar 2018 06:53:00 GMT https://www.uppmax.uu.se/changelog 2018-03-29T06:53:00Z [comp] advisor, ampilifier, inspector and itac upgraded https://www.uppmax.uu.se/changelog <p>advisor, ampilifier, inspector and itac upgraded has been upgraded to versions included in 2018 update 2.</p> Thu, 29 Mar 2018 06:51:00 GMT https://www.uppmax.uu.se/changelog 2018-03-29T06:51:00Z [parallel] openmpi/2.1.3 installed https://www.uppmax.uu.se/changelog <p>&nbsp;openmpi/2.1.3 installed on Rackham and Irma</p> Wed, 21 Mar 2018 09:50:00 GMT https://www.uppmax.uu.se/changelog 2018-03-21T09:50:00Z [bio] MultiQC/1.5 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://multiqc.info/">MultiQC</a> (aggregate results from bioinformatics analyses across many samples into a single report) version 1.5 is now installed as module MultiQC/1.5 on all systems.</p> Thu, 15 Mar 2018 23:33:00 GMT https://www.uppmax.uu.se/changelog 2018-03-15T23:33:00Z [bio] gvcftools/0.16.2 and gvcftools/0.17.0 available on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/sequencing/gvcftools">gvcftools</a> (utilities to analyse gVCF files) versions 0.16.2 and 0.17.0 are now available on all systems as modules gvcftools/0.16.2 and gvcftools/0.17.0.&nbsp; These were previously available on just milou.</p> Thu, 15 Mar 2018 11:36:00 GMT https://www.uppmax.uu.se/changelog 2018-03-15T11:36:00Z [bio] Stacks/1.48 and Stacks/2.0Beta9 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://catchenlab.life.illinois.edu/stacks/">Stacks</a> (RAD-Seq assembly and variant calling) versions 1.48 and 2.0Beta9 are now installed as modules Stacks/1.48 and Stacks/2.0Beta9 on all systems.</p> Tue, 06 Mar 2018 21:17:00 GMT https://www.uppmax.uu.se/changelog 2018-03-06T21:17:00Z [apps] PostgreSQL/10.3 installed on all systems https://www.uppmax.uu.se/changelog <p>PostgreSQL (open-source relational database) 10.3 is now installed as module PostgreSQL/10.3 on all systems.</p> Mon, 05 Mar 2018 22:37:00 GMT https://www.uppmax.uu.se/changelog 2018-03-05T22:37:00Z [bio] canu/1.7 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://canu.readthedocs.io">Canu</a> (assembler for long noisy read data) version 1.7 has been installed as module canu/1.7 on all systems.</p> Mon, 05 Mar 2018 17:19:00 GMT https://www.uppmax.uu.se/changelog 2018-03-05T17:19:00Z [apps] ImageMagick-6.9.9-35 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.imagemagick.org/">ImageMagick</a> (image manipulation) version 6.9.9-35 has been installed as module ImageMagick-6.9.9-35 on all systems.&nbsp; In addition to the ImageMagick executables, this module provides libraries and include files for building against ImageMagick (e.g., for the R package 'magick').&nbsp; The module also includes an installation of libwebp 0.6.1 which includes the cwebp/dwebp executables.</p> Mon, 05 Mar 2018 17:12:00 GMT https://www.uppmax.uu.se/changelog 2018-03-05T17:12:00Z [bio] Salmon/0.9.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://combine-lab.github.io/salmon/">Salmon</a> (RNA-seq transcript quantification) version 0.9.1 is now installed as module Salmon/0.9.1 on all systems.</p> Thu, 01 Mar 2018 18:57:00 GMT https://www.uppmax.uu.se/changelog 2018-03-01T18:57:00Z [bio] mergeSVcallers/161006-23533ef installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/zeeev/mergeSVcallers">mergeSVcallers</a> (Software for merging different Tabix merged VCF files) is now installed as module mergeSVcallers/161006-23533ef on all systems.</p> Thu, 01 Mar 2018 15:08:00 GMT https://www.uppmax.uu.se/changelog 2018-03-01T15:08:00Z [bio] gmap-gsnap/2018-02-12 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://research-pub.gene.com/gmap">Gmap and gsnap</a> (genomic alignment programs) version 2018-02-12 have been installed as module gmap-gsnap/2018-02-12 on all systems.&nbsp; As per the developer's website, versions 2018-mm-dd and later do not yet have support for mapping to genomes &gt;~4Gbp via the programs gmapl and gsnapl.&nbsp; For large genome support, load an earlier module version such as gmap-gsnap/2017-09-11.</p> Thu, 01 Mar 2018 12:32:00 GMT https://www.uppmax.uu.se/changelog 2018-03-01T12:32:00Z [comp] gcc/7.3.0 installed https://www.uppmax.uu.se/changelog <p>gcc 7.3.0 is now installed on Bianca, Irma, Milou and Rackham as gcc/7.3.0</p> Tue, 27 Feb 2018 12:17:00 GMT https://www.uppmax.uu.se/changelog 2018-02-27T12:17:00Z [apps] RStudio/1.1.423 installed on rackham, irma and bianca https://www.uppmax.uu.se/changelog <p><a href="https://www.rstudio.com/">RStudio</a> version 1.1.423 is installed on rackham, irma and bianca.&nbsp; This precompiled version cannot be installed on milou.</p> Tue, 20 Feb 2018 16:56:00 GMT https://www.uppmax.uu.se/changelog 2018-02-20T16:56:00Z [bio] canu/1.6 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://canu.readthedocs.io/">Canu</a> (assembler for long noisy reads) version 1.6 is now installed as module canu/1.6 on all systems.&nbsp; For this version and all canu module versions &gt;= 1.1, the global default for the useGrid option is set to be useGrid=false, to avoid problems with Canu's attempts to use SLURM to manage assembly jobs.&nbsp; This can be overridden via configuration files or command-line options.</p> Tue, 20 Feb 2018 16:21:00 GMT https://www.uppmax.uu.se/changelog 2018-02-20T16:21:00Z [bio] BEETL/1.1.0 installed on all systems https://www.uppmax.uu.se/changelog <p>BEETL (Burrows-Wheeler Extended Tool Library) version 1.1.0 is now installed as module BEETL/1.1.0 on all systems.</p> Tue, 20 Feb 2018 11:24:00 GMT https://www.uppmax.uu.se/changelog 2018-02-20T11:24:00Z [bio] artemis/16.0.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://www.sanger.ac.uk/science/tools/artemis">Artemis</a> (genome browser from Wellcome Sanger Institute) version 16.0.0 is now installed as module artemis/16.0.0 on all systems.</p> Mon, 19 Feb 2018 15:58:00 GMT https://www.uppmax.uu.se/changelog 2018-02-19T15:58:00Z [bio] phylophlan/0.99 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://bitbucket.org/nsegata/phylophlan/wiki/Home">PhyloPhlAn</a> (computational pipeline for reconstructing highly accurate and resolved phylogenetic trees based on whole-genome sequence information) version 0.99 is now installed as module phylophlan/0.99 on all systems.</p> Mon, 19 Feb 2018 13:53:00 GMT https://www.uppmax.uu.se/changelog 2018-02-19T13:53:00Z [bio] CheckM/1.0.11 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://ecogenomics.github.io/CheckM/">CheckM</a> (tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes) version 1.0.11 is now installed as module CheckM/1.0.11 on all systems.</p> Mon, 19 Feb 2018 13:07:00 GMT https://www.uppmax.uu.se/changelog 2018-02-19T13:07:00Z [bio] megahit/1.1.2 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/voutcn/megahit">MEGAHIT</a> (large and complex metagenomics assembly via succinct de Bruijn graph) 1.1.2 is now installed as megahit/1.1.2 on all systems.&nbsp; The installed version is CPU-only, as GPUs are not available at UPPMAX.</p> Sun, 18 Feb 2018 16:01:00 GMT https://www.uppmax.uu.se/changelog 2018-02-18T16:01:00Z [bio] beast/1.8.4 installed on all systems except for milou https://www.uppmax.uu.se/changelog <p><a href="http://beast.community/">BEAST</a> (Bayesian analysis of phylogenies using MCMC, independent from BEAST2) version 1.8.4 is installed on all systems except for milou as module beast/1.8.4.</p> Fri, 16 Feb 2018 16:47:00 GMT https://www.uppmax.uu.se/changelog 2018-02-16T16:47:00Z [bio] beast2/2.4.8 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.beast2.org/">BEAST2</a> (Bayesian evolutionary analysis by sample trees) version 2.4.8 is installed on all systems as module beast2/2.4.8.&nbsp; This module automatically loads the BEAGLE library module beagle/2.1.2.</p> Fri, 16 Feb 2018 16:44:00 GMT https://www.uppmax.uu.se/changelog 2018-02-16T16:44:00Z [bio] LUMPY/0.2.13-213a417 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/arq5x/lumpy-sv">LUMPY</a> (general probabilistic framework for structural variant discovery) version&nbsp;0.2.13-213a417, which is the 0.2.13 release updated to the most recent commit, is installed as module LUMPY/0.2.13-213a417 on all systems.</p> Fri, 16 Feb 2018 13:41:00 GMT https://www.uppmax.uu.se/changelog 2018-02-16T13:41:00Z [bio] supernova/2.0.0 installed on all systems https://www.uppmax.uu.se/changelog <p>The <a href="https://support.10xgenomics.com/de-novo-assembly/software/overview/latest/welcome">10X Chromium assembler Supernova</a> version 2.0.0 has been installed as module supernova/2.0.0 on all systems.&nbsp; The previous module versions supernova/{1.0.0,1.1.1,1.1.4} are also now available on all systems.</p> Mon, 12 Feb 2018 16:02:00 GMT https://www.uppmax.uu.se/changelog 2018-02-12T16:02:00Z [bio] bcl2fastq/2.20.0 installed on all systems https://www.uppmax.uu.se/changelog <p>The <a href="https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html">Illumina base caller bcl2fastq</a> version 2.20.0 is now installed as module bcl2fastq/2.20.0 on all systems.</p> Mon, 12 Feb 2018 16:00:00 GMT https://www.uppmax.uu.se/changelog 2018-02-12T16:00:00Z [bio] infernal/1.1.2 installed on all systems https://www.uppmax.uu.se/changelog <p>Infernal (Inference of RNA alignments) 1.1.2 is now installed on all systems as module infernal/1.1.2.&nbsp; The earlier version infernal/1.1.1 is also now available on all systems.</p> Fri, 09 Feb 2018 15:22:00 GMT https://www.uppmax.uu.se/changelog 2018-02-09T15:22:00Z [bio] prokka/1.12-12547ca installed on all systems https://www.uppmax.uu.se/changelog <p>The most recent Prokka (bacterial genome annotation package) is available as module prokka/1.12-12547ca on all systems.&nbsp; This is version 1.12 updated to the most recent source commit.</p> Fri, 09 Feb 2018 15:02:00 GMT https://www.uppmax.uu.se/changelog 2018-02-09T15:02:00Z [comp] git/2.16.1 now installed on all systems https://www.uppmax.uu.se/changelog <p>The most recent version of Git source control system is installed as module git/2.16.1 on all systems.</p> Fri, 09 Feb 2018 15:01:00 GMT https://www.uppmax.uu.se/changelog 2018-02-09T15:01:00Z [bio] tbl2asn/25.3 available on all systems, and version 24.9 removed from all systems https://www.uppmax.uu.se/changelog <p>The NCBI submission tool tbl2asn version 25.3 is now available on all systems, and the expired version 24.9 has been removed from all systems.</p> Fri, 09 Feb 2018 14:59:00 GMT https://www.uppmax.uu.se/changelog 2018-02-09T14:59:00Z [bio] aragorn/1.2.38 installed on all systems https://www.uppmax.uu.se/changelog <p>ARAGORN (tRNA and tmRNA&nbsp;detection) 1.2.38 is installed as module aragorn/1.2.38 on all systems.</p> Fri, 09 Feb 2018 14:57:00 GMT https://www.uppmax.uu.se/changelog 2018-02-09T14:57:00Z [bio] iqtree/1.5.4-omp-mpi installed on all systems https://www.uppmax.uu.se/changelog <p>IQ-TREE 1.5.4 (efficient software for phylogenomic inference) with executables for single-core, multi-core, MPI, and hybrid operation is installed as module iqtree/1.5.4-omp-mpi on all systems.&nbsp; See 'module help iqtree/1.5.4-omp-mpi' for more information.</p> Tue, 06 Feb 2018 15:37:00 GMT https://www.uppmax.uu.se/changelog 2018-02-06T15:37:00Z [bio] snakemake/4.5.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://snakemake.readthedocs.io/en/latest/">Snakemake</a> (A workflow management tool to create <strong>reproducible and scalable</strong> data analyses) version 4.5.0 is now installed as module snakemake/4.5.0 on all systems.</p> Thu, 01 Feb 2018 17:02:00 GMT https://www.uppmax.uu.se/changelog 2018-02-01T17:02:00Z [bio] samtools/1.6, bcftools/1.6, htslib/1.6 installed on all systems https://www.uppmax.uu.se/changelog <p>The most recent versions of the HTSlib collection of utilities have been installed as samtools/1.6, bcftools/1.6 and htslib/1.6 on all systems.</p> Tue, 30 Jan 2018 15:58:00 GMT https://www.uppmax.uu.se/changelog 2018-01-30T15:58:00Z [bio] spades/3.11.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://cab.spbu.ru/software/spades/">SPAdes</a> assembler version 3.11.1 is now installed as module spades/3.11.1 on all systems.</p> Tue, 23 Jan 2018 13:14:00 GMT https://www.uppmax.uu.se/changelog 2018-01-23T13:14:00Z [bio] CONSEL/0.2.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://http://stat.sys.i.kyoto-u.ac.jp/prog/consel/">CONSEL</a> (Program for assessing the confidence of phylogenetic tree selection) is now installed as module&nbsp;CONSEL/0.2.0 on all systems.</p> Tue, 09 Jan 2018 15:37:00 GMT https://www.uppmax.uu.se/changelog 2018-01-09T15:37:00Z [bio] plinkseq 0.10 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://atgu.mgh.harvard.edu/plinkseq/index.shtml">PLINK/SEQ</a> (A library for the analysis of genetic variation data; a toolset for working with human genetic variation data) version 0.10 is now installed as module plinkseq/0.10 on all systems.</p> <p></p> Fri, 22 Dec 2017 10:02:00 GMT https://www.uppmax.uu.se/changelog 2017-12-22T10:02:00Z [bio] ATSAS/2.8.3-1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.embl-hamburg.de/biosaxs/software.html">ATSAS</a> (program suite for small-angle scattering data analysis from biological macromolecules) 2.8.3-1 is now installed as module ATSAS/2.8.3-1 on all systems.</p> Wed, 20 Dec 2017 22:51:00 GMT https://www.uppmax.uu.se/changelog 2017-12-20T22:51:00Z [bio] BEDTools/2.27.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://bedtools.readthedocs.io/en/latest/">BEDTools</a> (a powerful toolset for genome arithmetic) version 2.27.1 is now installed as module BEDTools/2.27.1 on all systems.</p> Tue, 19 Dec 2017 14:21:00 GMT https://www.uppmax.uu.se/changelog 2017-12-19T14:21:00Z [bio] VCFaid/20170616-f0732ae installed on all systems https://www.uppmax.uu.se/changelog <p>VCFaid (Genotype likelihood based GQ estimation) version 20170616-f0732ae is now installed on all systems. See 'module help VCFaid/20170616-f0732ae' for details on how to run it.</p> Mon, 18 Dec 2017 11:12:00 GMT https://www.uppmax.uu.se/changelog 2017-12-18T11:12:00Z [bio] svprops/20171020-ebf6762 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/dellytools/svprops">svprops</a> (Computes various SV statistics from an input Delly VCF file) version 20171020-ebf6762 is now installed as module svprops/20171020-ebf6762 on all systems. See 'module help svprops/20171020-ebf6762' for details on running this.</p> Mon, 18 Dec 2017 10:56:00 GMT https://www.uppmax.uu.se/changelog 2017-12-18T10:56:00Z [bio] Strelka2/2.8.4 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/Illumina/strelka">Strelka2</a> (germline and somatic small variant caller) version 2.8.4 is now installed as module Strelka2/2.8.4 on all systems.</p> Mon, 18 Dec 2017 10:27:00 GMT https://www.uppmax.uu.se/changelog 2017-12-18T10:27:00Z [bio] GATK/4.beta.5 installed on all systems https://www.uppmax.uu.se/changelog <p>The Beta 5 version of <a href="https://software.broadinstitute.org/gatk/documentation/tooldocs/4.beta.5/">GATK 4</a> has been installed on all systems as module GATK/4.beta.5.&nbsp; This is used differently from earlier versions of GATK.&nbsp; See 'module help GATK/4.beta.5' for more information.</p> Wed, 13 Dec 2017 18:07:00 GMT https://www.uppmax.uu.se/changelog 2017-12-13T18:07:00Z [bio] pplacer/1.1.alpha19 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://matsen.github.io/pplacer/">pplacer</a> (place reads on a phylogenetic tree) version 1.1.alpha19 has been installed as module pplacer/1.1.alpha19 on all systems.</p> Fri, 08 Dec 2017 13:33:00 GMT https://www.uppmax.uu.se/changelog 2017-12-08T13:33:00Z [bio] freebayes/1.1.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/ekg/freebayes">Freebayes</a> 1.1.0 (variant calling) has been installed on all systems as module freebayes/1.1.0.</p> Thu, 07 Dec 2017 15:01:00 GMT https://www.uppmax.uu.se/changelog 2017-12-07T15:01:00Z [apps] R/3.4.3 and omnibus package module R_packages/3.4.3 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.r-project.org/">R</a> 3.4.3 together with the omnibus package module <a href="https://www.uppmax.uu.se/support-sv//r_packages-module-guide">R_packages</a> 3.4.3 have been installed on all systems as modules R/3.4.3 and R_packages/3.4.3, respectively.&nbsp; See the link for R_packages to see which packages are included.</p> Wed, 06 Dec 2017 14:53:00 GMT https://www.uppmax.uu.se/changelog 2017-12-06T14:53:00Z [bio] MEGAN/6.10.5 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://ab.inf.uni-tuebingen.de/software/megan6/">MEGAN</a> (interactive microbiome analysis tool) 6.10.5 Academic Edition is installed as module MEGAN/6.10.5 on all systems.</p> Tue, 05 Dec 2017 16:06:00 GMT https://www.uppmax.uu.se/changelog 2017-12-05T16:06:00Z [bio] cramtools/3.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/enasequence/cramtools">Cramtools</a> 3.0 is installed as module cramtools/3.0 on all systems.</p> Tue, 05 Dec 2017 09:57:00 GMT https://www.uppmax.uu.se/changelog 2017-12-05T09:57:00Z [apps] MariaDB/10.1.29 and /10.2.11 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://mariadb.org/">MariaDB</a> (open-source fork of MySQL) versions 10.1.29 and 10.2.11 have been installed as modules MariaDB/10.1.29 and MariaDB/10.2.11 on all systems.&nbsp; Uppmax does not allow&nbsp;persistent database servers beyond the extent of a single job; we recommend using sqlite for serverless SQL databases of convenience.&nbsp; These modules may also be useful for compiling software expecting to use a MySQL client to access remote databases.</p> Mon, 04 Dec 2017 15:19:00 GMT https://www.uppmax.uu.se/changelog 2017-12-04T15:19:00Z [bio] bowtie2/2.3.3.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://bowtie-bio.sourceforge.net/bowtie2/index.shtml">Bowtie2</a> 2.3.3.1 has been installed as module bowtie2/2.3.3.1 on all systems.</p> Mon, 04 Dec 2017 15:14:00 GMT https://www.uppmax.uu.se/changelog 2017-12-04T15:14:00Z [comp] java/sun_jdk1.8.0_151 installed on all systems https://www.uppmax.uu.se/changelog <p>The Sun Java Development Kit 8.0 release 151 has been installed as module&nbsp;java/sun_jdk1.8.0_151 on all systems.</p> Mon, 04 Dec 2017 12:35:00 GMT https://www.uppmax.uu.se/changelog 2017-12-04T12:35:00Z [apps] vim/8.0-1360 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://www.vim.org/">VIM</a> 8.0-1360 (version 8.0 through patch level 1360) has been installed as module vim/8.0-1360 on all systems.&nbsp; This installation includes support for python, python3, perl and tcl interpreters.&nbsp; See 'module help vim/8.0-1360 for more information.</p> Fri, 01 Dec 2017 15:58:00 GMT https://www.uppmax.uu.se/changelog 2017-12-01T15:58:00Z [bio] SMRT/5.0.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://www.pacb.com/support/software-downloads/">SMRT Link</a> v5.0.1 (PacBio software suite) is now installed as module SMRT/5.0.1 on all systems.&nbsp; This apparently includes all tools previously included in the SMRT Analysis set of tools.</p> Mon, 20 Nov 2017 15:37:00 GMT https://www.uppmax.uu.se/changelog 2017-11-20T15:37:00Z [bio] blasr/5.3-20171117-f72428d installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/PacificBiosciences/blasr/wiki">Blasr</a> 5.3.f72428d (PacBio long-read aligner) has been installed as module blasr/5.3-20171117-f72428d on all systems.</p> Mon, 20 Nov 2017 13:48:00 GMT https://www.uppmax.uu.se/changelog 2017-11-20T13:48:00Z [bio] pysam/0.13-python2.7.1 and pysam/0.13-python3.6.0 installed https://www.uppmax.uu.se/changelog <p><a href="http://pysam.readthedocs.io/en/latest/">PySam</a> version 0.13 has been installed on all systems as module pysam/0.13-python2.7.11 (for python/2.7.11) and pysam/0.13-python3.6.0 (for python/3.6.0).</p> Sat, 18 Nov 2017 11:49:00 GMT https://www.uppmax.uu.se/changelog 2017-11-18T11:49:00Z [bio] spaln/2.1.4 module now installed on all systems https://www.uppmax.uu.se/changelog <p>The SPALN spliced alignment tool version 2.1.4 is now installed as module spaln/2.1.4 on all systems.&nbsp; This module includes settings for compiling and linking against SPALN headers/libraries using gcc.&nbsp; The module was compiled with gcc/5.4.0.</p> Tue, 14 Nov 2017 10:58:00 GMT https://www.uppmax.uu.se/changelog 2017-11-14T10:58:00Z [bio] NCBI taxonomy databases now available https://www.uppmax.uu.se/changelog <p><a href="https://www.ncbi.nlm.nih.gov/guide/taxonomy/">NCBI taxonomy databases</a> are now available as local copies at Uppmax.&nbsp; See our <a href="https://www.uppmax.uu.se/resurser/databases/ncbi-taxonomy-databases">NCBI taxonomy databases</a> page for more information.</p> Tue, 14 Nov 2017 10:57:00 GMT https://www.uppmax.uu.se/changelog 2017-11-14T10:57:00Z [bio] UniVec and UniVec_Core databases now available https://www.uppmax.uu.se/changelog <p><a href="ftp://ftp.ncbi.nlm.nih.gov/pub/UniVec/README.uv">NCBI UniVec and UniVec_Core databases</a> have been added to the local copies of Blast databases available at **/sw/data/uppnex/blast_databases/**.&nbsp; As with other local copies of Blast databases, when one of the **blast** modules is loaded these databases are available by specifying '**-db UniVec**' or '**-db UniVec_Core**'.&nbsp; See our&nbsp;<a href="https://www.uppmax.uu.se/resurser/databases/blast-databases">Blast databases</a> page&nbsp;for more information.</p> Tue, 14 Nov 2017 10:51:00 GMT https://www.uppmax.uu.se/changelog 2017-11-14T10:51:00Z [bio] prank/170427 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://wasabiapp.org/software/prank/">PRANK</a> (probabilistic multiple alignment) 170427 is now installed as module prank/170427 on all systems.</p> Thu, 09 Nov 2017 15:55:00 GMT https://www.uppmax.uu.se/changelog 2017-11-09T15:55:00Z [bio] Minimap2 2.4 installed as minimap2/2.4 on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/lh3/minimap2">Minimap2</a> (versatile sequence alignment program, good for noisy long reads) 2.4 is installed as module minimap2/2.4 on all systems.</p> Thu, 09 Nov 2017 14:51:00 GMT https://www.uppmax.uu.se/changelog 2017-11-09T14:51:00Z [bio] bwa/0.7.17 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/lh3/bwa">BWA</a> 0.7.17 is installed as module bwa/0.7.17 on all systems.</p> Thu, 09 Nov 2017 14:33:00 GMT https://www.uppmax.uu.se/changelog 2017-11-09T14:33:00Z [bio] TrimGalore/0.4.4 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/">Trim Galore!</a> 0.4.4 has been installed as module TrimGalore/0.4.4 on all systems.</p> Thu, 09 Nov 2017 14:01:00 GMT https://www.uppmax.uu.se/changelog 2017-11-09T14:01:00Z [bio] Nextflow 0.26.0 has been installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.nextflow.io/">Nextflow</a> 0.26.0 has been installed as module Nextflow/0.26.0 on all systems.</p> Thu, 09 Nov 2017 14:00:00 GMT https://www.uppmax.uu.se/changelog 2017-11-09T14:00:00Z [bio] preseq/2.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://smithlabresearch.org/software/preseq/">Preseq</a> 2.0 has been installed as module preseq/2.0 on all systems.</p> Thu, 09 Nov 2017 13:58:00 GMT https://www.uppmax.uu.se/changelog 2017-11-09T13:58:00Z [bio] cutadapt/1.14 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://cutadapt.readthedocs.io/en/stable/#">Cutadapt</a> 1.14 has been installed as module cutadapt/1.14 on all systems.</p> Thu, 09 Nov 2017 13:57:00 GMT https://www.uppmax.uu.se/changelog 2017-11-09T13:57:00Z [bio] Kraken/1.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://ccb.jhu.edu/software/kraken/">Kraken</a> (system for assigning taxonomic labels to short DNA sequences) 1.0 has been installed as module Kraken/1.0 on all systems.</p> Sat, 04 Nov 2017 16:48:00 GMT https://www.uppmax.uu.se/changelog 2017-11-04T16:48:00Z [bio] MultiQC/1.3 installed on all systems https://www.uppmax.uu.se/changelog <p>MultiQC 1.3 has been installed on all systems as module MultiQC/1.3.</p> Fri, 03 Nov 2017 15:20:00 GMT https://www.uppmax.uu.se/changelog 2017-11-03T15:20:00Z [bio] Blast databases are now being updated https://www.uppmax.uu.se/changelog <p>After a long lull, the local copies of Blast databases are now being updated.&nbsp; Some additional databases have been added, and the WGS database (not updated locally since 2014) is no longer available.&nbsp; See the <a href="https://www.uppmax.uu.se/resurser/databases/blast-databases">resource page for local Blast databases</a>&nbsp;for more information.</p> Tue, 31 Oct 2017 11:43:00 GMT https://www.uppmax.uu.se/changelog 2017-10-31T11:43:00Z [bio] vsearch/2.5.2 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/torognes/vsearch">Vsearch</a> (open-source alternative to usearch) 2.5.2 has been installed as module vsearch/2.5.2 on all systems.</p> Mon, 30 Oct 2017 20:27:00 GMT https://www.uppmax.uu.se/changelog 2017-10-30T20:27:00Z [apps] packages added and updated in R_packages/3.4.0 https://www.uppmax.uu.se/changelog <p>Several packages have been added and many have been updated in the module R_packages/3.4.0.&nbsp; See&nbsp;<a href="https://www.uppmax.uu.se/support-sv//r_packages-module-guide">http://www.uppmax.uu.se/support/user-guides/r_packages-module-guide/</a> for a complete list of the available packages.</p> Mon, 30 Oct 2017 14:35:00 GMT https://www.uppmax.uu.se/changelog 2017-10-30T14:35:00Z [apps] GAMESS-US installed on Rackham https://www.uppmax.uu.se/changelog <p>GAMESS-US, a molecular dynamics package, is now installed on Rackham as module gamess/20170930.&nbsp;</p> Mon, 30 Oct 2017 13:48:00 GMT https://www.uppmax.uu.se/changelog 2017-10-30T13:48:00Z [libs] GLPK 4.63 linear programming package installed https://www.uppmax.uu.se/changelog <p>GLPK (GNU Linear Programming Kit) package&nbsp;for solving large-scale linear programming (LP), mixed integer programming (MIP), and related problems is now&nbsp;installed on Rackham, Irma, and Bianca as module glpk/4.63.</p> Mon, 30 Oct 2017 13:45:00 GMT https://www.uppmax.uu.se/changelog 2017-10-30T13:45:00Z [bio] sratools/2.8.2-1 installed on all systems https://www.uppmax.uu.se/changelog <p>The <a href="https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc">SRA Toolkit</a> version 2.8.2-1 has been installed as module sratools/2.8.2-1 on all systems.&nbsp; The SRA Toolkit provides access to SRA datasets as well as <a href="ftp://ftp.ncbi.nlm.nih.gov/blast/WGS_TOOLS/README_BLASTWGS.txt">special Blast+ tools</a> that enable searching against the WGS and TSA sequence databases.</p> Sun, 29 Oct 2017 12:10:00 GMT https://www.uppmax.uu.se/changelog 2017-10-29T12:10:00Z [bio] plink/1.90b4.9 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.cog-genomics.org/plink2">PLINK</a> 1.90b4.9 (beta version as of&nbsp;13 Oct 2017) is now available as module plink/1.90b4.9 on all systems.&nbsp; The previously available module plink/1.90 has been renamed plink/1.90b3n, to reflect its being an earlier beta version (11 May 2015).</p> Wed, 25 Oct 2017 13:20:00 GMT https://www.uppmax.uu.se/changelog 2017-10-25T13:20:00Z [ apps] VASP 5.4.4 and VASPsol 5.4.4 installed on Rackham https://www.uppmax.uu.se/changelog <h3>VASP version 5.4.4 and VASPsol version 5.4.4 have been installed as modules&nbsp; vasp/5.4.4_intel_mkl and vaspsol/5.4.4_intel_mkl on Rackham</h3> Wed, 25 Oct 2017 08:13:00 GMT https://www.uppmax.uu.se/changelog 2017-10-25T08:13:00Z [bio] NextGenMap/0.5.4 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://cibiv.github.io/NextGenMap/">NextGenMap</a> version 0.5.4 has been&nbsp;installed as module NextGenMap/0.5.4 as part of bioinfo-tools on all systems.</p> Tue, 24 Oct 2017 10:23:00 GMT https://www.uppmax.uu.se/changelog 2017-10-24T10:23:00Z [bio] Pilon/1.22 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/broadinstitute/pilon">Pilon</a> (automated genome assembly improvement and variant detection tool) version 1.22 is now installed as module Pilon/1.22 on all systems.</p> Sun, 22 Oct 2017 19:32:00 GMT https://www.uppmax.uu.se/changelog 2017-10-22T19:32:00Z [bio] REAPR/1.0.18 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://www.sanger.ac.uk/science/tools/reapr">REAPR</a> (tool that evaluates the accuracy of a genome assembly using mapped paired end reads) 1.0.18 has been installed as module REAPR/1.0.18 on all systems.</p> Sun, 22 Oct 2017 17:08:00 GMT https://www.uppmax.uu.se/changelog 2017-10-22T17:08:00Z [bio] SeqTools/4.44.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://www.sanger.ac.uk/science/tools/seqtools">SeqTools</a> (three sequence alignment visualisation tools from the Sanger Institute) 4.44.1 is now installed as module SeqTools/4.44.1 on all systems.</p> Thu, 19 Oct 2017 15:40:00 GMT https://www.uppmax.uu.se/changelog 2017-10-19T15:40:00Z [bio] ShoRAH/1.1.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/cbg-ethz/shorah">ShoRAH</a> (short reads assembly into haplotypes) 1.1.0 is now installed as module ShoRAH/1.1.0 on all systems.</p> Thu, 19 Oct 2017 14:52:00 GMT https://www.uppmax.uu.se/changelog 2017-10-19T14:52:00Z [bio] IGV/2.4.2 and IGVtools/2.3.98 installed on all systems https://www.uppmax.uu.se/changelog <p>The <a href="http://software.broadinstitute.org/software/igv/home">IGV genome viewer</a> version 2.4.2 and associated IGVtools 2.3.98 have been installed as modules IGV/2.4.2 and IGVtools/2.3.98 on all systems.&nbsp; The module IGV/3.0-beta is removed, as all of its additional features are now in IGV/2.4.2 and it is no longer available for download.</p> Tue, 17 Oct 2017 12:52:00 GMT https://www.uppmax.uu.se/changelog 2017-10-17T12:52:00Z [bio] velvet/1.2.10 and velvet/1.2.10_K128 offer more capabilities https://www.uppmax.uu.se/changelog <p>The modules for the most recent version of the <a href="https://www.ebi.ac.uk/~zerbino/velvet/">Velvet</a> assembler, velvet/1.2.10 and velvet/1.2.10_K128, now contain multiple velvetg and velveth versions with additional capabilities, including support for long sequences and big assemblies.&nbsp; See 'module help velvet/1.2.10' and 'module help velvet/1.2.10_K128' for more information.</p> Tue, 17 Oct 2017 10:10:00 GMT https://www.uppmax.uu.se/changelog 2017-10-17T10:10:00Z [misc] POV-Ray installed https://www.uppmax.uu.se/changelog <p>POV-Ray 3.7 (raytracing engine) has been installed on Rackham, Bianca, and Irma as module povray/3.7.</p> Mon, 16 Oct 2017 09:10:00 GMT https://www.uppmax.uu.se/changelog 2017-10-16T09:10:00Z [bio] LDhelmet/1.9 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://sourceforge.net/projects/ldhelmet/">LDhelmet</a> (fine-scale recombination estimates) version 1.9 is now installed as module LDhelmet/1.9 on all systems.</p> Sun, 15 Oct 2017 13:36:00 GMT https://www.uppmax.uu.se/changelog 2017-10-15T13:36:00Z [bio] MetaBat/2.12.1 is installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://bitbucket.org/berkeleylab/metabat">MetaBat</a> (tool for accurately reconstructing single genomes from complex microbial communities) 2.12.1 has been installed as module MetaBat/2.12.1 on all systems.</p> Sun, 15 Oct 2017 12:16:00 GMT https://www.uppmax.uu.se/changelog 2017-10-15T12:16:00Z [bio] ExpansionHunter/2.5.3 is installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/Illumina/ExpansionHunter">ExpansionHunter</a> (look for size differences in human-genome small-repeat regions) 2.5.3 is installed as ExpansionHunter/2.5.3 on all systems.&nbsp; See 'module help ExpansionHunter/2.5.3' for the location of repeat-specs for several human genome releases.</p> Thu, 12 Oct 2017 11:57:00 GMT https://www.uppmax.uu.se/changelog 2017-10-12T11:57:00Z [bio] maker/3.01.1-beta installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://www.yandell-lab.org/software/maker.html">MAKER</a> (genome annotation pipeline) version 3.01.1-beta has been installed as module maker/3.01.1-beta on all systems.</p> Mon, 09 Oct 2017 15:21:00 GMT https://www.uppmax.uu.se/changelog 2017-10-09T15:21:00Z [bio] RepeatMasker/4.0.7's RMBlast repaired via patch https://www.uppmax.uu.se/changelog <p>The RMBlast that is part of the <a href="http://www.repeatmasker.org/">RepeatMasker/4.0.7</a> module has been repaired.&nbsp;&nbsp;If you ever had rmblastn segfault with the message: &quot;Critical: (109.4) CObject::RemoveLastReference: CObject was referenced again&quot; while running RepeatMasker, this should correct that problem.</p> Mon, 09 Oct 2017 14:45:00 GMT https://www.uppmax.uu.se/changelog 2017-10-09T14:45:00Z [bio] GeneMark/4.33-es installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://exon.biology.gatech.edu/GeneMark/gmes_instructions.html">GeneMark-ES</a> (unsupervised gene-finding in eukaryotic genomes) version 4.33 is now installed as module GeneMark/4.33-es on all systems.</p> Mon, 09 Oct 2017 12:33:00 GMT https://www.uppmax.uu.se/changelog 2017-10-09T12:33:00Z [bio] trinotate/3.0.2 now installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://trinotate.github.io/">Trinotate</a> (transcript annotation) version 3.0.2 is now installed as module trinotate/3.0.2 on all systems.</p> Tue, 03 Oct 2017 16:37:00 GMT https://www.uppmax.uu.se/changelog 2017-10-03T16:37:00Z [bio] SignalP/4.1f is now installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://www.cbs.dtu.dk/services/SignalP/">SignalP</a> (signal peptide prediction) version 4.1f is now installed as module SignalP/4.1f on all systems.&nbsp; Use is restricted to academic users only.</p> Tue, 03 Oct 2017 09:33:00 GMT https://www.uppmax.uu.se/changelog 2017-10-03T09:33:00Z [bio] TransDecoder/5.0.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://transdecoder.github.io/">TransDecoder</a> (identifies candidate coding regions within transcript sequences) 5.0.1 is now installed as module TransDecoder/5.0.1 on all systems.</p> Tue, 03 Oct 2017 08:11:00 GMT https://www.uppmax.uu.se/changelog 2017-10-03T08:11:00Z [bio] MultiQC/1.2 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://multiqc.info/">MultiQC</a> 1.2 (comprehensive reporting for bioinformatics analyses) has been installed as module MultiQC/1.2 on all Uppmax systems.</p> Mon, 02 Oct 2017 21:08:00 GMT https://www.uppmax.uu.se/changelog 2017-10-02T21:08:00Z [bio] several more modules made available on all systems https://www.uppmax.uu.se/changelog <p>Several more modules that were previously available on milou only or a subset of systems are now available on all Uppmax systems (milou, rackham, irma, bianca):&nbsp;<!--?xml version="1.0" encoding="UTF-8"?-->RNAfold/{1.8.4,2.1.8,2.2.5,2.3.1} with ViennaRNA as an alias, vcftools/{0.1.12,0.1.13}, VAT/2.0.1, VarScan/{2.3.6,2.3.7}, R/3.0.2, star/2.3.1o, python/3.3.1 with python/3.3 as an alias</p> Sat, 30 Sep 2017 21:18:00 GMT https://www.uppmax.uu.se/changelog 2017-09-30T21:18:00Z [bio] MaSuRCA/3.2.3 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://www.genome.umd.edu/masurca.html">MaSuRCA</a> 3.2.3 (whole-genome assembler) has been installed as module MaSuRCA/3.2.3 on all systems.</p> Sat, 30 Sep 2017 20:47:00 GMT https://www.uppmax.uu.se/changelog 2017-09-30T20:47:00Z [comp] several more modules added to perl_modules/5.24.1 https://www.uppmax.uu.se/changelog <p>Several more modules have been added to the <a href="https://www.uppmax.uu.se/support-sv//perl_modules-5.24.1-module-guide">perl_modules/5.24.1</a> omnibus module, primarily within Statistics::*.</p> Thu, 28 Sep 2017 13:08:00 GMT https://www.uppmax.uu.se/changelog 2017-09-28T13:08:00Z [bio] VarScan/2.4.2 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://dkoboldt.github.io/varscan/">VarScan</a> (variant detection tool) version 2.4.2 has been installed as module VarScan/2.4.2 on all systems.</p> Tue, 26 Sep 2017 09:59:00 GMT https://www.uppmax.uu.se/changelog 2017-09-26T09:59:00Z [bio] several more modules made available on all systems https://www.uppmax.uu.se/changelog <p>Several more modules that were previously available on milou only or a subset of systems are now available on all Uppmax systems (milou, rackham, irma, bianca): IMPUTE2/2.3.2, beagle/2.1.2,&nbsp;<!--?xml version="1.0" encoding="UTF-8"?-->openblas/0.2.14a, openblas/0.2.19,&nbsp;<!--?xml version="1.0" encoding="UTF-8"?-->454-dataanalysis/{2.3,2.5.3,2.6,2.9}, 454-dataprocessing/2.3, bbmap/{33.41,35.14,35.40}, bcl2fastq/{1.8.4,2.15.0,2.16.0,2.17.1}, annovar/{2014.11.12,2015.06.17,2016.05.11},&nbsp;<!--?xml version="1.0" encoding="UTF-8"?-->CASAVA/{1.7.0,1.8.2}, chipster/webstart (also changed chipster/webstart to use 5g memory for java), gmap-gsnap/{2014-01-21,2015-09-28,2016-05-01}, cellranger/{1.1.0,1.3.0}, qctool/1.4, garli/2.1, iqtree/1.5.3-omp,&nbsp;<!--?xml version="1.0" encoding="UTF-8"?-->pear/{0.9.5,0.9.10}, msmc/0.1.0</p> Fri, 22 Sep 2017 13:50:00 GMT https://www.uppmax.uu.se/changelog 2017-09-22T13:50:00Z [bio] gmap-gsnap/2017-09-11 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://research-pub.gene.com/gmap/">GMAP-GSNAP</a> version 2017-09-11 has been installed as module gmap-gsnap/2017-09-11 on all systems.</p> Thu, 21 Sep 2017 16:03:00 GMT https://www.uppmax.uu.se/changelog 2017-09-21T16:03:00Z [bio] cellranger/2.0.2 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest">Chromium Cellranger</a> version 2.0.2 has been installed as module cellranger/2.0.2 on all systems. &nbsp;The directory structure has also changed slightly for earlier versions of the cellranger module and its associated data; please reload the module for new locations.</p> Thu, 21 Sep 2017 15:58:00 GMT https://www.uppmax.uu.se/changelog 2017-09-21T15:58:00Z [bio] annovar/2017.07.16 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://annovar.openbioinformatics.org/en/latest/">ANNOVAR</a> 2017.07.16 (comprehensive variant annotation) has been installed on all systems as module annovar/2017.07.16.&nbsp; A wide range of annotation databases has also been downloaded, for genome builds hg19 and hg38; see 'module help annovar/2017.07.16' for more information.</p> Wed, 20 Sep 2017 22:45:00 GMT https://www.uppmax.uu.se/changelog 2017-09-20T22:45:00Z [bio] bbmap/37.53 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://jgi.doe.gov/data-and-tools/bbtools/">BBTools/BBMap</a> (toolkit for read mapping and sequence analysis) has been installed as module bbmap/37.53 on all systems.</p> Tue, 19 Sep 2017 14:17:00 GMT https://www.uppmax.uu.se/changelog 2017-09-19T14:17:00Z [bio] AdapterRemoval/2.2.2 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/MikkelSchubert/adapterremoval">AdapterRemoval</a> (adapter removal and read merging) version 2.2.2 has been installed as module AdapterRemoval/2.2.2 on all systems. &nbsp;In addition, the earlier version AdapterRemoval/2.1.7, previously available only on milou, has also been installed on all systems.&nbsp;</p> Fri, 15 Sep 2017 09:27:00 GMT https://www.uppmax.uu.se/changelog 2017-09-15T09:27:00Z [bio] Vmatch/2.3.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://www.vmatch.de/">Vmatch</a> (large-scale sequence analysis software) 2.3.0 has been installed as module Vmatch/2.3.0 on all systems.</p> Thu, 14 Sep 2017 14:12:00 GMT https://www.uppmax.uu.se/changelog 2017-09-14T14:12:00Z [bio] BEDOPS/2.4.28 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://bedops.readthedocs.io/en/latest/">BEDOPS</a> (BAM file manipulation) version 2.4.28 has been installed as module BEDOPS/2.4.28 on all systems.</p> Thu, 14 Sep 2017 14:11:00 GMT https://www.uppmax.uu.se/changelog 2017-09-14T14:11:00Z [bio] several more modules made available on all systems https://www.uppmax.uu.se/changelog <p>Several more modules that were previously available on milou only or a subset of systems are now available on all Uppmax systems (milou, rackham, irma, bianca):&nbsp;sickle/1.210, samplefq/0.2, sambamba/0.5.9, SBT/0.3, scalpel/0.5.2, selscan/1.1.0,&nbsp;FastML/3.1, FastTree/2.1.8, BEDOPS/2.4.3, BEDTools/{2.23.0,2.25.0,2.26.0}, fermi/1.1-r751-beta, fermikit/{0.14-prerelease-96f7820,r178}, Tablet/1.15.09.01,&nbsp;phast/1.4, ncl/2.1.21-dev</p> Thu, 14 Sep 2017 14:03:00 GMT https://www.uppmax.uu.se/changelog 2017-09-14T14:03:00Z [bio] paml/4.9e is installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://abacus.gene.ucl.ac.uk/software/paml.html">PAML</a> (Phylogenetic Analysis by Maximum Likelihood) 4.9e is installed as module paml/4.9e on all systems.</p> Thu, 14 Sep 2017 13:21:00 GMT https://www.uppmax.uu.se/changelog 2017-09-14T13:21:00Z [bio] phylobayes/4.1c installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://megasun.bch.umontreal.ca/People/lartillot/www/download.html">PhyloBayes</a> version 4.1c has been installed as phylobayes/4.1c on all systems.</p> Thu, 14 Sep 2017 12:27:00 GMT https://www.uppmax.uu.se/changelog 2017-09-14T12:27:00Z [bio] phylobayesmpi/1.8 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/bayesiancook/pbmpi">PhyloBayes MPI</a> version 1.8 is now installed as module phylobayesmpi/1.8 on all systems.&nbsp;</p> Thu, 14 Sep 2017 12:26:00 GMT https://www.uppmax.uu.se/changelog 2017-09-14T12:26:00Z [bio] GATK-Queue/3.8-0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://software.broadinstitute.org/gatk/download/queue">GATK Queue</a> version 3.8-0 has been installed as module GATK-Queue/3.8-0 on all systems.</p> Wed, 13 Sep 2017 15:42:00 GMT https://www.uppmax.uu.se/changelog 2017-09-13T15:42:00Z [apps] RStudio/1.1.233-buggy now available on milou https://www.uppmax.uu.se/changelog <p>RStudio version 1.1.233 has been built from source and installed as module RStudio/1.1.233-buggy on milou. &nbsp;The most recent prebuilt version available for milou cannot manage figures produced by more recent versions of R. &nbsp;This module version of RStudio can interact with more recent R versions, but has a buggy and incomplete interface, particularly with respect to fonts used in the interface. &nbsp;This will not be the default module version for RStudio on milou. &nbsp;Use at your own risk, or better yet use RStudio on another Uppmax system.</p> Wed, 13 Sep 2017 15:15:00 GMT https://www.uppmax.uu.se/changelog 2017-09-13T15:15:00Z [bio] GATK/3.8-0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://software.broadinstitute.org/gatk/">Genome Analysis Toolkit</a> version 3.8-0 is installed on all systems as module GATK/3.8-0. &nbsp;In addition to other improvements, this version corrects <a href="https://gatkforums.broadinstitute.org/gatk/discussion/9947/crashes-with-segmentation-fault-in-shipped-libvectorloglesspairhmm-so">core dumps within the PairHMM library</a> that some users have reported.</p> Wed, 13 Sep 2017 15:13:00 GMT https://www.uppmax.uu.se/changelog 2017-09-13T15:13:00Z [comp] pgi/17.7 installed https://www.uppmax.uu.se/changelog <p>pgi/17.7 installed on Milou and Rackham</p> Wed, 13 Sep 2017 13:47:00 GMT https://www.uppmax.uu.se/changelog 2017-09-13T13:47:00Z [bio] local data caches for vep/84, vep/86 greatly reduced https://www.uppmax.uu.se/changelog <p>The local data caches for vep/84 and vep/86 have been reduced to just homo_sapiens. &nbsp;The local data caches for vep/87 and vep/89 remain complete. &nbsp;For more information, see&nbsp;<a href="http://www.uppmax.uu.se/resources/databases/other-uppnex-oriented-local-data-resources/">http://www.uppmax.uu.se/resources/databases/other-uppnex-oriented-local-data-resources/</a>&nbsp;and 'module help vep'.</p> Mon, 11 Sep 2017 16:31:00 GMT https://www.uppmax.uu.se/changelog 2017-09-11T16:31:00Z [bio] BioPerl/1.7.1_Perl5.24.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://bioperl.org/">BioPerl</a> 1.7.1 for Perl 5.24.1&nbsp;has been installed as module BioPerl/1.7.1_Perl5.24.1 on all systems.</p> Mon, 11 Sep 2017 14:56:00 GMT https://www.uppmax.uu.se/changelog 2017-09-11T14:56:00Z [bio] spaln/2.3.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/">Spaln</a> (space-efficient spliced alignment) version 2.3.1 is now installed as module spaln/2.3.1 on all systems.</p> Thu, 07 Sep 2017 14:05:00 GMT https://www.uppmax.uu.se/changelog 2017-09-07T14:05:00Z [bio] sickle/1.33-20-g4b0dc85-mullins installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/MullinsLab/sickle">Sickle</a> (short read quality-based correction) version&nbsp;1.33-20-g4b0dc85-mullins, based off a maintained fork of the original source tree, has been installed as module&nbsp;sickle/1.33-20-g4b0dc85-mullins on all systems.</p> Tue, 05 Sep 2017 15:41:00 GMT https://www.uppmax.uu.se/changelog 2017-09-05T15:41:00Z [bio] SHORE/0.9.3 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://shore.sourceforge.net/wiki/">SHORE</a> (mapping and analysis pipeline for short DNA sequences) 0.9.3 is now installed as module SHORE/0.9.3 on all systems.</p> Tue, 05 Sep 2017 15:40:00 GMT https://www.uppmax.uu.se/changelog 2017-09-05T15:40:00Z [bio] sambamba/0.6.6 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://lomereiter.github.io/sambamba/">Sambamba</a> 0.6.6 (SAM/BAM file processing) has been installed as module sambamba/0.6.6 on all systems.</p> Tue, 05 Sep 2017 15:38:00 GMT https://www.uppmax.uu.se/changelog 2017-09-05T15:38:00Z [bio] scalpel/0.5.3 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://sourceforge.net/p/scalpel/wiki/Manual/">Scalpel</a> (indel detection) 0.5.3 has been installed as module scalpel/0.5.3 on all systems.</p> Tue, 05 Sep 2017 15:37:00 GMT https://www.uppmax.uu.se/changelog 2017-09-05T15:37:00Z Several more modules now available on all systems https://www.uppmax.uu.se/changelog <p>Several more modules, previously available only on milou or on milou and a subset of other systems, are now available on all systems (milou, rackham, irma, bianca): jellyfish/1.1.11, Kraken/0.10.5-beta, Krona/2.7, SGA/0.10.14, soapdenovo-trans/{1.03,1.04}, soapcorrector/1.0, soapdenovo/2.04-r240, StringTie/{1.2.0,1.3.3}, trinity/2014-07-17, h5utils/1.12.1, jemalloc/3.6.0, swig/3.0.7, SCons/2.5.0, blas/3.6.0, gsl/2.1, gsl/2.3, libcurl/7.45.0, diamond/0.8.26, maq/0.7.1, MUMmer/3.2.2, MafFilter/1.1.2, last/847, Vmatch/2.2.5,&nbsp;multiz/012109&nbsp;</p> <div><!--?xml version="1.0" encoding="UTF-8" standalone="no"?--></div> Mon, 04 Sep 2017 11:29:00 GMT https://www.uppmax.uu.se/changelog 2017-09-04T11:29:00Z [bio] MAFFT/7.310 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://mafft.cbrc.jp/alignment/software/">MAFFT</a> 7.310 (multiple sequence aligner) is installed as module MAFFT/7.310 on all systems.</p> Mon, 04 Sep 2017 11:12:00 GMT https://www.uppmax.uu.se/changelog 2017-09-04T11:12:00Z [libs] jemalloc/5.0.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://jemalloc.net/">Jemalloc</a> 5.0.1 (general purpose malloc implementation) has been installed as module jemalloc/5.0.1 on all systems. &nbsp;The earlier installed module version jemalloc/3.6.0 is also now available on all systems.</p> Mon, 04 Sep 2017 08:27:00 GMT https://www.uppmax.uu.se/changelog 2017-09-04T08:27:00Z [bio] trinity/2.4.0 installed on all systems https://www.uppmax.uu.se/changelog <p>Trinity 2.4.0 (transcriptome assembler) is installed as module trinity/2.4.0 on all systems.</p> Sun, 03 Sep 2017 19:56:00 GMT https://www.uppmax.uu.se/changelog 2017-09-03T19:56:00Z [bio] khmer/2.1.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://[bio] khmer/2.1.1 installed on all systems">Khmer</a> 2.1.1 (k-mer counting library) is installed as module khmer/2.1.1 on all systems.</p> Sun, 03 Sep 2017 12:35:00 GMT https://www.uppmax.uu.se/changelog 2017-09-03T12:35:00Z [bio] NGSadmin/32 and fastNGSadmin/20170825-099ab7f are installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://www.popgen.dk/software/index.php/NgsAdmix">NGSadmix</a> version 32 and <a href="http://www.popgen.dk/software/index.php/FastNGSadmix">fastNGSadmix</a> (versioned based on repository date/commit hash) are available as modules NGSadmix/32 and fastNGSadmix/20170825-099ab7f on all systems.</p> Sat, 02 Sep 2017 18:44:00 GMT https://www.uppmax.uu.se/changelog 2017-09-02T18:44:00Z [bio] lastz/1.04.00 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.bx.psu.edu/~rsharris/lastz/">LASTZ</a> 1.04.00 (pairwise sequence aligner) has been installed as module lastz/1.04.00 on all systems.</p> Fri, 01 Sep 2017 15:25:00 GMT https://www.uppmax.uu.se/changelog 2017-09-01T15:25:00Z [bio] rtgcore/3.8.3 installed on all systems https://www.uppmax.uu.se/changelog <p>The non-commercial version of&nbsp;<a href="https://www.realtimegenomics.com/products/rtg-core-non-commercial">RTG Core</a> version 3.8.3 has been installed as module rtgcore/3.8.3 on all systems. &nbsp;This includes all functionality of rtgtools/3.8.3 as well as additional commands.</p> Fri, 01 Sep 2017 12:49:00 GMT https://www.uppmax.uu.se/changelog 2017-09-01T12:49:00Z [bio] rtgtools/3.8.3 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.realtimegenomics.com/products/rtg-tools">RTG Tools</a> version 3.8.3 has been installed as module rtgtools/3.8.3 on all systems.</p> Fri, 01 Sep 2017 12:48:00 GMT https://www.uppmax.uu.se/changelog 2017-09-01T12:48:00Z [bio] fastq_screen/0.11.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/">FastQ Screen</a> version 0.11.1 has been installed as module fastq_screen/0.11.1 on all systems.</p> Fri, 01 Sep 2017 10:58:00 GMT https://www.uppmax.uu.se/changelog 2017-09-01T10:58:00Z [bio] anfo/0.98 now available for all systems https://www.uppmax.uu.se/changelog <p><a href="https://bioinf.eva.mpg.de/anfo/">Anfo</a> (short-read mapper for divergent reads) version 0.98 is now available as module anfo/0.98 on all systems. &nbsp;This module was installed for the now-decommissioned kalkyl but didn't work properly for milou, and this is now corrected for all systems. The earlier module version anfo/0.97 is removed. &nbsp;This version of the program&nbsp;is quite old (~8 y).</p> Fri, 01 Sep 2017 09:53:00 GMT https://www.uppmax.uu.se/changelog 2017-09-01T09:53:00Z [apps] gnuplot/5.0.7 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://www.gnuplot.info/">Gnuplot</a> 5.0.7 is installed as module gnuplot/5.0.7 on all systems.</p> Thu, 31 Aug 2017 15:03:00 GMT https://www.uppmax.uu.se/changelog 2017-08-31T15:03:00Z [apps] awscli/1.11.140 now available on all systems https://www.uppmax.uu.se/changelog <p><a href="https://aws.amazon.com/cli/">Amazon Web Services Command-Line Interface</a> version 1.11.140 is now installed as module awscli/1.11.140 on all systems.</p> Fri, 25 Aug 2017 14:56:00 GMT https://www.uppmax.uu.se/changelog 2017-08-25T14:56:00Z Several more modules now available on all systems https://www.uppmax.uu.se/changelog <p>Several more modules that were previously available only on milou, or only milou and rackham, are now available on all systems: guile/1.8.8, agrep/3.41.5, mcl/14-137, JAGS/4.2.0 and&nbsp;mbuffer/20151002.</p> Fri, 25 Aug 2017 14:50:00 GMT https://www.uppmax.uu.se/changelog 2017-08-25T14:50:00Z [bio] htseq/0.9.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://htseq.readthedocs.io/">HTSeq</a> version 0.9.1 has been installed as module htseq/0.9.1 on all systems.</p> Fri, 25 Aug 2017 11:43:00 GMT https://www.uppmax.uu.se/changelog 2017-08-25T11:43:00Z [comp] gcc/6.4.0 installed https://www.uppmax.uu.se/changelog <p>gcc 6.4.0 is now installed on Bianca, Irma, Milou and Rackham as gcc/6.4.0</p> Fri, 25 Aug 2017 10:19:00 GMT https://www.uppmax.uu.se/changelog 2017-08-25T10:19:00Z [bio] ITSx/1.0.11 and ITSx/1.1-beta installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://microbiology.se/software/itsx/">ITSx</a> (detection of ITS regions in ribosomal sequences) versions 1.0.11 and 1.1-beta are now installed on all systems. &nbsp;Both versions are new installations for all systems; note that 1.1-beta is a beta (preliminary) release.</p> Fri, 25 Aug 2017 09:23:00 GMT https://www.uppmax.uu.se/changelog 2017-08-25T09:23:00Z [bio] rseqc/2.6.4 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://rseqc.sourceforge.net/">RSeQC</a> 2.6.4 (RNA-Seq quality control) is now installed as module rseqc/2.6.4 on all systems.</p> Thu, 24 Aug 2017 12:50:00 GMT https://www.uppmax.uu.se/changelog 2017-08-24T12:50:00Z [bio] MaSuRCA/3.2.2 installed on all systems https://www.uppmax.uu.se/changelog <p>The <a href="http://www.genome.umd.edu/masurca.html">MaSuRCA assembler</a> version 3.2.2 is now installed as module MaSuRCA/3.2.2 on all systems.</p> Mon, 21 Aug 2017 13:22:00 GMT https://www.uppmax.uu.se/changelog 2017-08-21T13:22:00Z [bio] KAT/2.3.4 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://www.earlham.ac.uk/kat-tools">KAT (K-mer Analysis Toolkit)</a> version 2.3.4 has been installed as module KAT/2.3.4 on all systems.</p> Wed, 16 Aug 2017 14:12:00 GMT https://www.uppmax.uu.se/changelog 2017-08-16T14:12:00Z [comp] gcc/7.2.0 installed https://www.uppmax.uu.se/changelog <p>gcc 7.2.0 is now installed in Bianca, Irma, Milou and Rackham as gcc/7.2.0.</p> Tue, 15 Aug 2017 10:58:00 GMT https://www.uppmax.uu.se/changelog 2017-08-15T10:58:00Z [bio] RealTime Genomics reference databases now available https://www.uppmax.uu.se/changelog <p><a href="https://www.realtimegenomics.com/news/pre-formatted-reference-datasets">RealTime Genomics'&nbsp;preformatted reference databases</a> are now available on Uppmax systems. &nbsp;See 'module help rtgtools/3.8.1' for more information.</p> Sat, 12 Aug 2017 12:28:00 GMT https://www.uppmax.uu.se/changelog 2017-08-12T12:28:00Z [bio] pblat-cluster/0.3 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://icebert.github.io/pblat-cluster/">Pblat-cluster</a> (blat aligner with hybrid parallel support via MPI) version 0.3 has been installed as pblat-cluster/0.3 on all systems. &nbsp;Note that module pblat/2.0, with single-node multithreading,&nbsp;is also available.</p> Fri, 11 Aug 2017 09:27:00 GMT https://www.uppmax.uu.se/changelog 2017-08-11T09:27:00Z [bio] pblat/2.0 installed on all clusters https://www.uppmax.uu.se/changelog <p><a href="http://icebert.github.io/pblat/">Pblat</a> (threaded version of blat aligner) version 2.0 has been installed as module pblat/2.0 on all systems.</p> Fri, 11 Aug 2017 09:25:00 GMT https://www.uppmax.uu.se/changelog 2017-08-11T09:25:00Z [bio] all bioinformatics modules will default to the latest version https://www.uppmax.uu.se/changelog <p>Previously, several bioinformatics modules had default versions fixed to earlier module versions; the default version is that loaded when no version is specified when using 'module load'. &nbsp;All such restrictions on default versions have now been removed. &nbsp;To improve reproducibility of results, a specific module version should&nbsp;<em><strong>always</strong></em>&nbsp;be specified when loading tools via the module system.</p> Thu, 10 Aug 2017 14:14:00 GMT https://www.uppmax.uu.se/changelog 2017-08-10T14:14:00Z [apps] Matlab R2017a installed https://www.uppmax.uu.se/changelog <p>Matlab R2017a has been installed as module matlab/R2017a on Milou and Rackham.</p> Wed, 09 Aug 2017 12:05:00 GMT https://www.uppmax.uu.se/changelog 2017-08-09T12:05:00Z [bio] EPACTS/3.3.0-a5209db installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://genome.sph.umich.edu/wiki/EPACTS">EPACTS</a> 3.3.0-a5209db (version based off of latest bug-fix commit) has been installed as module EPACTS/3.3.0-a5209db on all systems.</p> Tue, 08 Aug 2017 14:52:00 GMT https://www.uppmax.uu.se/changelog 2017-08-08T14:52:00Z [bio] MELT/2.0.2 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://melt.igs.umaryland.edu/">MELT</a> (Mobile Element Locator Tool) version 2.0.2 has been installed as module MELT/2.0.2 on all systems.</p> Tue, 08 Aug 2017 12:46:00 GMT https://www.uppmax.uu.se/changelog 2017-08-08T12:46:00Z [bio] AMOS/3.0.0, AMOS/3.1.0, blat/34 and blat/35 now on rackham, irma, bianca https://www.uppmax.uu.se/changelog <p>The modules AMOS/3.0.0, AMOS/3.1.0, blat/34 and blat/35, previously available only on milou, are now on rackham, irma, bianca.</p> Mon, 07 Aug 2017 15:42:00 GMT https://www.uppmax.uu.se/changelog 2017-08-07T15:42:00Z [bio] kallisto/0.43.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://pachterlab.github.io/kallisto/">The RNA-seq pseudoalignment tool&nbsp;kallisto</a> version 0.43.1 has been installed on all systems as module&nbsp;kallisto/0.43.1.</p> Mon, 07 Aug 2017 15:40:00 GMT https://www.uppmax.uu.se/changelog 2017-08-07T15:40:00Z [bio] cufflinks/2.2.1-b55bb21 installed on all systems https://www.uppmax.uu.se/changelog <p>An updated version of cufflinks has been installed as module&nbsp;cufflinks/2.2.1-b55bb21 on all systems. &nbsp;This contains a fix for an unusual case in which extremely long runtimes have been observed; more information is available <a href="https://github.com/UPPMAX/install-methods/blob/master/apps/bioinfo/cufflinks/cufflinks-2.2.1-b55bb21-install-README.md">here</a>.</p> Mon, 07 Aug 2017 13:38:00 GMT https://www.uppmax.uu.se/changelog 2017-08-07T13:38:00Z [apps] several packages added to R_packages/3.4.0 https://www.uppmax.uu.se/changelog <p>The R packages&nbsp;Lahman, RJSONIO, ecodist, gee, hflights, igraph, optparse, proto, and reshape and the BioConductor packages&nbsp;ROC, TCC, baySeq,&nbsp;multtest, and&nbsp;phyloseq, together with their dependencies, have been added to the R_packages/3.4.0 module. &nbsp;For a complete list of packages available, see the&nbsp;<a href="https://www.uppmax.uu.se/support-sv//r_packages-module-guide">R_packages user guide</a>.</p> Mon, 31 Jul 2017 14:33:00 GMT https://www.uppmax.uu.se/changelog 2017-07-31T14:33:00Z [bio] picard/2.10.3 installed on all systems https://www.uppmax.uu.se/changelog <p>The most recent version of <a href="https://broadinstitute.github.io/picard/">Picard tools</a> has been installed as module picard/2.10.3 on all systems.</p> Thu, 20 Jul 2017 21:48:00 GMT https://www.uppmax.uu.se/changelog 2017-07-20T21:48:00Z [bio] samtools/1.5, htslib/1.5, bcftools/1.5 installed on all systems https://www.uppmax.uu.se/changelog <p>The modules <a href="https://github.com/samtools/samtools">samtools/1.5</a>, <a href="https://github.com/samtools/htslib">htslib/1.5</a>, and&nbsp;<a href="https://github.com/samtools/bcftools">bcftools/1.5</a>&nbsp;have been installed on all systems. &nbsp;Note that the most recent versions of the tabix and bgzip tools are now found in the htslib module, and not the tabix module.</p> Thu, 20 Jul 2017 21:45:00 GMT https://www.uppmax.uu.se/changelog 2017-07-20T21:45:00Z [bio] augustus/3.2.2 available on irma, bianca, rackham https://www.uppmax.uu.se/changelog <p>The module augustus/3.2.2, previously available only on milou, is now also available on irma, bianca and rackham.</p> Tue, 18 Jul 2017 21:27:00 GMT https://www.uppmax.uu.se/changelog 2017-07-18T21:27:00Z [bio] Longranger upgraded to 2.1.4 on all systems https://www.uppmax.uu.se/changelog <p>10X Longranger 2.1.4 (set of analysis pipelines to process Chromium sequencing output) is installed in module longranger/2.1.4 on all systems.</p> Wed, 12 Jul 2017 07:37:00 GMT https://www.uppmax.uu.se/changelog 2017-07-12T07:37:00Z [bio] bismark/0.18.2 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.bioinformatics.babraham.ac.uk/projects/download.html#bismark">Bismark</a> 0.18.2 has been installed as module bismark/0.18.2 on all systems. &nbsp;The earlier&nbsp;bismark module versions&nbsp;0.14.5, 0.15.0, 0.16.1 and 0.16.2 are also installed on rackham; they were previously available on milou, bianca and irma.</p> Wed, 28 Jun 2017 12:05:00 GMT https://www.uppmax.uu.se/changelog 2017-06-28T12:05:00Z [bio] vsearch/2.4.3 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/torognes/vsearch">vsearch</a> 2.4.3 has been installed as module vsearch/2.4.3 on all systems.</p> Tue, 27 Jun 2017 12:36:00 GMT https://www.uppmax.uu.se/changelog 2017-06-27T12:36:00Z [bio] VEP 89 upgraded https://www.uppmax.uu.se/changelog <p>VEP (Variant Effect Predictor) has been upgraded to version&nbsp;89 on all systems.</p> Tue, 27 Jun 2017 10:44:00 GMT https://www.uppmax.uu.se/changelog 2017-06-27T10:44:00Z STAR-Fusion Installed on all the systems https://www.uppmax.uu.se/changelog <p>STAR-Fusion/1.0.0 is Installed and is available on all the systems.</p> Thu, 22 Jun 2017 16:22:00 GMT https://www.uppmax.uu.se/changelog 2017-06-22T16:22:00Z Eigensoft upgraded to 7.2.0 https://www.uppmax.uu.se/changelog <p>eigensoft/7.2.0 is now available on all the systems.</p> Thu, 22 Jun 2017 16:19:00 GMT https://www.uppmax.uu.se/changelog 2017-06-22T16:19:00Z STAR upgraded to 2.5.3a https://www.uppmax.uu.se/changelog <p>star/2.5.3a is now available on all the systems.</p> Wed, 21 Jun 2017 17:25:00 GMT https://www.uppmax.uu.se/changelog 2017-06-21T17:25:00Z HISAT2 upgraded to 2.1.0 https://www.uppmax.uu.se/changelog <p>HISAT2/2.1.0 is now available on all the systems.</p> Wed, 21 Jun 2017 09:23:00 GMT https://www.uppmax.uu.se/changelog 2017-06-21T09:23:00Z [geo] libgeotiff/1.4.1 available on rackham https://www.uppmax.uu.se/changelog <p>The libgeotiff/1.4.1 module is now available on rackham; it was previously available only on milou.</p> Fri, 16 Jun 2017 14:34:00 GMT https://www.uppmax.uu.se/changelog 2017-06-16T14:34:00Z [geo] GEOS/3.4.0, GDAL/2.1.0, PROJ.4/4.9.2, FYBA/4.1.1 now on all systems https://www.uppmax.uu.se/changelog <p>The geospatial modules GEOS/3.4.0, GDAL/2.1.0, PROJ.4/4.9.2, and FYBA/4.1.1 are now available on rackham. &nbsp;These were already available on milou and were previously available on tintin. &nbsp;These are fresh installations of the modules from tintin, so are not necessarily the latest versions of these tools.</p> Fri, 16 Jun 2017 13:55:00 GMT https://www.uppmax.uu.se/changelog 2017-06-16T13:55:00Z delly upgraded to 0.7.7 https://www.uppmax.uu.se/changelog <p>delly/0.7.7 has been installed on all the systems.</p> Wed, 07 Jun 2017 08:13:00 GMT https://www.uppmax.uu.se/changelog 2017-06-07T08:13:00Z [bio] rtgtools/3.8.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/RealTimeGenomics/rtg-tools">RTG Tools</a> 3.8.1 (utilities for accurate VCF comparison and manipulation) has been installed as module rtgtools/3.8.1 on all systems.</p> Mon, 05 Jun 2017 14:00:00 GMT https://www.uppmax.uu.se/changelog 2017-06-05T14:00:00Z [bio] MAGeCK/0.5.6 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://sourceforge.net/projects/mageck/">MAGeCK</a> 0.5.6 (Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout) is now installed as module MAGeCK/0.5.6 on all systems.</p> Mon, 05 Jun 2017 13:39:00 GMT https://www.uppmax.uu.se/changelog 2017-06-05T13:39:00Z [bio] cufflinks/2.2.1 installed on all systems https://www.uppmax.uu.se/changelog <p>Cufflinks 2.2.1 has been installed as module cufflinks/2.2.1 on all systems. &nbsp;The earlier version cufflinks/2.1.1 has also been installed on rackham; it was all ready available on all other systems.</p> Fri, 02 Jun 2017 22:54:00 GMT https://www.uppmax.uu.se/changelog 2017-06-02T22:54:00Z [bio] bowtie2/2.3.2 installed on all systems https://www.uppmax.uu.se/changelog <p>Bowtie2 2.3.2 has been installed as module bowtie2/2.3.2 on all systems.</p> Fri, 02 Jun 2017 22:51:00 GMT https://www.uppmax.uu.se/changelog 2017-06-02T22:51:00Z [bio] bowtie/1.2.0 installed on all systems https://www.uppmax.uu.se/changelog <p>Bowtie 1.2.0 has been installed as module bowtie/1.2.0 on all systems.</p> Fri, 02 Jun 2017 22:47:00 GMT https://www.uppmax.uu.se/changelog 2017-06-02T22:47:00Z [bio] tophat/2.1.1 installed on all systems https://www.uppmax.uu.se/changelog <p>Tophat 2.1.1 has been installed as module tophat/2.1.1 on all systems. &nbsp;The earlier versions tophat/2.0.10 and tophat/2.0.12 have also been made available on rackham, irma and/or bianca.</p> Fri, 02 Jun 2017 22:41:00 GMT https://www.uppmax.uu.se/changelog 2017-06-02T22:41:00Z [bio] MrBayes installed on Rackham https://www.uppmax.uu.se/changelog <p><a href="http://mrbayes.sourceforge.net">MrBayes</a> (Bayesian inference and model choice) is now installed on Rackham as module mrbayes/3.2.6.&nbsp;</p> Fri, 02 Jun 2017 08:21:00 GMT https://www.uppmax.uu.se/changelog 2017-06-02T08:21:00Z [bio]Beagle-lib installed on Rackham https://www.uppmax.uu.se/changelog <p><a href="https://github.com/beagle-dev/beagle-lib">Beagle-lib</a>&nbsp;(general purpose library for evaluating the likelihood of sequence evolution on trees) is now installed on Rackham as module beagle/2.1.2.&nbsp;</p> Fri, 02 Jun 2017 08:18:00 GMT https://www.uppmax.uu.se/changelog 2017-06-02T08:18:00Z [bio] MultiQC/1.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://multiqc.info/">MultiQC</a>&nbsp;1.0 (aggregates results from bioinformatics analyses across many samples into a single report) is now installed as module MultiQC/1.0 on all systems.</p> Tue, 30 May 2017 12:24:00 GMT https://www.uppmax.uu.se/changelog 2017-05-30T12:24:00Z [bio] several bioinfo-tools/misc modules now also available on rackham https://www.uppmax.uu.se/changelog <p>Several bioinformatics modules from the bioinfo-tools/misc subgroup available on milou were previously installed on bianca and irma but not on rackham; these are now also made available on rackham. The modules are:&nbsp;ANGSD/0.917, ANGSD/0.917-g6522d3e, biopython/1.68, biopython/1.68-py3, deepTools/2.2.3, deepTools/2.3.1, ngsplot/2.61, phantompeakqualtools/1.1, preseq/0.1.0, prodigal/2.6.3, pysam/0.9.1.4, RepeatModeler/1.0.8_RM4.0.7, SPP/1.11, strelka/1.0.15, tabix/0.2.6</p> Wed, 24 May 2017 15:21:00 GMT https://www.uppmax.uu.se/changelog 2017-05-24T15:21:00Z [bio] deepTools/2.5.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/fidelram/deepTools">deepTools</a> 2.5.1 is now installed as module deepTools/2.5.1 on all systems.</p> Wed, 24 May 2017 15:16:00 GMT https://www.uppmax.uu.se/changelog 2017-05-24T15:16:00Z [bio] deepTools/2.4.3 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/fidelram/deepTools">deepTools</a> 2.4.3 has been installed as module deepTools/2.4.3 on all systems.</p> Wed, 24 May 2017 15:02:00 GMT https://www.uppmax.uu.se/changelog 2017-05-24T15:02:00Z [bio] seqtk/1.2-r101 available on all systems https://www.uppmax.uu.se/changelog <p>The <a href="https://github.com/lh3/seqtk">seqtk</a> tool version 1.2-r101 has been installed on all systems as module seqtk/1.2-r101. &nbsp;The earlier version 1.0-r57 has also been installed on all systems as module seqtk/1.0-r57, and&nbsp;the module versions seqtk/1.0-r31 and&nbsp;seqtk/1.0-r68e, previously available only on milou,&nbsp;have been installed on rackham, irma and bianca.</p> Wed, 24 May 2017 11:36:00 GMT https://www.uppmax.uu.se/changelog 2017-05-24T11:36:00Z [comp] pgi/17.4 installed https://www.uppmax.uu.se/changelog <p>pgi/17.4 installed on Milou and Rackham</p> Wed, 24 May 2017 10:01:00 GMT https://www.uppmax.uu.se/changelog 2017-05-24T10:01:00Z [parallel] openmpi/2.1.1 https://www.uppmax.uu.se/changelog <p>openmpi/2.1.1 has been installed on Irma, Milou and Rackham</p> Wed, 24 May 2017 06:36:00 GMT https://www.uppmax.uu.se/changelog 2017-05-24T06:36:00Z [comp] advisor, ampilifier, inspector and itac upgraded https://www.uppmax.uu.se/changelog <p>advisor, ampilifier, inspector and itac upgraded</p> Wed, 24 May 2017 06:35:00 GMT https://www.uppmax.uu.se/changelog 2017-05-24T06:35:00Z [comp] intel/17.4 installed https://www.uppmax.uu.se/changelog <p>intel/17.4 has been installed on all systems.</p> Wed, 24 May 2017 06:33:00 GMT https://www.uppmax.uu.se/changelog 2017-05-24T06:33:00Z [bio] TEtools/1.0.0-283c1ca installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/l-modolo/TEtools">TEtools</a> 1.0.0 up through commit 283c1ca has been installed as module&nbsp;TEtools/1.0.0-283c1ca on all systems. &nbsp;The <a href="https://github.com/douglasgscofield/TEtools">local UPPMAX version</a> has been modified to move some options provided only in config files to command-line options.</p> Fri, 19 May 2017 14:23:00 GMT https://www.uppmax.uu.se/changelog 2017-05-19T14:23:00Z [comp] perl_modules/5.24.1 installed on all systems https://www.uppmax.uu.se/changelog <p>The omnibus module <a href="https://www.uppmax.uu.se/support-sv//perl_modules-5.24.1-module-guide">perl_modules/5.24.1</a> has been installed on all systems. &nbsp;This module contains many commonly-used and not-so-commonly used perl modules, for use with the perl/5.24.1 module, which is also loaded. &nbsp;Note that perl/5.24.1 uses 64-bit integers and pointers. &nbsp;See the linked page for a list of the contents of this omnibus module.</p> Mon, 15 May 2017 14:16:00 GMT https://www.uppmax.uu.se/changelog 2017-05-15T14:16:00Z [comp] perl6/rakudo-star-2017.04 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://perl6.org">Perl6</a>&nbsp;<a href="http://rakudo.org/2017/05/01/announce-rakudo-star-release-2017-04/">Rakudo Star 2017.04</a>&nbsp;has been installed as module perl6/rakudo-star-2017.04 on all systems. &nbsp;This module also modifies the environment for development against MoarVM if so desired.</p> Mon, 15 May 2017 10:25:00 GMT https://www.uppmax.uu.se/changelog 2017-05-15T10:25:00Z [apps] emacs/25.2 installed on all systems https://www.uppmax.uu.se/changelog <p>The editor <a href="https://www.gnu.org/software/emacs/">emacs</a> has been installed as module emacs/25.2 on all systems. &nbsp;Emacs is already installed on all systems but this module provides the most recent version.</p> Sun, 14 May 2017 01:18:00 GMT https://www.uppmax.uu.se/changelog 2017-05-14T01:18:00Z [libs] giflib/5.1.4 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://sourceforge.net/projects/giflib/">GIFLIB</a> (library providing GIF support via libgif) is now installed as module libgif/5.1.4 on all systems.</p> Sun, 14 May 2017 01:16:00 GMT https://www.uppmax.uu.se/changelog 2017-05-14T01:16:00Z [bio] ATLAS_aDNA/20170510 installed on all systems https://www.uppmax.uu.se/changelog <p>The <a href="https://bitbucket.org/phaentu/atlas/wiki/Home">ATLAS</a> tool for working with ancient DNA has been installed as module ATLAS_aDNA/20170510 on all systems. &nbsp;Note the module name is <strong>ATLAS_aDNA</strong>, because the name ATLAS has already being given to a module for the&nbsp;widely used numeric library.</p> Sat, 13 May 2017 17:55:00 GMT https://www.uppmax.uu.se/changelog 2017-05-13T17:55:00Z [libs] Armadillo/7.900.0 installed on all systems https://www.uppmax.uu.se/changelog <p>The <a href="http://arma.sourceforge.net/">Armadillo</a> C++ linear algebra library has been installed as module Armadillo/7.900.0 on all systems.</p> Sat, 13 May 2017 17:54:00 GMT https://www.uppmax.uu.se/changelog 2017-05-13T17:54:00Z [bio] hmmer/3.1b2-intel installed on all systems https://www.uppmax.uu.se/changelog <p>HMMER 3.1b2 compiled with the Intel compiler and OpenMPI support (with the intel/17.2 and openmpi/2.1.0 modules) has been installed as module hmmer/3.1b2-intel on all systems.</p> Sat, 13 May 2017 09:43:00 GMT https://www.uppmax.uu.se/changelog 2017-05-13T09:43:00Z [bio] MethylDackel/0.2.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/dpryan79/MethylDackel">MethylDackel</a>&nbsp;0.2.1 (renamed continuation of methylation detection tool PileOMeth) is now installed as module MethylDackel/0.2.1 on all systems.</p> Thu, 11 May 2017 16:52:00 GMT https://www.uppmax.uu.se/changelog 2017-05-11T16:52:00Z [comp] perl/5.24.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.perl.org/">Perl</a> 5.24.1 (the most recent stable distribution) has been installed as perl/5.24.1 on all systems. &nbsp;Perl modules perl/5.22.2 and perl/5.24.0, previously available only on milou, are now also available on rackham, irma and bianca. &nbsp; All perl modules with versions 5.24+ are built with 64-bit integers and pointers.</p> Thu, 11 May 2017 16:47:00 GMT https://www.uppmax.uu.se/changelog 2017-05-11T16:47:00Z [bio] vcftools/0.1.15 installed on all systems https://www.uppmax.uu.se/changelog <p>VCFtools version 0.1.15 is now installed as module vcftools/0.1.15 on all systems. &nbsp;vcftools/0.1.14 has also been provided on rackham; it was previously available on milou, bianca and irma.</p> Thu, 11 May 2017 16:09:00 GMT https://www.uppmax.uu.se/changelog 2017-05-11T16:09:00Z [build] m4/1.4.17 and libtool/2.4.6 installed on all systems https://www.uppmax.uu.se/changelog <p>The scripting language <a href="https://www.gnu.org/software/m4/m4.html">m4</a> &nbsp;and the build tool <a href="https://www.gnu.org/software/libtool/">libtool</a> are now installed as modules m4/1.4.17 and libtool/2.4.6&nbsp;on all systems.</p> Thu, 11 May 2017 14:58:00 GMT https://www.uppmax.uu.se/changelog 2017-05-11T14:58:00Z [build] cmake/3.5.1 available on rackham, bianca and irma https://www.uppmax.uu.se/changelog <p>CMake 3.5.1, previously available only on milou, is now available as module cmake/3.5.1 on rackham, bianca and irma as well.</p> Thu, 11 May 2017 14:12:00 GMT https://www.uppmax.uu.se/changelog 2017-05-11T14:12:00Z [comp] gcc/7.1.0 installed https://www.uppmax.uu.se/changelog <p>gcc/7.1.0 installed on all systems.</p> Thu, 11 May 2017 11:59:00 GMT https://www.uppmax.uu.se/changelog 2017-05-11T11:59:00Z [bio] malder/1.0 installed on milou https://www.uppmax.uu.se/changelog <p><a href="https://github.com/joepickrell/malder">MALDER</a> has been installed as module malder/1.0 on milou.</p> Tue, 09 May 2017 09:20:00 GMT https://www.uppmax.uu.se/changelog 2017-05-09T09:20:00Z [apps] p7zip/16.02 now installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://sourceforge.net/projects/p7zip/">p7zip</a> (Linux port of popular 7zip archiver from Windows) 16.02 is now installed as module p7zip/16.02 on all systems. &nbsp;The executable file is named <strong>7za</strong>.</p> Mon, 08 May 2017 11:21:00 GMT https://www.uppmax.uu.se/changelog 2017-05-08T11:21:00Z [bio] ProtExcluder/1.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Repeat_Library_Construction-Basic">ProtExcluder</a> 1.1 (scripts to remove fragmented proteins during repeat library construction) is installed as module ProtExcluder/1.1 on all systems.</p> Sat, 06 May 2017 22:57:00 GMT https://www.uppmax.uu.se/changelog 2017-05-06T22:57:00Z [bio] mirdeep2/2.0.0.8 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.mdc-berlin.de/8551903/en/">miRDeep2</a> (miRNA discovery) version 2.0.0.8 is now installed as module mirdeep2/2.0.0.8 on all systems.</p> Sat, 06 May 2017 16:58:00 GMT https://www.uppmax.uu.se/changelog 2017-05-06T16:58:00Z [bio] MetaSV/0.5.4 installed on all systems https://www.uppmax.uu.se/changelog <p>The most recent version of <a href="https://github.com/bioinform/metasv">MetaSV</a> (accurate and integrative structural-variant caller for next generation sequencing) has now been installed as module MetaSV/0.5.4 on all systems.</p> Sat, 06 May 2017 11:37:00 GMT https://www.uppmax.uu.se/changelog 2017-05-06T11:37:00Z [bio] spades/3.10.1 installed on all systems https://www.uppmax.uu.se/changelog <p>The latest <a href="http://bioinf.spbau.ru/spades">SPAdes</a> assembler is now installed as spades/3.10.1 on all systems. &nbsp;Earlier versions 3.6.0, 3.8.0, 3.8.1, 3.9.0 and 3.10.0 are also now available on rackham, irma and bianca.</p> Sat, 06 May 2017 10:52:00 GMT https://www.uppmax.uu.se/changelog 2017-05-06T10:52:00Z [bio] AGE/0.4 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/abyzovlab/AGE">AGE</a> (sequence alignment in the presence of structural variants) 0.4 is installed as module AGE/0.4 on all systems. &nbsp;The executable <strong>age_align</strong> is built without parallel support, while the executable <strong>age_align_omp</strong> is built with parallel support. &nbsp;See 'module help AGE/0.4' for more information.</p> Sat, 06 May 2017 09:58:00 GMT https://www.uppmax.uu.se/changelog 2017-05-06T09:58:00Z [apps] eLSA/20160907-febe2d7a57c8 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://bitbucket.org/charade/elsa/wiki/Home">eLSA</a> (extended local similarity analysis) has been installed as module&nbsp;eLSA/20160907-febe2d7a57c8 on all systems.</p> Sat, 06 May 2017 09:21:00 GMT https://www.uppmax.uu.se/changelog 2017-05-06T09:21:00Z [bio] GEMINI/0.20.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://gemini.readthedocs.io/en/latest/">GEMINI</a> (comprehensive genome variant annotation) 0.20.0 has been installed as module GEMINI/0.20.0 on all systems. &nbsp;The earlier versions GEMINI/0.18.3 and GEMINI/0.20.0 have also been extended to rackham, irma and bianca. &nbsp;As before, the additional CADD and GERP annotation datasets have been included.</p> Sat, 06 May 2017 01:58:00 GMT https://www.uppmax.uu.se/changelog 2017-05-06T01:58:00Z [bio] vep/87 and local caches installed on rackham, irma and bianca https://www.uppmax.uu.se/changelog <p>The Variant Effects Predictor module vep/87 and its local caches have been installed on rackham, irma and bianca. &nbsp;The module was previously installed only on milou.</p> Fri, 05 May 2017 11:25:00 GMT https://www.uppmax.uu.se/changelog 2017-05-05T11:25:00Z [bio] fermikit/0.14-prerelease-96f7820 installed on all systems https://www.uppmax.uu.se/changelog <p>The most recent version of the <a href="https://github.com/lh3/fermikit">fermikit</a> assembly-based variant calling pipeline is now installed as module&nbsp;fermikit/0.14-prerelease-96f7820 on all systems. &nbsp;The previously installed fermikit/r178 is now also available on rackham, irma and bianca.</p> Fri, 05 May 2017 11:13:00 GMT https://www.uppmax.uu.se/changelog 2017-05-05T11:13:00Z [bio] SpeedSeq/0.1.2-20170504-30f8dc6 installed on all systems https://www.uppmax.uu.se/changelog <p>The latest <a href="https://github.com/hall-lab/speedseq/">SpeedSeq</a> (rapid genome analysis and interpretation) is installed as module&nbsp;SpeedSeq/0.1.2-20170504-30f8dc6 on all systems. &nbsp;The module version reflects the most recent release, as well as the date and commit of the repository clone for this installed module. &nbsp;See 'module help&nbsp;SpeedSeq/0.1.2-20170504-30f8dc6' for more information on available data.</p> Fri, 05 May 2017 09:52:00 GMT https://www.uppmax.uu.se/changelog 2017-05-05T09:52:00Z [bio] CNVnator/0.3.3 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/abyzovlab/CNVnator">CNVnator</a> 0.3.3 (copy-number variant detection) has been installed as module CNVnator/0.3.3 on all systems.</p> Thu, 04 May 2017 09:45:00 GMT https://www.uppmax.uu.se/changelog 2017-05-04T09:45:00Z [apps] ROOT/6.06.08 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://root.cern.ch/">ROOT</a> 6.06.08 (data analysis framework from CERN) has been installed as ROOT/6.06.08 on all systems.</p> Thu, 04 May 2017 09:44:00 GMT https://www.uppmax.uu.se/changelog 2017-05-04T09:44:00Z [libs] cairo/1.14.8 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.cairographics.org/">Cairo</a> 1.14.8 (device-independent graphics rendering library) has been installed as module cairo/1.14.8 on all systems.</p> Thu, 04 May 2017 09:42:00 GMT https://www.uppmax.uu.se/changelog 2017-05-04T09:42:00Z [libs] Poppler/0.54.0 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://poppler.freedesktop.org/">Poppler</a> 0.54.0 (library for rendering PDF) has been installed as module Poppler/0.54.0 on all systems.</p> Thu, 04 May 2017 09:41:00 GMT https://www.uppmax.uu.se/changelog 2017-05-04T09:41:00Z [bio] Salmon/0.8.2 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://combine-lab.github.io/salmon/">Salmon</a> 0.8.2 is now installed as module Salmon/0.8.2 on all systems.</p> Tue, 02 May 2017 09:37:00 GMT https://www.uppmax.uu.se/changelog 2017-05-02T09:37:00Z [bio] LEON-BIS 20130322 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://www.lbgi.fr/~julie/LEON-BIS/">LEON-BIS</a> (identify conserved areas in protein alignments) is now installed as module LEON-BIS/20130322 on all systems. &nbsp;See 'module help LEON-BIS/20130322' for more information.</p> Tue, 02 May 2017 07:47:00 GMT https://www.uppmax.uu.se/changelog 2017-05-02T07:47:00Z [libs] ATLAS/3.10.3 available on all systems https://www.uppmax.uu.se/changelog <p><a href="http://math-atlas.sourceforge.net/">ATLAS</a> (Automatically Tuned Linear Algebra Software) library version 3.10.3 is now installed on all systems. It was previously available only on milou. It has been tuned separately for milou, rackham and irma, and the bianca version is linked to the rackham build.</p> Thu, 27 Apr 2017 14:14:00 GMT https://www.uppmax.uu.se/changelog 2017-04-27T14:14:00Z [bio] pysam/0.9.1.4 and pysam/0.10.0 available on all systems https://www.uppmax.uu.se/changelog <p>Pysam 0.9.1.4 and 0.10.0 are now available on all systems&nbsp;as pysam/0.9.1.4 and pysam/0.10.0. &nbsp;Both are built to run against python/2.7.6. &nbsp;They were previously available only on milou and/or irma.</p> Thu, 27 Apr 2017 14:07:00 GMT https://www.uppmax.uu.se/changelog 2017-04-27T14:07:00Z [bio] MethPipe/3.4.3 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://smithlabresearch.org/software/methpipe/">MethPipe</a> 3.4.3 (computational pipeline for analyzing bisulfite sequencing data) is now installed as module MethPipe/3.4.3 on all systems.</p> Wed, 26 Apr 2017 07:45:00 GMT https://www.uppmax.uu.se/changelog 2017-04-26T07:45:00Z [bio] raxml/8.2.10-gcc, raxml/8.2.10-gcc-mpi installed on all systems https://www.uppmax.uu.se/changelog <p>The standard <a href="https://github.com/stamatak/standard-RAxML">RAxML</a> has been updated to version 8.2.10 both with and without MPI support on all systems. &nbsp;The modules are raxml/8.2.10-gcc and raxml/8.2.10-gcc-mpi.</p> Tue, 25 Apr 2017 16:41:00 GMT https://www.uppmax.uu.se/changelog 2017-04-25T16:41:00Z [bio] RAxML-NG/0.2.0b-mpi installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/amkozlov/raxml-ng">RAxML-NG</a> (reimplementation of RAxML) 0.2.0b is installed on all systems. &nbsp;The default module ins installed as RAxML-NG/0.2.0b, and the module enabled for MPI is installed as RAxML-NG/0.2.0b-mpi.</p> Tue, 25 Apr 2017 14:11:00 GMT https://www.uppmax.uu.se/changelog 2017-04-25T14:11:00Z [bio] wise2/2.2.0, wise2/2.4.1, geneid/1.4.4 installed on rackham, irma, bianca https://www.uppmax.uu.se/changelog <p>The modules wise2/2.2.0, wise2/2.4.1, and geneid/1.4.4 have been installed on rackham, irma and bianca.</p> Tue, 25 Apr 2017 09:19:00 GMT https://www.uppmax.uu.se/changelog 2017-04-25T09:19:00Z [bio] cegma/2.5 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://korflab.ucdavis.edu/datasets/cegma/">CEGMA</a> 2.5 (tool for assessing assembly completeness) is now installed as cegma/2.5 on all systems.</p> Tue, 25 Apr 2017 09:17:00 GMT https://www.uppmax.uu.se/changelog 2017-04-25T09:17:00Z [bio] BUSCO/2.0.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://busco.ezlab.org/">BUSCO</a> 2.0.1 has been installed as module BUSCO/2.0.1 on all systems. &nbsp;There is an extensive list of BUSCO lineage sets available, see the module help. &nbsp;BUSCO/1.22 has also been installed on rackham, irma and bianca.</p> Tue, 25 Apr 2017 07:19:00 GMT https://www.uppmax.uu.se/changelog 2017-04-25T07:19:00Z [bio] bowtie and bowtie2 modules available on rackham https://www.uppmax.uu.se/changelog <p>Several versions of the&nbsp;<a href="http://bowtie-bio.sourceforge.net/index.shtml">bowtie</a> and <a href="http://bowtie-bio.sourceforge.net/bowtie2/index.shtml">bowtie2</a>&nbsp;modules have been made available on rackham, irma and bianca. &nbsp;Available are bowtie/0.12.9, bowtie/1.1.2, bowtie2/2.1.0, bowtie2/2.2.9.</p> Mon, 24 Apr 2017 13:27:00 GMT https://www.uppmax.uu.se/changelog 2017-04-24T13:27:00Z [bio] samtools/1.4 and htslib/1.4 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/samtools/samtools">samtools</a> 1.4 and <a href="https://github.com/samtools/htslib">htslib</a> 1.4 have been installed as samtools/1.4 and htslib/1.4 on all systems.</p> Mon, 24 Apr 2017 11:21:00 GMT https://www.uppmax.uu.se/changelog 2017-04-24T11:21:00Z [bio] samblaster/0.1.22 and /0.1.24 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/GregoryFaust/samblaster">samblaster</a> 0.1.22 and 0.1.24 have been installed on all systems as modules samblaster/0.1.22 and samblaster/0.1.24. &nbsp;Previously, only samblaster/0.1.22 was available, and only on milou.</p> Mon, 24 Apr 2017 09:17:00 GMT https://www.uppmax.uu.se/changelog 2017-04-24T09:17:00Z [bio] seqmonk/1.37.1 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/">SeqMonk</a> 1.37.1 is now installed as module seqmonk/1.37.1 on all systems.</p> Fri, 21 Apr 2017 18:14:00 GMT https://www.uppmax.uu.se/changelog 2017-04-21T18:14:00Z [bio] maker/2.31.9 installed https://www.uppmax.uu.se/changelog <p><a href="http://www.yandell-lab.org/software/maker.html">MAKER</a> 2.31.9 has been installed on all systems as module maker/2.31.9. &nbsp;This module also uses updated versions of several&nbsp;external modules (RepeatMasker/4.0.7, augustus/3.2.3, snap/2013-11-29, blast/2.4.0+, openmpi/2.1.0 [if used])&nbsp;and adds GeneMark/4.32-es as a <em>de novo</em> gene finder.</p> Thu, 20 Apr 2017 08:41:00 GMT https://www.uppmax.uu.se/changelog 2017-04-20T08:41:00Z [bio] SignalP/4.1c installed on rackham, irma, bianca https://www.uppmax.uu.se/changelog <p><a href="http://www.cbs.dtu.dk/services/SignalP/">SignalP</a> 4.1c has been installed on rackham, irma and bianca. &nbsp;This version was previously available on milou, and given the version number 4.1. &nbsp;On all systems, this module can be loaded with SignalP/4.1c.</p> Thu, 20 Apr 2017 08:38:00 GMT https://www.uppmax.uu.se/changelog 2017-04-20T08:38:00Z [bio] tRNAscan-SE/1.3.1 installed on rackham, irma and bianca https://www.uppmax.uu.se/changelog <p><a href="http://eddylab.org/software.html">tRNAscan-SE</a> 1.3.1 has been installed on rackham, irma and bianca as module tRNAscan-SE/1.3.1.</p> Wed, 19 Apr 2017 12:40:00 GMT https://www.uppmax.uu.se/changelog 2017-04-19T12:40:00Z [comp] binutils/2.28 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://www.gnu.org/software/binutils/">GNU binutils</a>&nbsp;2.28 is now installed as module binutils/2.28 on all systems.</p> Wed, 19 Apr 2017 09:14:00 GMT https://www.uppmax.uu.se/changelog 2017-04-19T09:14:00Z [bio] augustus/3.2.3 installed on all systems https://www.uppmax.uu.se/changelog <p>The <a href="http://bioinf.uni-greifswald.de/augustus/">augustus</a> gene discovery tool version 3.2.3 is now installed on milou, rackham, irma and bianca. &nbsp;This is an update for milou and a new installation for the other systems.</p> Tue, 18 Apr 2017 14:03:00 GMT https://www.uppmax.uu.se/changelog 2017-04-18T14:03:00Z [bio] bamtools/2.3.0 installed on rackham, irma, bianca https://www.uppmax.uu.se/changelog <p>bamtools/2.3.0, already available on milou, has now been installed on rackham, irma and bianca.</p> Tue, 18 Apr 2017 14:02:00 GMT https://www.uppmax.uu.se/changelog 2017-04-18T14:02:00Z [bio] snap/2013-11-29 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://korflab.ucdavis.edu/software.html">SNAP</a> (gene prediction tool) version 2013-11-29 is now installed as module snap/2013-11-29 on all systems.</p> Thu, 13 Apr 2017 15:58:00 GMT https://www.uppmax.uu.se/changelog 2017-04-13T15:58:00Z [bio] usearch/9.2.64 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="http://www.drive5.com/usearch/">USEARCH</a> 9.2.64 (32-bit version) has been installed on all systems as module usearch/9.2.64. &nbsp;All previously installed versions are also now available on all systems.</p> Thu, 13 Apr 2017 15:18:00 GMT https://www.uppmax.uu.se/changelog 2017-04-13T15:18:00Z [bio] delly/0.7.6 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/dellytools/delly">Delly</a> (structural variant discovery) 0.7.6 is installed on all systems as delly/0.7.6. &nbsp;The additional tools delly-suave and delly-maze have not been installed.</p> Thu, 06 Apr 2017 23:21:00 GMT https://www.uppmax.uu.se/changelog 2017-04-06T23:21:00Z [bio] MUMmer 3.23 and 3.9.4alpha installed on rackham, irma, bianca https://www.uppmax.uu.se/changelog <p>The MUMmer/3.23 and MUMmer/3.9.4alpha modules have been installed on rackham, irma and bianca.</p> Thu, 06 Apr 2017 23:04:00 GMT https://www.uppmax.uu.se/changelog 2017-04-06T23:04:00Z [bio] blast/2.2.26 and blast/2.2.31+ installed on rackham, bianca, irma https://www.uppmax.uu.se/changelog <p>The legacy Blast version 2.2.26 is now available on rackham, bianca and irma as module blast/2.2.26, and the Blast+ version 2.2.31+ is now available on rackham as module blast/2.2.31+.</p> Thu, 06 Apr 2017 21:02:00 GMT https://www.uppmax.uu.se/changelog 2017-04-06T21:02:00Z [bio] last/847 installed on all systems https://www.uppmax.uu.se/changelog <p>The <a href="http://last.cbrc.jp/">last</a>&nbsp;pairwise sequence aligner version 847 is now installed as module last/847 on all systems.</p> Thu, 06 Apr 2017 21:00:00 GMT https://www.uppmax.uu.se/changelog 2017-04-06T21:00:00Z [bio] vcflib/2017-04-04 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/vcflib/vcflib">vcflib</a> (VCF file filtering) is now updated on milou and installed on all other systems as vcflib/2017-04-04.</p> Thu, 06 Apr 2017 12:18:00 GMT https://www.uppmax.uu.se/changelog 2017-04-06T12:18:00Z [apps] gawk/4.1.4 installed https://www.uppmax.uu.se/changelog <p><a href="https://www.gnu.org/software/gawk/">Gnu awk</a> 4.1.4 is now installed as module gawk/4.1.4 on all systems.</p> Tue, 04 Apr 2017 12:20:00 GMT https://www.uppmax.uu.se/changelog 2017-04-04T12:20:00Z [bio] ExAC 0.3.1 and CDD 3.16 installed https://www.uppmax.uu.se/changelog <p>Two&nbsp;<a href="http://www.uppmax.uu.se/resources/databases/other-uppnex-oriented-local-data-resources/">UPPMAX-local database copies</a>&nbsp;have been updated: ExAC to version 0.3.1 and CDD to version 3.16.&nbsp;</p> Mon, 03 Apr 2017 00:05:00 GMT https://www.uppmax.uu.se/changelog 2017-04-03T00:05:00Z [bio] Pfam 31.0 and pfam_scan/1.6 installed https://www.uppmax.uu.se/changelog <p>The <a href="http://pfam.xfam.org/">Pfam</a> protein family database version 31.0 is now <a href="http://www.uppmax.uu.se/resources/databases/other-uppnex-oriented-local-data-resources/">installed locally</a> on Uppmax. &nbsp;The <a href="https://xfam.wordpress.com/2017/03/08/pfam-31-0-is-released">pfam_scan</a> module is updated to pfam_scan/1.6 to handle new formats in the new Pfam release.</p> Mon, 03 Apr 2017 00:00:00 GMT https://www.uppmax.uu.se/changelog 2017-04-03T00:00:00Z [bio] vep/87 and local caches installed https://www.uppmax.uu.se/changelog <p><a href="http://www.ensembl.org/info/docs/tools/vep/index.html">Variant Effects Predictor</a> version 87 is now installed as module vep/87 on all systems. &nbsp;Locally-cached databases and plugins are also available. &nbsp;Note that this version still uses the script from the Ensembl package&nbsp;(varient_effects_predictor.pl) rather than the new script from the now-separate, beta version&nbsp;(vep).</p> Sun, 02 Apr 2017 11:43:00 GMT https://www.uppmax.uu.se/changelog 2017-04-02T11:43:00Z [bio] IGV/3.0-beta installed https://www.uppmax.uu.se/changelog <p><a href="http://software.broadinstitute.org/software/igv/igv3.0">IGV 3.0-beta</a> (Integrated Genome Viewer with support for long reads) is now installed as module IGV/3.0-beta on all systems.</p> Sat, 01 Apr 2017 14:04:00 GMT https://www.uppmax.uu.se/changelog 2017-04-01T14:04:00Z [bio] IGV/2.3.92 and IGVtools/2.3.91 installed https://www.uppmax.uu.se/changelog <p><a href="http://software.broadinstitute.org/software/igv/">IGV</a> (Integrated Genome Viewer) 2.3.92 and IGVtools 2.3.91 are now installed as modules IGV/2.3.92 and IGVtools/2.3.91, respectively, on all systems.</p> Sat, 01 Apr 2017 14:02:00 GMT https://www.uppmax.uu.se/changelog 2017-04-01T14:02:00Z [apps] R/3.3.2 available on irma and bianca https://www.uppmax.uu.se/changelog <p>The R/3.3.2 module is now available on irma and bianca.</p> Tue, 28 Mar 2017 10:05:00 GMT https://www.uppmax.uu.se/changelog 2017-03-28T10:05:00Z [bio] jellyfish/2.2.6 installed on all systems https://www.uppmax.uu.se/changelog <p><a href="https://github.com/gmarcais/Jellyfish">Jellyfish</a> (flexible kmer counter) 2.2.6 is now installed as module jellyfish/2.2.6 on milou, rackham, irma and bianca.</p> Tue, 28 Mar 2017 10:03:00 GMT https://www.uppmax.uu.se/changelog 2017-03-28T10:03:00Z [apps] R_packages/3.3.2 now uses R_LIBS_SITE https://www.uppmax.uu.se/changelog <p>The R_packages/3.3.2 module now prepends a new path to R_LIBS_SITE, rather than appends a new path to R_LIBS_USER. &nbsp;BioConductor is now able to install additional packages not included in R_packages/3.3.2 into users' personal library directories.</p> Sun, 26 Mar 2017 11:41:00 GMT https://www.uppmax.uu.se/changelog 2017-03-26T11:41:00Z [apps] vim/8.0-16 installed on rackham https://www.uppmax.uu.se/changelog <p>The vim/8.0-16 module is now installed on rackham.</p> Thu, 23 Mar 2017 17:11:00 GMT https://www.uppmax.uu.se/changelog 2017-03-23T17:11:00Z [apps] haskell-stack/1.4.0 installed https://www.uppmax.uu.se/changelog <p><a href="https://docs.haskellstack.org/en/stable/README/">Haskell Tool Stack</a> 1.4.0 is installed as module haskell-stack/1.4.0 on milou and rackham.</p> Thu, 23 Mar 2017 16:40:00 GMT https://www.uppmax.uu.se/changelog 2017-03-23T16:40:00Z [apps] texlive/2016 installed https://www.uppmax.uu.se/changelog <p><a href="https://www.tug.org/texlive/">Texlive</a>&nbsp;2016 is now installed as module texlive/2016 on milou and rackham.</p> Thu, 23 Mar 2017 16:29:00 GMT https://www.uppmax.uu.se/changelog 2017-03-23T16:29:00Z [bio] Subread 1.5.2 https://www.uppmax.uu.se/changelog <p>tool kit for processing next-gen sequencing data</p> Wed, 22 Mar 2017 13:25:00 GMT https://www.uppmax.uu.se/changelog 2017-03-22T13:25:00Z [bio] GCTA 1.26.0 https://www.uppmax.uu.se/changelog <p>Genome-wide Complex Trait Analysis</p> Thu, 16 Mar 2017 12:37:00 GMT https://www.uppmax.uu.se/changelog 2017-03-16T12:37:00Z [bio] deepTools 2.4.3 https://www.uppmax.uu.se/changelog <p>tools for exploring deep sequencing data</p> Tue, 21 Mar 2017 07:54:00 GMT https://www.uppmax.uu.se/changelog 2017-03-21T07:54:00Z [bio] ucsc-utilities/v345 installed https://www.uppmax.uu.se/changelog <p>The <a href="http://hgdownload.soe.ucsc.edu/admin/exe/">UCSC 'Kent' utilities</a> version 345 are now installed as module ucsc-utilities/v345 on milou.</p> Tue, 21 Mar 2017 13:27:00 GMT https://www.uppmax.uu.se/changelog 2017-03-21T13:27:00Z [bio] exonerate/2.2.0 and ucsc-utilities/v287 modules installed on rackham https://www.uppmax.uu.se/changelog <p>The exonerate/2.2.0 and ucsc-utilities/v287 modules are now available on rackham.</p> Tue, 21 Mar 2017 13:25:00 GMT https://www.uppmax.uu.se/changelog 2017-03-21T13:25:00Z [bio] Redundans/0.13a-20170321 installed https://www.uppmax.uu.se/changelog <p><a href="https://github.com/Gabaldonlab/redundans">Redundans</a> (pipeline that assists assembly of heterozygous/polymorphic genomes)&nbsp;0.13a-20170321 (version 9.13a with commits up to today) is now installed on milou and rackham.</p> Tue, 21 Mar 2017 10:05:00 GMT https://www.uppmax.uu.se/changelog 2017-03-21T10:05:00Z [bio] RepeatModeler/1.0.8_RM4.0.7 installed https://www.uppmax.uu.se/changelog <p><a href="http://www.repeatmasker.org/RepeatModeler.html">RepeatModeler</a> 1.0.8_RM4.0.7 is now installed on milou and rackham. &nbsp;This is the existing RepeatModeler 1.0.8, configured to use the newer RepeatMasker/4.0.7 and updated versions of the auxiliary tools.</p> Mon, 20 Mar 2017 17:24:00 GMT https://www.uppmax.uu.se/changelog 2017-03-20T17:24:00Z [bio] hmmer/3.1b2 installed on rackham https://www.uppmax.uu.se/changelog <p>hmmer 3.1b2 is now also available on rackham.</p> Mon, 20 Mar 2017 16:17:00 GMT https://www.uppmax.uu.se/changelog 2017-03-20T16:17:00Z [bio] RepeatMasker/4.0.7 installed https://www.uppmax.uu.se/changelog <p><a href="http://www.repeatmasker.org/">RepeatMasker</a> 4.0.7 is now installed on Milou and Rackham. &nbsp;This module version also contains updated rmblastn and trf tools and provides nhmmer and cross_match as additional search tools.</p> Mon, 20 Mar 2017 16:15:00 GMT https://www.uppmax.uu.se/changelog 2017-03-20T16:15:00Z [bio] StringTie/1.3.3 installed https://www.uppmax.uu.se/changelog <p>StringTie 1.3.3 is now installed on milou, rackham, irma and bianca and will be available as the module system refreshes.</p> Mon, 20 Mar 2017 15:30:00 GMT https://www.uppmax.uu.se/changelog 2017-03-20T15:30:00Z [libs] blas/3.6.0 installed on rackham https://www.uppmax.uu.se/changelog <p>blas/3.6.0, which includes BLAS and CBLAS, is now also installed on rackham.</p> Mon, 20 Mar 2017 13:42:00 GMT https://www.uppmax.uu.se/changelog 2017-03-20T13:42:00Z [bio] STAR 2.5.2b https://www.uppmax.uu.se/changelog <p>RNA-seq aligner</p> Thu, 16 Mar 2017 13:11:00 GMT https://www.uppmax.uu.se/changelog 2017-03-16T13:11:00Z [bio] barrnap 0.8 https://www.uppmax.uu.se/changelog <p>[bio] barrnap 0.8</p> Mon, 06 Mar 2017 12:56:00 GMT https://www.uppmax.uu.se/changelog 2017-03-06T12:56:00Z [bio] Trimmomatic 0.36 https://www.uppmax.uu.se/changelog <p>trim&nbsp;Illumina NGS data</p> Mon, 20 Mar 2017 10:03:00 GMT https://www.uppmax.uu.se/changelog 2017-03-20T10:03:00Z [libs] hdf5/1.8.18 and hdf5/1.8.18_gcc6.3.0 installed https://www.uppmax.uu.se/changelog <p><a href="https://support.hdfgroup.org/HDF5/">HDF5</a> (high-performance data file format) 1.8.18 is now installed on milou and rackham. &nbsp;SZIP is supported via the szip/2.1.1 module and GZIP is supported via the gzip/1.2.11 module.&nbsp;On both clusters there are two module versions available. &nbsp;<strong>hdf5/1.8.18</strong> is compiled with the system GCC compiler, and <strong>hdf5/1.8.18_gcc6.3.0</strong> is compiled with the gcc/6.3.0 module.</p> Thu, 16 Mar 2017 14:07:00 GMT https://www.uppmax.uu.se/changelog 2017-03-16T14:07:00Z [libs] freetype/2.7.1 installed https://www.uppmax.uu.se/changelog <p><a href="https://www.freetype.org/">freetype</a> (open-source type rendering library) 2.7.1 is now installed on milou and rackham.</p> Thu, 16 Mar 2017 11:07:00 GMT https://www.uppmax.uu.se/changelog 2017-03-16T11:07:00Z [libs] szip/2.1.1 installed https://www.uppmax.uu.se/changelog <p><a href="https://support.hdfgroup.org/doc_resource/SZIP/">szip</a> (high-performance compression library) 2.1.1 is now installed on milou and rackham.</p> Thu, 16 Mar 2017 10:35:00 GMT https://www.uppmax.uu.se/changelog 2017-03-16T10:35:00Z [libs] zlib/1.2.11 installed https://www.uppmax.uu.se/changelog <p><a href="http://www.zlib.net/">zlib</a> (general compression library) 1.2.11 is installed on milou and rackham. &nbsp;zlib/1.2.8 remains the default module version on milou.</p> Thu, 16 Mar 2017 09:53:00 GMT https://www.uppmax.uu.se/changelog 2017-03-16T09:53:00Z [bio] Ragout/2.0-20170312 installed https://www.uppmax.uu.se/changelog <p><a href="https://github.com/fenderglass/Ragout">Ragout</a> (chromosome assembly using multiple references)&nbsp;2.0-20170312 is now installed as module Ragout/2.0-20170312 on milou and rackham.</p> Mon, 13 Mar 2017 01:32:00 GMT https://www.uppmax.uu.se/changelog 2017-03-13T01:32:00Z [bio] SiBELia/3.0.6 installed https://www.uppmax.uu.se/changelog <p><a href="http://bioinf.spbau.ru/sibelia">SiBELia</a> (synteny exploration tool) 3.0.6 is now installed as module SiBELia/3.0.6 on milou and rackham.</p> Sun, 12 Mar 2017 19:45:00 GMT https://www.uppmax.uu.se/changelog 2017-03-12T19:45:00Z [bio] AdmixTools/5.0-20170312 installed https://www.uppmax.uu.se/changelog <p><a href="https://github.com/DReichLab/AdmixTools">AdmixTools</a> tools (admixture in human populations) version 5.0-20170312 is now installed on milou as module AdmisTools/5.0-20170312.</p> Sun, 12 Mar 2017 18:24:00 GMT https://www.uppmax.uu.se/changelog 2017-03-12T18:24:00Z [bio] iqtree/1.5.3-omp installed https://www.uppmax.uu.se/changelog <p><a href="http://www.iqtree.org/">IQ-TREE</a> 1.5.3 (phylogenomic software by maximum likelihood) is installed as module&nbsp;iqtree/1.5.3-omp as part of the phylogeny subgroup of bioinfo-tools on milou and rackham. &nbsp;The multicore&nbsp;executable is available as <strong>iqtree-omp</strong> and the single core executable as <strong>iqtree</strong>.</p> Sun, 12 Mar 2017 13:47:00 GMT https://www.uppmax.uu.se/changelog 2017-03-12T13:47:00Z [bio] Meerkat/0.189 installed https://www.uppmax.uu.se/changelog <p><a href="http://compbio.med.harvard.edu/Meerkat/">Meerkat</a> 0.189 (detection of somatic structural variants) has been installed as module Meerkat/0.189 on milou.</p> Wed, 22 Feb 2017 21:16:00 GMT https://www.uppmax.uu.se/changelog 2017-02-22T21:16:00Z [bio] Primer3/2.3.7 installed https://www.uppmax.uu.se/changelog <p><a href="http://primer3.sourceforge.net/">Primer3</a> 2.3.7 (package for designing PCR primers) is now installed as module Primer3/2.3.7 on milou.</p> Wed, 22 Feb 2017 21:04:00 GMT https://www.uppmax.uu.se/changelog 2017-02-22T21:04:00Z [bio] BEDTools 2.26.0 https://www.uppmax.uu.se/changelog <p>utilities&nbsp;for a range of genomics analysis tasks</p> Wed, 08 Feb 2017 18:23:00 GMT https://www.uppmax.uu.se/changelog 2017-02-08T18:23:00Z [bio] khmer 2.0 https://www.uppmax.uu.se/changelog <p>In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more</p> Wed, 08 Feb 2017 18:17:00 GMT https://www.uppmax.uu.se/changelog 2017-02-08T18:17:00Z [bio] bwa 0.7.15 https://www.uppmax.uu.se/changelog <p>Burrow-Wheeler Aligner for pairwise alignment between DNA sequences</p> Tue, 21 Feb 2017 18:07:00 GMT https://www.uppmax.uu.se/changelog 2017-02-21T18:07:00Z [bio] 10X Supernova 1.1.4 https://www.uppmax.uu.se/changelog <p>de novo assembly from Chromium Linked-Reads</p> Fri, 17 Feb 2017 18:04:00 GMT https://www.uppmax.uu.se/changelog 2017-02-17T18:04:00Z [bio] 10X Cellranger 1.3.0 https://www.uppmax.uu.se/changelog <p>set of analysis pipelines to&nbsp;process&nbsp;Chromium single cell 3’ RNA-seq output</p> Fri, 17 Feb 2017 17:59:00 GMT https://www.uppmax.uu.se/changelog 2017-02-17T17:59:00Z [lib] boost 1.63.0 https://www.uppmax.uu.se/changelog <p>widely-used C++ library</p> Wed, 15 Feb 2017 16:40:00 GMT https://www.uppmax.uu.se/changelog 2017-02-15T16:40:00Z [parallel] gnuparallel 20170122 https://www.uppmax.uu.se/changelog <p>scripts for running parallel jobs</p> Mon, 13 Feb 2017 16:34:00 GMT https://www.uppmax.uu.se/changelog 2017-02-13T16:34:00Z OpenFOAM v1612+ now installed on Rackham https://www.uppmax.uu.se/changelog <p>OpenFOAM v1612+ is now available on Rackham as a module. Please run "module load openfoam/v1612+" to load OpenFOAM v1612+.</p> Tue, 21 Feb 2017 14:51:00 GMT https://www.uppmax.uu.se/changelog 2017-02-21T14:51:00Z [bio] eigensoft/6.1.4 installed https://www.uppmax.uu.se/changelog <p><a href="https://www.hsph.harvard.edu/alkes-price/software/">Eigensoft</a> 6.1.4 is now installed on milou and tintin. &nbsp;As with 6.0.1, this version has support for longer IDs.</p> Wed, 08 Feb 2017 12:13:00 GMT https://www.uppmax.uu.se/changelog 2017-02-08T12:13:00Z [bio] A5-miseq/20160825 installed https://www.uppmax.uu.se/changelog <p><a href="https://sourceforge.net/projects/ngopt/">A5-miseq</a> version 20160825 is now installed on milou and tintin.</p> Fri, 27 Jan 2017 18:30:00 GMT https://www.uppmax.uu.se/changelog 2017-01-27T18:30:00Z [apps] sqlite/3.11.1 and sqlite/3.16.2 installed https://www.uppmax.uu.se/changelog <p><a href="https://sqlite.org/">SQLite</a> versions 3.11.1 and 3.16.2 are now installed on milou and tintin. &nbsp;These provide both an <strong>sqlite3</strong> executable as well as libraries and include files for development.</p> Fri, 20 Jan 2017 14:08:00 GMT https://www.uppmax.uu.se/changelog 2017-01-20T14:08:00Z [bio] OrthoMCL/2.0.9 now installed https://www.uppmax.uu.se/changelog <p><a href="https://github.com/douglasgscofield/OrthoMCL">OrthoMCL</a> 2.0.9 is now available on milou. &nbsp;This uses SQLite by default, rather than MySQL or Oracle, which should work much better at UPPMAX.</p> Fri, 20 Jan 2017 13:42:00 GMT https://www.uppmax.uu.se/changelog 2017-01-20T13:42:00Z [comp] Apache Ant 1.9.8 and 1.10.0 https://www.uppmax.uu.se/changelog <p>build tool</p> Fri, 20 Jan 2017 10:01:00 GMT https://www.uppmax.uu.se/changelog 2017-01-20T10:01:00Z [bio] RTG Tools (new) https://www.uppmax.uu.se/changelog <p>utilities to&nbsp;manipulate/compare&nbsp;VCF files and other NGS formats</p> Thu, 19 Jan 2017 09:03:00 GMT https://www.uppmax.uu.se/changelog 2017-01-19T09:03:00Z [bio] manta 1.0.3 https://www.uppmax.uu.se/changelog <p>structural variant and indel caller for mapped sequencing data</p> Fri, 20 Jan 2017 08:59:00 GMT https://www.uppmax.uu.se/changelog 2017-01-20T08:59:00Z [bio] Mothur 1.38.1 https://www.uppmax.uu.se/changelog <p>software collection for gene sequence analysis</p> Fri, 20 Jan 2017 08:51:00 GMT https://www.uppmax.uu.se/changelog 2017-01-20T08:51:00Z [bio] RNAfold/2.3.1 (alias ViennaRNA/2.3.1) installed https://www.uppmax.uu.se/changelog <p>RNAfold (aka ViennaRNA) 2.3.1 is now installed on milou and tintin. &nbsp;This is an update for both systems.</p> Wed, 21 Dec 2016 17:06:00 GMT https://www.uppmax.uu.se/changelog 2016-12-21T17:06:00Z [bio] InterProScan/5.20-59.0 disabled https://www.uppmax.uu.se/changelog <p>This version of InterProScan&nbsp;requires glibc 2.14. Milou and Tintin only have 2.12 and cannot be upgraded in any reasonable way. Older versions of&nbsp;InterProScan are still installed and appear to function normall.&nbsp;Newer clusters, such as the upcoming Rackham, will have a newer glibc so should be able to run this and perhaps some later versions of&nbsp;InterProScan.</p> Tue, 20 Dec 2016 08:41:00 GMT https://www.uppmax.uu.se/changelog 2016-12-20T08:41:00Z [bio] GATK/3.7 installed https://www.uppmax.uu.se/changelog Mon, 19 Dec 2016 13:12:00 GMT https://www.uppmax.uu.se/changelog 2016-12-19T13:12:00Z [bio] GATK-Queue/3.7 installed https://www.uppmax.uu.se/changelog Mon, 19 Dec 2016 13:11:00 GMT https://www.uppmax.uu.se/changelog 2016-12-19T13:11:00Z [bio] plink repository for custom compilation on milou https://www.uppmax.uu.se/changelog <p><a href="https://www.cog-genomics.org/plink2">PLINK version 1.90</a>&nbsp;is available as module plink/1.90 and is installed from the prebuilt binaries. &nbsp;For custom compilations, a fork of its source repository has been created to ease compiling on milou at <a href="https://github.com/douglasgscofield/plink-ng">https://github.com/douglasgscofield/plink-ng</a>.</p> Sat, 17 Dec 2016 10:13:00 GMT https://www.uppmax.uu.se/changelog 2016-12-17T10:13:00Z [libs] ATLAS/3.10.3 installed https://www.uppmax.uu.se/changelog <p><a href="http://math-atlas.sourceforge.net/">ATLAS</a> (Automatically Tuned Linear Algebra Software) 3.10.3 is now installed as module ATLAS/3.10.3 on milou and tintin.</p> Sat, 17 Dec 2016 10:05:00 GMT https://www.uppmax.uu.se/changelog 2016-12-17T10:05:00Z [libs] blas/3.6.0 installed https://www.uppmax.uu.se/changelog <p>The <a href="http://www.netlib.org/blas/">BLAS</a> library (Basic Linear Algebra Subroutines) 3.6.0 together with CBLAS (C-language interface to BLAS) is now installed as module blas/3.6.0 on milou and tintin. &nbsp;The openblas and ATLAS modules provide tuned versions of BLAS/CBLAS.</p> Sat, 17 Dec 2016 10:00:00 GMT https://www.uppmax.uu.se/changelog 2016-12-17T10:00:00Z [bio] Trinity 2.3.2 https://www.uppmax.uu.se/changelog <p>assembles transcript sequences from Illumina RNA-Seq data</p> Fri, 16 Dec 2016 06:50:00 GMT https://www.uppmax.uu.se/changelog 2016-12-16T06:50:00Z [bio] Transrate 1.0.3 https://www.uppmax.uu.se/changelog <p>de-novo&nbsp;transcriptome assembly quality analysis</p> Tue, 13 Dec 2016 07:30:00 GMT https://www.uppmax.uu.se/changelog 2016-12-13T07:30:00Z [bio] default blast https://www.uppmax.uu.se/changelog <p>Default version of blast changed from latest "legacy blast" to latest version overall, i.e.,&nbsp;"blast+".</p> Tue, 13 Dec 2016 07:24:00 GMT https://www.uppmax.uu.se/changelog 2016-12-13T07:24:00Z [bio] GATK-Queue/3.6 installed https://www.uppmax.uu.se/changelog <p><a href="http://gatkforums.broadinstitute.org/gatk/discussion/1306/overview-of-queue">GATK-Queue</a> 3.6 (GATK + Queue parallelism) is now installed on all systems. &nbsp;This is an update for milou and a new module for tintin et al.</p> Fri, 09 Dec 2016 13:01:00 GMT https://www.uppmax.uu.se/changelog 2016-12-09T13:01:00Z [bio] EnsEMBL-API/87 installed https://www.uppmax.uu.se/changelog <p>The <a href="http://www.ensembl.org/info/docs/api/index.html">EnsEMBL Perl API</a> for EnsEMBL release 87 has been installed as&nbsp;EnsEMBL-API/87.</p> Thu, 08 Dec 2016 14:23:00 GMT https://www.uppmax.uu.se/changelog 2016-12-08T14:23:00Z [bio] Satsuma2 https://www.uppmax.uu.se/changelog <p>FFT cross-correlation based synteny aligner</p> Wed, 07 Dec 2016 14:50:00 GMT https://www.uppmax.uu.se/changelog 2016-12-07T14:50:00Z [bio] SeqMonk 1.36.0 https://www.uppmax.uu.se/changelog <p>visualise and analyse high throughput mapped sequence data</p> Tue, 06 Dec 2016 12:31:00 GMT https://www.uppmax.uu.se/changelog 2016-12-06T12:31:00Z [bio] 10X Supernova 1.1.1 https://www.uppmax.uu.se/changelog <p>de novo assembly from Chromium Linked-Reads</p> Sat, 24 Sep 2016 07:44:00 GMT https://www.uppmax.uu.se/changelog 2016-09-24T07:44:00Z [bio] 10X Supernova 1.0.0 https://www.uppmax.uu.se/changelog <p><em>de novo</em>&nbsp;assembly from Chromium Linked-Reads</p> Tue, 05 Jul 2016 07:41:00 GMT https://www.uppmax.uu.se/changelog 2016-07-05T07:41:00Z [bio] 10X Cellranger 1.1.0 https://www.uppmax.uu.se/changelog <p>set of analysis pipelines to&nbsp;process&nbsp;Chromium single cell 3’ RNA-seq output</p> Tue, 05 Jul 2016 06:57:00 GMT https://www.uppmax.uu.se/changelog 2016-07-05T06:57:00Z [bio] 10X Longranger 2.0.1 https://www.uppmax.uu.se/changelog <p>set of analysis pipelines to process Chromium sequencing output</p> Tue, 05 Jul 2016 06:46:00 GMT https://www.uppmax.uu.se/changelog 2016-07-05T06:46:00Z [bio] 10X Longranger 2.1.1 https://www.uppmax.uu.se/changelog <p>set of analysis pipelines to process Chromium sequencing output</p> Sat, 24 Sep 2016 06:44:00 GMT https://www.uppmax.uu.se/changelog 2016-09-24T06:44:00Z [bio] 10X Longranger 2.1.2 https://www.uppmax.uu.se/changelog <p>set of analysis pipelines to process&nbsp;Chromium sequencing output</p> Tue, 06 Dec 2016 07:32:00 GMT https://www.uppmax.uu.se/changelog 2016-12-06T07:32:00Z [bio] Prodigal 2.6.3 https://www.uppmax.uu.se/changelog <p>protein-coding gene prediction for prokaryotic genomes</p> Wed, 12 Oct 2016 08:48:00 GMT https://www.uppmax.uu.se/changelog 2016-10-12T08:48:00Z [bio] InterProScan 5.20-59.0 https://www.uppmax.uu.se/changelog <p>scan the InterPro&nbsp;database of&nbsp;protein&nbsp;function&nbsp;prediction</p> Tue, 25 Oct 2016 08:41:00 GMT https://www.uppmax.uu.se/changelog 2016-10-25T08:41:00Z [bio] FastQ Screen 0.9.2 https://www.uppmax.uu.se/changelog <p>screen&nbsp;sequences&nbsp;against a database</p> <p></p> Thu, 27 Oct 2016 08:32:00 GMT https://www.uppmax.uu.se/changelog 2016-10-27T08:32:00Z [bio] blast/2.5.0+ installed https://www.uppmax.uu.se/changelog <p><a href="https://blast.ncbi.nlm.nih.gov/Blast.cgi">Blast</a> 2.5.0+ has been installed on all systems.</p> Sun, 04 Dec 2016 09:57:00 GMT https://www.uppmax.uu.se/changelog 2016-12-04T09:57:00Z [bio] PileOMeth 0.1.13 https://www.uppmax.uu.se/changelog <p>methylation extractor for BS-seq experiments</p> Mon, 21 Nov 2016 18:11:00 GMT https://www.uppmax.uu.se/changelog 2016-11-21T18:11:00Z [bio] bwa-meth 0.2.0 https://www.uppmax.uu.se/changelog <p>BS-Seq&nbsp;alignment</p> Mon, 21 Nov 2016 18:07:00 GMT https://www.uppmax.uu.se/changelog 2016-11-21T18:07:00Z [bio] piper 1.5.0 (milou) https://www.uppmax.uu.se/changelog <p>NGI pipeline</p> Tue, 22 Nov 2016 18:02:00 GMT https://www.uppmax.uu.se/changelog 2016-11-22T18:02:00Z [bio] piper 1.5.0 (fix) https://www.uppmax.uu.se/changelog <p>NGI pipeline</p> Sat, 24 Sep 2016 16:59:00 GMT https://www.uppmax.uu.se/changelog 2016-09-24T16:59:00Z [bio] piper 1.5.0 https://www.uppmax.uu.se/changelog <p>NGI pipeline</p> Tue, 06 Sep 2016 16:49:00 GMT https://www.uppmax.uu.se/changelog 2016-09-06T16:49:00Z [bio] PLINK/SEQ 0.10 https://www.uppmax.uu.se/changelog <p>C/C++ library for working with human genetic variation data</p> Fri, 02 Dec 2016 17:36:00 GMT https://www.uppmax.uu.se/changelog 2016-12-02T17:36:00Z [bio] SRA Tools 2.8.0 https://www.uppmax.uu.se/changelog <p>Collection of tools and libraries for using data in the INSDC Sequence Read Archives</p> Fri, 02 Dec 2016 17:11:00 GMT https://www.uppmax.uu.se/changelog 2016-12-02T17:11:00Z [comp] python/2.7.11 installed https://www.uppmax.uu.se/changelog <p>Python 2.7.11 is now installed on milou and tintin.</p> Fri, 02 Dec 2016 17:40:00 GMT https://www.uppmax.uu.se/changelog 2016-12-02T17:40:00Z [bio] vsearch/2.3.2 installed https://www.uppmax.uu.se/changelog <p><a href="https://github.com/torognes/vsearch">Vsearch</a> 2.3.2 (open source tool comparable to usearch) is now installed as vsearch/2.3.2 on milou and tintin. &nbsp;This is a new module for both systems.</p> Thu, 01 Dec 2016 14:09:00 GMT https://www.uppmax.uu.se/changelog 2016-12-01T14:09:00Z [bio] progressiveCactus/2016-11-30 installed https://www.uppmax.uu.se/changelog <p><a href="https://github.com/glennhickey/progressiveCactus">progressiveCactus</a> as of 2016-11-30 is now installed on milou and tintin. &nbsp;This is an update for both systems. &nbsp;If it can be made to work successfully, an additional module version with SLURM support is forthcoming.</p> Thu, 01 Dec 2016 14:06:00 GMT https://www.uppmax.uu.se/changelog 2016-12-01T14:06:00Z [bio] hal/20161130 installed https://www.uppmax.uu.se/changelog <p>The <a href="https://github.com/ComparativeGenomicsToolkit/hal">hal</a> module (Hierarchical Alignment Format API) as of 20161130 has been installed as module hal/20161130 on milou and tintin. &nbsp;This is an update for both systems.</p> Thu, 01 Dec 2016 13:55:00 GMT https://www.uppmax.uu.se/changelog 2016-12-01T13:55:00Z [bio] phast/1.4 installed https://www.uppmax.uu.se/changelog <p><a href="http://compgen.cshl.edu/phast/">Phast</a> 1.4 (phylogenetic analysis with space/time modules) is now installed on milou and tintin. &nbsp;This is an update for milou and a new module for tintin.</p> Wed, 30 Nov 2016 16:26:00 GMT https://www.uppmax.uu.se/changelog 2016-11-30T16:26:00Z [bio] blasr/5.3 https://www.uppmax.uu.se/changelog <p>The <a href="https://github.com/PacificBiosciences/blasr">blasr</a> aligner (alignment of long, error-prone reads) version 5.3&nbsp;is now installed on milou as blasr/5.3. This is an update, created via the PacBio pitchfork build process. This installation represents blasr&nbsp;5.3.e901e48.</p> Sun, 20 Nov 2016 18:53:00 GMT https://www.uppmax.uu.se/changelog 2016-11-20T18:53:00Z [bio] FALCON-integrate/20161113 installed https://www.uppmax.uu.se/changelog <p><a href="https://github.com/PacificBiosciences/FALCON-integrate">FALCON-integrate</a><strong>&nbsp;as of the latest commit on 2016-11-13&nbsp;is now installed as FALCON/20161113&nbsp;on milou. This replaces the FALCON/20161112 module.</strong></p> Sun, 20 Nov 2016 18:28:00 GMT https://www.uppmax.uu.se/changelog 2016-11-20T18:28:00Z [bio] HISAT2/2.0.5 installed https://www.uppmax.uu.se/changelog <p><a href="https://ccb.jhu.edu/software/hisat2/index.shtml">HISAT2</a> 2.0.5 is now installed on milou and tintin. This is an update.</p> Sat, 12 Nov 2016 22:14:00 GMT https://www.uppmax.uu.se/changelog 2016-11-12T22:14:00Z [bio] diamond/0.8.26 installed https://www.uppmax.uu.se/changelog <p><a href="https://github.com/bbuchfink/diamond">DIAMOND 0.8.26</a> (fast protein database search) is now installed as diamond/0.8.26 on milou and tintin. &nbsp;See 'module help diamond' for more on availability of prebuilt databases.</p> Sat, 12 Nov 2016 21:09:00 GMT https://www.uppmax.uu.se/changelog 2016-11-12T21:09:00Z [comp] git/2.10.2 installed https://www.uppmax.uu.se/changelog <p><a href="https://github.com/git/git">Git</a> 2.10.2 is now available as module git/2.10.2 on milou and tintin. &nbsp;This is an update.</p> Sat, 12 Nov 2016 21:07:00 GMT https://www.uppmax.uu.se/changelog 2016-11-12T21:07:00Z [bio] FALCON-integrate/20161112 installed https://www.uppmax.uu.se/changelog <p><strong><em>This module is superseded by FALCON-integrate/20161113.</em></strong></p> <p><a href="https://github.com/PacificBiosciences/FALCON-integrate">FALCON-integrate</a> as of the latest commit on 2016-11-12 is now installed as FALCON/20161112 on milou. This is an updated version of the FALCON assembler for PacBio data.</p> Sat, 12 Nov 2016 21:00:00 GMT https://www.uppmax.uu.se/changelog 2016-11-12T21:00:00Z [bio] Krona/2.7 installed https://www.uppmax.uu.se/changelog <p><a href="https://github.com/marbl/Krona">Krona 2.7</a> (exploration of metagenomic datasets) is now installed as Krona/2.7 on milou and tintin.</p> Fri, 11 Nov 2016 19:30:00 GMT https://www.uppmax.uu.se/changelog 2016-11-11T19:30:00Z [bio] SortMeRNA/2.1b https://www.uppmax.uu.se/changelog <p><a href="http://bioinfo.lifl.fr/RNA/sortmerna/">SortMeRNA 2.1b</a> (NGS read filtering, alignment and OTU clustering) is now installed as module SortMeRNA/2.1b on milou and tintin. This is a new module for both systems.</p> Fri, 11 Nov 2016 17:56:00 GMT https://www.uppmax.uu.se/changelog 2016-11-11T17:56:00Z [comp] advisor, ampilifier, inspector and itac upgraded https://www.uppmax.uu.se/changelog <p>advisor, ampilifier, inspector and itac upgraded&nbsp;</p> Thu, 10 Nov 2016 09:12:00 GMT https://www.uppmax.uu.se/changelog 2016-11-10T09:12:00Z [comp] intel/17.1 installed https://www.uppmax.uu.se/changelog <p>intel/17.1 installed</p> Thu, 10 Nov 2016 09:11:00 GMT https://www.uppmax.uu.se/changelog 2016-11-10T09:11:00Z [parallel] intelmpi/17.1 installed https://www.uppmax.uu.se/changelog <p>intelmpi/17.1 has been installed on Milou and Tintin</p> Thu, 10 Nov 2016 09:07:00 GMT https://www.uppmax.uu.se/changelog 2016-11-10T09:07:00Z [apps] JAGS/4.2.0 installed https://www.uppmax.uu.se/changelog <p><a href="http://mcmc-jags.sourceforge.net/">JAGS 4.2.0</a> (Just Another Gibbs Sampler) is now installed as JAGS/4.2.0 on milou,&nbsp;tintin and irma. This is a new module for all systems.</p> Thu, 03 Nov 2016 22:07:00 GMT https://www.uppmax.uu.se/changelog 2016-11-03T22:07:00Z [bio] MACE/1.2 installed https://www.uppmax.uu.se/changelog <p><a href="http://chipexo.sourceforge.net/">MACE 1.2</a> (analyze ChIP-exo data) has been installed as MACE/1.2 on milou and tintin. &nbsp;This is a new module for all systems.</p> Sun, 30 Oct 2016 10:14:00 GMT https://www.uppmax.uu.se/changelog 2016-10-30T10:14:00Z [bio] GEM/2.7 installed https://www.uppmax.uu.se/changelog <p><a href="https://groups.csail.mit.edu/cgs/gem">GEM 2.7</a>&nbsp;(high-resolution peak calling and motif discovery for ChIP-seq and ChIP-exo data) has been installed as module GEM/2.7 on milou and tintin. &nbsp;This is a new module for both systems.</p> Sun, 30 Oct 2016 10:12:00 GMT https://www.uppmax.uu.se/changelog 2016-10-30T10:12:00Z [apps] R/3.3.1 and R_packages/3.3.1 installed https://www.uppmax.uu.se/changelog <p><a href="https://www.r-project.org/">R</a> 3.3.1 has been installed on milou and tintin, as has <a href="https://www.uppmax.uu.se/support-sv//r_packages-module-guide">R_packages</a> 3.3.1.</p> Sun, 23 Oct 2016 21:06:00 GMT https://www.uppmax.uu.se/changelog 2016-10-23T21:06:00Z jobstats script updated https://www.uppmax.uu.se/changelog <p>The <a href="https://www.uppmax.uu.se/support-sv//jobstats-user-guide">jobstats</a> tool has been updated to calculate maximum memory used as reported by SLURM when available&nbsp;and to include this information as an additional trace in plots (black dotted line).</p> Sun, 23 Oct 2016 12:26:00 GMT https://www.uppmax.uu.se/changelog 2016-10-23T12:26:00Z [bio] Scipio/1.4 installed https://www.uppmax.uu.se/changelog <p><a href="http://www.webscipio.org/">Scipio 1.4</a> (eukaryotic gene detection) is now installed&nbsp;on milou.</p> Tue, 11 Oct 2016 08:43:00 GMT https://www.uppmax.uu.se/changelog 2016-10-11T08:43:00Z [bio] Vmatch/2.2.5 installed https://www.uppmax.uu.se/changelog <p><a href="http://www.vmatch.de/">Vmatch 2.2.5</a> (sequence matching tool) has been installed on milou and tintin.</p> Sun, 09 Oct 2016 23:33:00 GMT https://www.uppmax.uu.se/changelog 2016-10-09T23:33:00Z [bio] clusterflow/0.4 installed https://www.uppmax.uu.se/changelog <p><a href="http://clusterflow.io/">Clusterflow 0.4 installed</a> on milou, irma and bianca. &nbsp;This is an update.</p> Fri, 07 Oct 2016 13:54:00 GMT https://www.uppmax.uu.se/changelog 2016-10-07T13:54:00Z [bio] nextflow/0.22.2 installed https://www.uppmax.uu.se/changelog <p><a href="https://www.nextflow.io/">Nextflow</a> 0.22.2 is now installed as module nextflow/0.22.2 on milou. &nbsp;Our local installation has been modified to require that the&nbsp;NXF_TEMP variable be set prior to running nextflow to indicate a directory into which&nbsp;temporary files should be written. A message is produced when loading the module as a reminder.</p> Thu, 06 Oct 2016 11:07:00 GMT https://www.uppmax.uu.se/changelog 2016-10-06T11:07:00Z pgi/16.9 installed https://www.uppmax.uu.se/changelog <p>The portland compiler has been upgraded to pgi/16.9 on Milou and Tintin.</p> Fri, 30 Sep 2016 07:25:00 GMT https://www.uppmax.uu.se/changelog 2016-09-30T07:25:00Z [bio] vt/0.5772 installed https://www.uppmax.uu.se/changelog <p><a href="http://genome.sph.umich.edu/wiki/Vt">vt 0.5772</a> (short variant discovery from NGS data) is now installed as vt/0.5772 on milou and tintin. &nbsp;This is a new module for both systems.</p> Thu, 29 Sep 2016 21:33:00 GMT https://www.uppmax.uu.se/changelog 2016-09-29T21:33:00Z [bio] GenomeSTRiP/2.00.1685 installed https://www.uppmax.uu.se/changelog <p><a href="http://software.broadinstitute.org/software/genomestrip/index.html">GenomeSTRiP&nbsp;2.00.1685</a> (structural variant pipeline) has been installed as module GenomeSTRiP/2.00.1685 on milou. This is an update.</p> Thu, 29 Sep 2016 20:54:00 GMT https://www.uppmax.uu.se/changelog 2016-09-29T20:54:00Z [apps] vim/8.0-16 https://www.uppmax.uu.se/changelog <p><a href="http://www.vim.org/">Vim 8.0</a> through patch 16 is now installed as module vim/8.0-16 on milou and tintin. This is an update for both systems.</p> Tue, 27 Sep 2016 09:31:00 GMT https://www.uppmax.uu.se/changelog 2016-09-27T09:31:00Z [parallel] openmpi/1.10.4 and openmpi/2.0.1 https://www.uppmax.uu.se/changelog <p>openmpi/1.10.4 and openmpi/2.0.1 has been installed for a number of different compilers on Irma, Milou and Tintin.</p> Mon, 26 Sep 2016 07:52:00 GMT https://www.uppmax.uu.se/changelog 2016-09-26T07:52:00Z [parallel] intelmpi/17.0 installed https://www.uppmax.uu.se/changelog <p>intelmpi/17.0 has been installed on Milou and Tintin.</p> Mon, 26 Sep 2016 07:50:00 GMT https://www.uppmax.uu.se/changelog 2016-09-26T07:50:00Z [comp] advisor, ampilifier, inspector and itac upgraded https://www.uppmax.uu.se/changelog <p>As parts of Intel Parallel Studio XE Cluster edition advisor/17.1.0 amplifier/17.0 inspector/17.1.0 and itac/17.0 has been installed on Tintin and Milou.</p> Mon, 26 Sep 2016 07:44:00 GMT https://www.uppmax.uu.se/changelog 2016-09-26T07:44:00Z [bio] gvcftools/0.17.0 installed https://www.uppmax.uu.se/changelog <p><a href="https://sites.google.com/site/gvcftools/home">gvcftools&nbsp;0.17.0</a> installed on milou and tintin. &nbsp;This is an upgrade for both systems.</p> Sun, 25 Sep 2016 16:52:00 GMT https://www.uppmax.uu.se/changelog 2016-09-25T16:52:00Z [comp] python/3.4.3 for tintin https://www.uppmax.uu.se/changelog <p>Python 3.4.3 is now available on tintin.</p> Fri, 23 Sep 2016 14:19:00 GMT https://www.uppmax.uu.se/changelog 2016-09-23T14:19:00Z [bio] biopython/1.68 and biopython/1.68-py3 https://www.uppmax.uu.se/changelog <p><a href="http://biopython.org/">BioPython&nbsp;1.68</a>&nbsp;has been installed on milou and tintin as modules biopython/1.68 (requiring python/2.7.6) and biopython/1.68-py3 (requiring python/3.4.3). &nbsp;This is an update for both systems.</p> Fri, 23 Sep 2016 14:13:00 GMT https://www.uppmax.uu.se/changelog 2016-09-23T14:13:00Z [bio] MetAMOS/1.5rc3 installed https://www.uppmax.uu.se/changelog <p><a href="http://metamos.readthedocs.io/en/v1.5rc3/index.html">MetAMOS 1.5rc3</a> has been installed with core prerequisites as module&nbsp;MetAMOS/1.5rc3 on milou. &nbsp;This is a new module. &nbsp;Additional functionality may be available by loading other modules available on milou; see 'module help MetAMOS' for more details.</p> Fri, 23 Sep 2016 06:57:00 GMT https://www.uppmax.uu.se/changelog 2016-09-23T06:57:00Z [bio] strelka/1.0.15 installed https://www.uppmax.uu.se/changelog <p><a href="https://sites.google.com/site/strelkasomaticvariantcaller/home">Strelka 1.0.15</a> (somatic variant detection via tumour-normal sequencing) is now installed as module strelka/1.0.15 on milou and tintin. &nbsp;This is a new module for both systems.</p> Wed, 21 Sep 2016 10:33:00 GMT https://www.uppmax.uu.se/changelog 2016-09-21T10:33:00Z [bio] Metaxa2/2.1.3 installed https://www.uppmax.uu.se/changelog <p><a href="http://microbiology.se/software/metaxa2/">Metaxa2 2.1.3</a> (classification of rRNA in metagenomic data) is now installed as module Metaxa2/2.1.3 as part of bioinfo-tools on milou and tintin. &nbsp;This is a new module for both systems.</p> Tue, 20 Sep 2016 21:23:00 GMT https://www.uppmax.uu.se/changelog 2016-09-20T21:23:00Z [bio] SHAPEIT/v2.r837 installed https://www.uppmax.uu.se/changelog <p><a href="https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html">SHAPEIT v2.r837</a> (haplotype phasing) is now installed as part of bioinfo-tools on milou and tintin. This is a new module for both systems.</p> Tue, 20 Sep 2016 20:50:00 GMT https://www.uppmax.uu.se/changelog 2016-09-20T20:50:00Z [bio] augustus/3.2.2 installed https://www.uppmax.uu.se/changelog <p><a href="http://bioinf.uni-greifswald.de/augustus/">augustus/3.2.2</a> for de novo gene prediction is now installed on milou and tintin.</p> Tue, 20 Sep 2016 08:15:00 GMT https://www.uppmax.uu.se/changelog 2016-09-20T08:15:00Z R_packages/3.3.0 updated with additional packages https://www.uppmax.uu.se/changelog <p><a href="https://www.uppmax.uu.se/support-sv//r_packages-module-guide">R_packages/3.3.0</a> now contains additional packages for RNA-seq analysis, including&nbsp;Gviz,&nbsp;gplots,&nbsp;<span style="font-size:1em; line-height:1.5em">edgeR,&nbsp;</span><span style="font-size:1em; line-height:1.5em">DEXSeq,&nbsp;</span><span style="font-size:1em; line-height:1.5em">goseq,&nbsp;</span><span style="font-size:1em; line-height:1.5em">GO.db,&nbsp;reactome.db,&nbsp;</span><span style="font-size:1em; line-height:1.5em">org.Mm.eg.db</span></p> Mon, 19 Sep 2016 13:14:00 GMT https://www.uppmax.uu.se/changelog 2016-09-19T13:14:00Z [comp] julia/0.4.6 installed https://www.uppmax.uu.se/changelog <p>julia/0.4.6</p> Fri, 16 Sep 2016 13:34:00 GMT https://www.uppmax.uu.se/changelog 2016-09-16T13:34:00Z [comp] intel/17.0 installed https://www.uppmax.uu.se/changelog <p>intel/17.0</p> Thu, 15 Sep 2016 08:18:00 GMT https://www.uppmax.uu.se/changelog 2016-09-15T08:18:00Z [comp] gcc/6.2.0 installed https://www.uppmax.uu.se/changelog <p>gcc/6.2.0</p> Thu, 15 Sep 2016 07:22:00 GMT https://www.uppmax.uu.se/changelog 2016-09-15T07:22:00Z [bio] Metassembler/1.5 installed on tintin https://www.uppmax.uu.se/changelog <p><a href="https://sourceforge.net/p/metassembler">Metassembler 1.5</a>&nbsp;is installed on tintin; it was previously available only on milou.</p> Fri, 09 Sep 2016 12:28:00 GMT https://www.uppmax.uu.se/changelog 2016-09-09T12:28:00Z [bio] MUMmer/3.9.4alpha installed https://www.uppmax.uu.se/changelog <p><a href="https://github.com/gmarcais/mummer">MUMmer&nbsp;3.9.4alpha</a>&nbsp;(the latest alpha version of 'MUMmer4') is now&nbsp;installed on milou and tintin. The default version remains MUMmer/3.23</p> Fri, 09 Sep 2016 09:11:00 GMT https://www.uppmax.uu.se/changelog 2016-09-09T09:11:00Z [bio] KAT/2.1.1 installed https://www.uppmax.uu.se/changelog <p><a href="https://github.com/TGAC/KAT">KAT 2.1.1</a> (kmer analysis toolkit) has been installed on milou and tintin. &nbsp;This is an upgrade for both systems.</p> Fri, 02 Sep 2016 14:12:00 GMT https://www.uppmax.uu.se/changelog 2016-09-02T14:12:00Z [bio] concaterpillar/1.4 updated https://www.uppmax.uu.se/changelog <p><a href="http://hierarchical likelihood ratio test for phylogenetic congruence">Concaterpillar 1.4</a> (<em>hierarchical likelihood ratio test for phylogenetic congruence</em>) is updated to work on milou and is now also installed on tintin.</p> Thu, 01 Sep 2016 06:58:00 GMT https://www.uppmax.uu.se/changelog 2016-09-01T06:58:00Z [bio] subread/1.5.1 https://www.uppmax.uu.se/changelog <p><a href="http://subread.sourceforge.net/">Subread 1.5.1</a> is now installed on milou and tintin</p> Tue, 30 Aug 2016 08:32:00 GMT https://www.uppmax.uu.se/changelog 2016-08-30T08:32:00Z [bio] vcflib/2016-08-29 installed https://www.uppmax.uu.se/changelog <p><a href="https://github.com/vcflib/vcflib">vcflib 2016-08-29</a> installed on milou and tintin</p> <p></p> Mon, 29 Aug 2016 09:38:00 GMT https://www.uppmax.uu.se/changelog 2016-08-29T09:38:00Z [apps] tinyutils/1.4 https://www.uppmax.uu.se/changelog <p>tinyutils 1.4 (tiny utilities for manipulating data) installed</p> Wed, 24 Aug 2016 12:52:00 GMT https://www.uppmax.uu.se/changelog 2016-08-24T12:52:00Z [bio] IQ-TREE 1.4.3-pomo https://www.uppmax.uu.se/changelog <p>Efficient phylogenomic software by maximum likelihood&nbsp;(polymorphism-aware version)</p> Fri, 05 Aug 2016 13:44:00 GMT https://www.uppmax.uu.se/changelog 2016-08-05T13:44:00Z [bio] blast 2.4.0+ https://www.uppmax.uu.se/changelog <p>Basic Local Alignment Search Tool</p> Thu, 28 Jul 2016 09:39:00 GMT https://www.uppmax.uu.se/changelog 2016-07-28T09:39:00Z [bio] AdmixTools https://www.uppmax.uu.se/changelog <p>test whether admixture occurred</p> Wed, 03 Aug 2016 09:00:00 GMT https://www.uppmax.uu.se/changelog 2016-08-03T09:00:00Z [bio] MACS 2.1.0 (irma) https://www.uppmax.uu.se/changelog <p>Model-based Analysis of ChIP-Seq</p> Wed, 03 Aug 2016 08:55:00 GMT https://www.uppmax.uu.se/changelog 2016-08-03T08:55:00Z [bio] ngsplot 2.61 (irma) https://www.uppmax.uu.se/changelog <p>mining and visualization of NGS data</p> Wed, 03 Aug 2016 08:51:00 GMT https://www.uppmax.uu.se/changelog 2016-08-03T08:51:00Z [bio] SHRiMP 2.2.3 https://www.uppmax.uu.se/changelog <p>SHort Read Mapping Package</p> Fri, 05 Aug 2016 08:43:00 GMT https://www.uppmax.uu.se/changelog 2016-08-05T08:43:00Z [bio] GATK temp https://www.uppmax.uu.se/changelog <p>Genome Analysis Toolkit</p> Wed, 27 Jul 2016 06:58:00 GMT https://www.uppmax.uu.se/changelog 2016-07-27T06:58:00Z [bio] spades/3.9.0 https://www.uppmax.uu.se/changelog <p><a href="http://bioinf.spbau.ru/spades">Spades 3.9.0</a></p> <p>a flexible assembler for small genomes</p> Wed, 27 Jul 2016 19:38:00 GMT https://www.uppmax.uu.se/changelog 2016-07-27T19:38:00Z [apps] tinyutils/1.3 https://www.uppmax.uu.se/changelog <p><a href="https://github.com/douglasgscofield/tinyutils">Tinyutils 1.3</a></p> <p>small utilities for working with data</p> Wed, 27 Jul 2016 14:48:00 GMT https://www.uppmax.uu.se/changelog 2016-07-27T14:48:00Z [bio] MEMEsuite/4.11.2_1 https://www.uppmax.uu.se/changelog <p><a href="http://meme-suite.org/tools/meme">MEME Suite 4.11.2 patch level 1</a></p> <p>motif-based sequence analysis tools</p> Mon, 25 Jul 2016 17:00:00 GMT https://www.uppmax.uu.se/changelog 2016-07-25T17:00:00Z [bio] ucsc-utilities/v334 https://www.uppmax.uu.se/changelog <p><a href="http://hgdownload.cse.ucsc.edu/admin/exe/">UCSC utilities version 334</a></p> Mon, 25 Jul 2016 14:21:00 GMT https://www.uppmax.uu.se/changelog 2016-07-25T14:21:00Z [bio] deepTools 2.3.1 https://www.uppmax.uu.se/changelog <p>Tools to process and analyze deep sequencing data</p> Sun, 24 Jul 2016 14:31:00 GMT https://www.uppmax.uu.se/changelog 2016-07-24T14:31:00Z [bio] deepTools 2.2.3 (irma) https://www.uppmax.uu.se/changelog <p>Tools to process and analyze deep sequencing data</p> Sun, 24 Jul 2016 12:41:00 GMT https://www.uppmax.uu.se/changelog 2016-07-24T12:41:00Z [bio] DICE https://www.uppmax.uu.se/changelog <p>estimate of demography and contamination for nuclear ancient DNA</p> Fri, 08 Jul 2016 12:24:00 GMT https://www.uppmax.uu.se/changelog 2016-07-08T12:24:00Z [bio] verifyBamID 1.1.2 https://www.uppmax.uu.se/changelog <p>verifies whether the reads match previously known genotypes</p> Wed, 06 Jul 2016 12:05:00 GMT https://www.uppmax.uu.se/changelog 2016-07-06T12:05:00Z [bio] pear 0.9.10 https://www.uppmax.uu.se/changelog <p>Paired-End reAd mergeR</p> Wed, 20 Jul 2016 11:54:00 GMT https://www.uppmax.uu.se/changelog 2016-07-20T11:54:00Z [bio] MultiQC 0.7 https://www.uppmax.uu.se/changelog <p>aggregate bioinformatics results into single report</p> Tue, 05 Jul 2016 11:29:00 GMT https://www.uppmax.uu.se/changelog 2016-07-05T11:29:00Z [bio] MultiQC 0.6 (irma) https://www.uppmax.uu.se/changelog <p>aggregate bioinformatics results into single report</p> Sat, 04 Jun 2016 10:56:00 GMT https://www.uppmax.uu.se/changelog 2016-06-04T10:56:00Z [bio] MultiQC 0.6 https://www.uppmax.uu.se/changelog <p>aggregate bioinformatics results into single report</p> Fri, 29 Apr 2016 10:45:00 GMT https://www.uppmax.uu.se/changelog 2016-04-29T10:45:00Z [bio] phylobayesmpi 1.7a https://www.uppmax.uu.se/changelog <p>Bayesian monte carlo markov chain&nbsp;sampler for phylogenetic reconstruction (MPI version)</p> Tue, 19 Jul 2016 10:25:00 GMT https://www.uppmax.uu.se/changelog 2016-07-19T10:25:00Z [bio] Bismark 0.16.2 (bugfix) https://www.uppmax.uu.se/changelog <p>bisulfite read mapper and methylation caller</p> Tue, 19 Jul 2016 09:59:00 GMT https://www.uppmax.uu.se/changelog 2016-07-19T09:59:00Z [bio] SPP 1.11 (irma) https://www.uppmax.uu.se/changelog <p>ChIP-seq processing pipeline</p> Wed, 13 Jul 2016 09:48:00 GMT https://www.uppmax.uu.se/changelog 2016-07-13T09:48:00Z [bio] phantompeakqualtools 1.1 (Irma) https://www.uppmax.uu.se/changelog <p>ChIP-Seq enrichment and quality measures</p> Wed, 13 Jul 2016 09:33:00 GMT https://www.uppmax.uu.se/changelog 2016-07-13T09:33:00Z [bio] pysam 0.9.1.4 https://www.uppmax.uu.se/changelog <p>Python module for reading and manipulating samfiles</p> Sun, 24 Jul 2016 09:20:00 GMT https://www.uppmax.uu.se/changelog 2016-07-24T09:20:00Z [bio] vep/84 installed https://www.uppmax.uu.se/changelog <p><a href="http://www.ensembl.org/info/docs/tools/vep/index.html">Variant Effect Predictor version 84</a></p> Wed, 20 Jul 2016 16:50:00 GMT https://www.uppmax.uu.se/changelog 2016-07-20T16:50:00Z [bio] GEMINI/0.19.0 installed https://www.uppmax.uu.se/changelog <p><a href="http://gemini.readthedocs.io/en/latest/index.html">GEMINI/0.19.0 (flexible framework for exploring genome variation) installed.</a></p> Mon, 18 Jul 2016 14:25:00 GMT https://www.uppmax.uu.se/changelog 2016-07-18T14:25:00Z [libs] GEOS/3.5.0 installed https://www.uppmax.uu.se/changelog <p><a href="https://trac.osgeo.org/geos/">GEOS/3.5.0 open-source genometry engine&nbsp;installed</a></p> Mon, 18 Jul 2016 11:28:00 GMT https://www.uppmax.uu.se/changelog 2016-07-18T11:28:00Z [bio] spades/3.8.1 https://www.uppmax.uu.se/changelog <p><a href="http://bioinf.spbau.ru/spades">SPAdes 3.8.1 (feature-rich assembler for small genomes)</a></p> <p>is now installed as module spades/3.8.1 as part of the assembly subgroup of bioinfo-tools on milou and tintin. &nbsp;This is an update for both systems. &nbsp;/douglas</p> Fri, 01 Jul 2016 16:18:00 GMT https://www.uppmax.uu.se/changelog 2016-07-01T16:18:00Z [bio] MetaBat 0.26.3 https://www.uppmax.uu.se/changelog <p>An Efficient Tool for Accurately Reconstructing Single Genomes from Complex Microbial Communities</p> Wed, 29 Jun 2016 09:27:00 GMT https://www.uppmax.uu.se/changelog 2016-06-29T09:27:00Z [tool] SCons 2.5.0 https://www.uppmax.uu.se/changelog <p>Software construction tool (like make)</p> Wed, 29 Jun 2016 08:44:00 GMT https://www.uppmax.uu.se/changelog 2016-06-29T08:44:00Z [bio] tbl2asn https://www.uppmax.uu.se/changelog <p>Automates the creation of sequence records for submission to GenBank</p> Tue, 14 Jun 2016 07:23:00 GMT https://www.uppmax.uu.se/changelog 2016-06-14T07:23:00Z [bio] ngsF-HMM https://www.uppmax.uu.se/changelog <p>Estimate per-individual inbreeding tracts using a two-state Hidden Markov Model</p> Tue, 14 Jun 2016 07:14:00 GMT https://www.uppmax.uu.se/changelog 2016-06-14T07:14:00Z [lib] boost 1.61.0 (gcc 5.3.0) https://www.uppmax.uu.se/changelog <p>Widely-used C++ library</p> Mon, 13 Jun 2016 07:05:00 GMT https://www.uppmax.uu.se/changelog 2016-06-13T07:05:00Z [lib] sparsehash 2.0.3 https://www.uppmax.uu.se/changelog <p>Various hash-map implementations</p> Mon, 20 Jun 2016 06:53:00 GMT https://www.uppmax.uu.se/changelog 2016-06-20T06:53:00Z [bio] blobtools 0.9.17 https://www.uppmax.uu.se/changelog <p>Visualisation of draft assemblies using TAGC plots</p> Thu, 16 Jun 2016 06:46:00 GMT https://www.uppmax.uu.se/changelog 2016-06-16T06:46:00Z [bio] MinCED 0.2.0 https://www.uppmax.uu.se/changelog <p>Mining CRISPRs in Environmental Datasets</p> Wed, 15 Jun 2016 06:40:00 GMT https://www.uppmax.uu.se/changelog 2016-06-15T06:40:00Z [bio] Installations for Irma https://www.uppmax.uu.se/changelog <p>Various bio packages installed for Irma, either by linking to packages on Milou or local compilation.</p> Tue, 21 Jun 2016 05:56:00 GMT https://www.uppmax.uu.se/changelog 2016-06-21T05:56:00Z [bio] LoFreq 2.1.2 https://www.uppmax.uu.se/changelog <p>Fast and sensitive variant calling from next-gen sequencing data</p> Mon, 27 Jun 2016 15:39:00 GMT https://www.uppmax.uu.se/changelog 2016-06-27T15:39:00Z [bio] RNAfold (aka ViennaRNA) 2.2.5 installed https://www.uppmax.uu.se/changelog <p><a href="http://www.tbi.univie.ac.at/RNA/index.html">The ViennaRNA package for prediction and comparison of RNA secondary structures</a></p> <p>is now installed as module RNAfold/2.2.5, with alias ViennaRNA/2.2.5, on milou and tintin. &nbsp;This is an update for milou and a new module for tintin. &nbsp;/douglas</p> Sun, 19 Jun 2016 16:31:00 GMT https://www.uppmax.uu.se/changelog 2016-06-19T16:31:00Z [bio] CleaveLand4/4.3 installed https://www.uppmax.uu.se/changelog <h4><a href="http://sites.psu.edu/axtell/software/cleaveland4/">CleaveLand4 (analysis of degradome data to find sliced miRNA and siRNA targets)</a></h4> <p>is now installed as module CleaveLand4/4.3 as part of the misc subgroup of bioinfo-tools on milou and tintin. &nbsp;This is a new module for both systems. &nbsp;/douglas</p> Sun, 19 Jun 2016 10:15:00 GMT https://www.uppmax.uu.se/changelog 2016-06-19T10:15:00Z [comp] binutils/2.26 installed https://www.uppmax.uu.se/changelog <p><a href="https://www.gnu.org/software/binutils">Gnu binutils</a></p> <p>have&nbsp;been installed as module binutils/2.26 as part of compilers&nbsp;on milou and tintin. The module has been configured with --enable-plugins so that the contained utilities support plugins. &nbsp;This module updates the installed versions on both systems. &nbsp;/douglas</p> Sun, 19 Jun 2016 07:54:00 GMT https://www.uppmax.uu.se/changelog 2016-06-19T07:54:00Z [apps] doxygen/1.8.11 installed https://www.uppmax.uu.se/changelog <p><a href="http://www.stack.nl/~dimitri/doxygen/">Doxygen</a>&nbsp;version 1.8.11 (tool for generating documentation from source code) has been installed as module doxygen/1.8.11 on milou and tintin. &nbsp;This is an update for both systems. &nbsp;/douglas</p> Sun, 19 Jun 2016 05:02:00 GMT https://www.uppmax.uu.se/changelog 2016-06-19T05:02:00Z [bio] kallisto/0.43.0 installed https://www.uppmax.uu.se/changelog <p><a href="https://pachterlab.github.io/kallisto/">Kallisto</a></p> <p>has been upgraded to version 0.43.0 and compiled with gcc/5.3.0, and is now installed as module kallisto/0.43.0 on milou and tintin. &nbsp;/douglas</p> Sat, 18 Jun 2016 13:58:00 GMT https://www.uppmax.uu.se/changelog 2016-06-18T13:58:00Z [apps] vim/7.4-1941 installed https://www.uppmax.uu.se/changelog <p><a href="http://www.vim.org/">VIM 7.4-1941</a></p> <p>... (a text editor and more, version 7.4 through patch 1941)&nbsp;has been&nbsp;installed as module vim/7.4-1941 on milou and tintin. &nbsp;This is a new module for both systems; VIM is available on the system, but this is a more up-to-date version than the default. &nbsp;Using 'gvim' or 'gview'&nbsp;will open an X-windows version. &nbsp;/douglas</p> Thu, 16 Jun 2016 14:01:00 GMT https://www.uppmax.uu.se/changelog 2016-06-16T14:01:00Z [stats] R_packages/3.3.0 installed https://www.uppmax.uu.se/changelog <p><a href="https://www.uppmax.uu.se/support-sv//r_packages-module-guide">A module containing a modest collection of useful&nbsp;R packages</a></p> <p>... for R/3.3.0 is now installed as module R_packages/3.3.0 on milou and tintin. This is a new module for both systems.</p> Thu, 16 Jun 2016 09:39:00 GMT https://www.uppmax.uu.se/changelog 2016-06-16T09:39:00Z [bio] DWGSIM/0.1.11-6e9a361 installed https://www.uppmax.uu.se/changelog <p><a href="https://github.com/nh13/DWGSIM">The DWGSIM sequence simulator</a>&nbsp;... version 0.1.11 commit&nbsp;6e9a361&nbsp;(sequence simulation) has been installed as module DWGSIM/0.1.11-6e9a361 as part of the misc subgroup of bioinfo-tools on milou and tintin. The version reflects the last commit after version 0.1.11 when the repository was cloned. This is a new module for both systems. /douglas</p> Thu, 16 Jun 2016 07:16:00 GMT https://www.uppmax.uu.se/changelog 2016-06-16T07:16:00Z [bio] BAM-matcher installed https://www.uppmax.uu.se/changelog <p>Determine&nbsp;whether two BAM files&nbsp;contain reads sequenced from the same sample or patient</p> Sat, 11 Jun 2016 14:43:00 GMT https://www.uppmax.uu.se/changelog 2016-06-11T14:43:00Z [bio] EEMS installed https://www.uppmax.uu.se/changelog <p>Estimating Effective Migration Surfaces</p> Sun, 05 Jun 2016 15:10:00 GMT https://www.uppmax.uu.se/changelog 2016-06-05T15:10:00Z Bismark has been upgraded to version 0.16.1 https://www.uppmax.uu.se/changelog <p>&nbsp;(bisulfite read mapper and methylation caller)</p> Fri, 03 Jun 2016 12:21:00 GMT https://www.uppmax.uu.se/changelog 2016-06-03T12:21:00Z rnaQUAST has been installed https://www.uppmax.uu.se/changelog <p>&nbsp;(Quality Assessment Tool for Transcriptome Assemblies)&nbsp;</p> Thu, 02 Jun 2016 12:20:00 GMT https://www.uppmax.uu.se/changelog 2016-06-02T12:20:00Z Infernal has been installed https://www.uppmax.uu.se/changelog <p>(INFERence of RNA ALignment: search DNA for RNA structure and sequence similarities)</p> Thu, 02 Jun 2016 12:19:00 GMT https://www.uppmax.uu.se/changelog 2016-06-02T12:19:00Z Barrnap has been upgraded to version 0.6 https://www.uppmax.uu.se/changelog <p>(predicts the location of ribosomal RNA genes in genomes)</p> Thu, 02 Jun 2016 12:18:00 GMT https://www.uppmax.uu.se/changelog 2016-06-02T12:18:00Z Bridger has been installed https://www.uppmax.uu.se/changelog <p>&nbsp;(de-novo RNA-Seq assembly)</p> Thu, 02 Jun 2016 12:18:00 GMT https://www.uppmax.uu.se/changelog 2016-06-02T12:18:00Z NGSUtils 0.5.9 installed https://www.uppmax.uu.se/changelog <p>(suite of software tools for working with next-generation sequencing datasets)&nbsp;</p> Tue, 31 May 2016 12:17:00 GMT https://www.uppmax.uu.se/changelog 2016-05-31T12:17:00Z SPAdes 3.8.0 is now installed https://www.uppmax.uu.se/changelog <p>(flexible small-genome assembly, now with plasmid assembly option)&nbsp;</p> Tue, 31 May 2016 12:16:00 GMT https://www.uppmax.uu.se/changelog 2016-05-31T12:16:00Z mrCaNaVeR 0.51 is now installed https://www.uppmax.uu.se/changelog <p>(copy-number caller using whole-genome read mappings)&nbsp;</p> Tue, 31 May 2016 12:15:00 GMT https://www.uppmax.uu.se/changelog 2016-05-31T12:15:00Z mrFAST 2.6.1.0 is now installed https://www.uppmax.uu.se/changelog <p>(short-read aligner)</p> Tue, 31 May 2016 12:14:00 GMT https://www.uppmax.uu.se/changelog 2016-05-31T12:14:00Z Bandage 0.8.0 is now installed https://www.uppmax.uu.se/changelog <p>&nbsp;(assembly graph visualisation tool)</p> Tue, 31 May 2016 12:14:00 GMT https://www.uppmax.uu.se/changelog 2016-05-31T12:14:00Z Perl 5.24.0 is now installed https://www.uppmax.uu.se/changelog Mon, 30 May 2016 12:13:00 GMT https://www.uppmax.uu.se/changelog 2016-05-30T12:13:00Z Perl 5.22.2 is now installed https://www.uppmax.uu.se/changelog Mon, 30 May 2016 12:13:00 GMT https://www.uppmax.uu.se/changelog 2016-05-30T12:13:00Z Our local copy of iGenomes is being updated https://www.uppmax.uu.se/changelog Sun, 29 May 2016 12:12:00 GMT https://www.uppmax.uu.se/changelog 2016-05-29T12:12:00Z Java JDK 1.8 release 92 is now installed https://www.uppmax.uu.se/changelog <p>Java JDK 1.8 release 92 is now installed as module&nbsp;java/sun_jdk1.8.0_92&nbsp;as part of&nbsp;compilerson milou and tintin. This is an update for both systems. /douglas</p> Sat, 28 May 2016 12:11:00 GMT https://www.uppmax.uu.se/changelog 2016-05-28T12:11:00Z KAT has been updated to version 2.0.8 https://www.uppmax.uu.se/changelog <p>(Kmer Analysis Toolkit)</p> Wed, 25 May 2016 12:10:00 GMT https://www.uppmax.uu.se/changelog 2016-05-25T12:10:00Z Roary 3.6.2 (high speed stand alone pan genome pipeline) is now installed https://www.uppmax.uu.se/changelog Wed, 25 May 2016 12:09:00 GMT https://www.uppmax.uu.se/changelog 2016-05-25T12:09:00Z GNU parallel 20150522 is now installed https://www.uppmax.uu.se/changelog Tue, 24 May 2016 12:08:00 GMT https://www.uppmax.uu.se/changelog 2016-05-24T12:08:00Z The GNU coreutils 8.25 (core Linux utilities) is now available https://www.uppmax.uu.se/changelog Tue, 24 May 2016 12:08:00 GMT https://www.uppmax.uu.se/changelog 2016-05-24T12:08:00Z cutadapt 1.9.1 (flexible adapter trimming) is now installed https://www.uppmax.uu.se/changelog Tue, 24 May 2016 12:07:00 GMT https://www.uppmax.uu.se/changelog 2016-05-24T12:07:00Z Trim Galore! 0.4.1 (QC wrapper script for FastQC and cutadapt) is now installed https://www.uppmax.uu.se/changelog Tue, 24 May 2016 12:06:00 GMT https://www.uppmax.uu.se/changelog 2016-05-24T12:06:00Z FastQC 0.4.11 (quality control for FastQ sequences) is now installed https://www.uppmax.uu.se/changelog Tue, 24 May 2016 12:06:00 GMT https://www.uppmax.uu.se/changelog 2016-05-24T12:06:00Z SPAdes 3.7.1 (flexible small-genome assembly) is now installed https://www.uppmax.uu.se/changelog Tue, 24 May 2016 12:05:00 GMT https://www.uppmax.uu.se/changelog 2016-05-24T12:05:00Z libgeotiff 1.4.1 (TIFF-based interchange format for georeferenced raster imagery) is now installed https://www.uppmax.uu.se/changelog Sat, 21 May 2016 12:04:00 GMT https://www.uppmax.uu.se/changelog 2016-05-21T12:04:00Z Poppler 0.43.0 (PDF rendering library) is now installed https://www.uppmax.uu.se/changelog Sat, 21 May 2016 12:04:00 GMT https://www.uppmax.uu.se/changelog 2016-05-21T12:04:00Z NetCDF 4.4.0 (software libraries and data formats that support array-oriented scientific data) is now available https://www.uppmax.uu.se/changelog Sat, 21 May 2016 12:02:00 GMT https://www.uppmax.uu.se/changelog 2016-05-21T12:02:00Z FreeType 2.6 (library to render fonts) is now available https://www.uppmax.uu.se/changelog Fri, 20 May 2016 12:02:00 GMT https://www.uppmax.uu.se/changelog 2016-05-20T12:02:00Z FYBA 4.1.1 (open-source library to read and write files in the National geodata standard format SOSI from the National Mapping Authority of Norway [Statens kartverk]) is now installed https://www.uppmax.uu.se/changelog Fri, 20 May 2016 12:01:00 GMT https://www.uppmax.uu.se/changelog 2016-05-20T12:01:00Z PROJ.4 4.9.2 (Cartographic Projections Library) is now installed https://www.uppmax.uu.se/changelog Fri, 20 May 2016 12:00:00 GMT https://www.uppmax.uu.se/changelog 2016-05-20T12:00:00Z GDAL 2.1.0 (Geospatial Data Abstraction library) is now installed https://www.uppmax.uu.se/changelog Fri, 20 May 2016 12:00:00 GMT https://www.uppmax.uu.se/changelog 2016-05-20T12:00:00Z R 3.3.0 (flexible statistical language) is now installed https://www.uppmax.uu.se/changelog Thu, 19 May 2016 11:59:00 GMT https://www.uppmax.uu.se/changelog 2016-05-19T11:59:00Z PCRE 8.38 (library providing Perl-compatible regular expressions) is now available https://www.uppmax.uu.se/changelog Thu, 19 May 2016 11:59:00 GMT https://www.uppmax.uu.se/changelog 2016-05-19T11:59:00Z zlib 1.2.8 (widely used general purpose compression library) has been available https://www.uppmax.uu.se/changelog Thu, 19 May 2016 11:58:00 GMT https://www.uppmax.uu.se/changelog 2016-05-19T11:58:00Z XZ Utils 5.2.2 (high-performance general-purpose compression) is now installed https://www.uppmax.uu.se/changelog Thu, 19 May 2016 11:57:00 GMT https://www.uppmax.uu.se/changelog 2016-05-19T11:57:00Z Bzip2 1.0.6 (general-purpose compression) is now installed https://www.uppmax.uu.se/changelog Thu, 19 May 2016 11:55:00 GMT https://www.uppmax.uu.se/changelog 2016-05-19T11:55:00Z Openmpi 1.10.2 was installed for gcc/6.1.0 https://www.uppmax.uu.se/changelog <p>Openmpi 1.10.2 was installed for gcc/6.1.0 as module openmpi/1.10.2 on tintin, milou and irma. /agback</p> Fri, 29 Apr 2016 11:53:00 GMT https://www.uppmax.uu.se/changelog 2016-04-29T11:53:00Z gcc 6.1.0 was installed https://www.uppmax.uu.se/changelog <p>gcc 6.1.0 was installed as module gcc/6.1.0 on milou, tintin and irma. /agback</p> Fri, 29 Apr 2016 11:53:00 GMT https://www.uppmax.uu.se/changelog 2016-04-29T11:53:00Z pgi 16.4 was installed https://www.uppmax.uu.se/changelog <p>pgi 16.4 was installed as module pgi/16.4 on milou and tintin. /agback</p> Thu, 28 Apr 2016 11:52:00 GMT https://www.uppmax.uu.se/changelog 2016-04-28T11:52:00Z Piper (NGI pipeline) has been installed for Irma https://www.uppmax.uu.se/changelog Wed, 27 Apr 2016 11:51:00 GMT https://www.uppmax.uu.se/changelog 2016-04-27T11:51:00Z GSL (Gnu Scientific Library) has been upgraded to version 2.1 https://www.uppmax.uu.se/changelog Wed, 27 Apr 2016 11:50:00 GMT https://www.uppmax.uu.se/changelog 2016-04-27T11:50:00Z VarDictJava 1.4.5 is now installed https://www.uppmax.uu.se/changelog Mon, 25 Apr 2016 11:50:00 GMT https://www.uppmax.uu.se/changelog 2016-04-25T11:50:00Z Schmutzi (maximum a posteriori estimate of contamination for ancient samples) has been installed https://www.uppmax.uu.se/changelog Sun, 24 Apr 2016 11:49:00 GMT https://www.uppmax.uu.se/changelog 2016-04-24T11:49:00Z Platypus (haplotype-based variant caller) has been installed https://www.uppmax.uu.se/changelog Fri, 22 Apr 2016 11:47:00 GMT https://www.uppmax.uu.se/changelog 2016-04-22T11:47:00Z Haskell Tool Stack (cross-platform program for developing Haskell programming projects) has been installed. https://www.uppmax.uu.se/changelog Thu, 21 Apr 2016 11:46:00 GMT https://www.uppmax.uu.se/changelog 2016-04-21T11:46:00Z MEGAN (MEtaGenome ANalyzer) has been upgraded to version 5 https://www.uppmax.uu.se/changelog Thu, 21 Apr 2016 11:46:00 GMT https://www.uppmax.uu.se/changelog 2016-04-21T11:46:00Z Several prebuilt databases have been added for use with the DIAMOND tool. https://www.uppmax.uu.se/changelog Wed, 20 Apr 2016 11:44:00 GMT https://www.uppmax.uu.se/changelog 2016-04-20T11:44:00Z DIAMOND (protein database alignment much faster than BLAST) updated to version 0.7.12 https://www.uppmax.uu.se/changelog Wed, 20 Apr 2016 11:43:00 GMT https://www.uppmax.uu.se/changelog 2016-04-20T11:43:00Z RNA-SeQC (computes quality control metrics for RNA-seq) has been installed https://www.uppmax.uu.se/changelog Tue, 19 Apr 2016 11:42:00 GMT https://www.uppmax.uu.se/changelog 2016-04-19T11:42:00Z The deepTools package (user-friendly tools for the normalization and visualization of deep-sequencing data) updated to version 2.2.3 https://www.uppmax.uu.se/changelog Mon, 18 Apr 2016 11:40:00 GMT https://www.uppmax.uu.se/changelog 2016-04-18T11:40:00Z BEAST2 (bayesian phylogenetic analysis of molecular sequences) has been upgraded to version 2.4.0 https://www.uppmax.uu.se/changelog Fri, 15 Apr 2016 11:40:00 GMT https://www.uppmax.uu.se/changelog 2016-04-15T11:40:00Z MultiQC (aggregate bioinformatics results into single report) has been updated to version 0.5 https://www.uppmax.uu.se/changelog Thu, 07 Apr 2016 11:37:00 GMT https://www.uppmax.uu.se/changelog 2016-04-07T11:37:00Z BCFtools (VCF and BCF manipulation) has been upgraded to version 1.3 https://www.uppmax.uu.se/changelog Thu, 07 Apr 2016 11:37:00 GMT https://www.uppmax.uu.se/changelog 2016-04-07T11:37:00Z Miniasm (ultrafast de novo assembly for long noisy reads, though having no consensus step) and minimap (experimental tool to find approximate mapping positions between long sequences) are now installed https://www.uppmax.uu.se/changelog Tue, 05 Apr 2016 11:35:00 GMT https://www.uppmax.uu.se/changelog 2016-04-05T11:35:00Z HTSlib (C library for high-throughput sequencing data formats) has been installed https://www.uppmax.uu.se/changelog Mon, 04 Apr 2016 11:34:00 GMT https://www.uppmax.uu.se/changelog 2016-04-04T11:34:00Z Latent Strain Analysis (pre-assembly tool for partitioning metagenomic reads) is now installed https://www.uppmax.uu.se/changelog Mon, 04 Apr 2016 11:33:00 GMT https://www.uppmax.uu.se/changelog 2016-04-04T11:33:00Z CMake (comprehensive configuration and build tool) upgraded to 3.5.1 https://www.uppmax.uu.se/changelog Mon, 04 Apr 2016 11:32:00 GMT https://www.uppmax.uu.se/changelog 2016-04-04T11:32:00Z SHORE 0.9.3 (Next Generation Sequencing data analysis suite) is now installed https://www.uppmax.uu.se/changelog Tue, 29 Mar 2016 11:18:00 GMT https://www.uppmax.uu.se/changelog 2016-03-29T11:18:00Z The tinyutils 1.2 collection of small utilities for working on columns of numbers is now installed https://www.uppmax.uu.se/changelog Tue, 29 Mar 2016 11:17:00 GMT https://www.uppmax.uu.se/changelog 2016-03-29T11:17:00Z Quast (Quality Assessment Tool for Genome Assemblies) was updated to version 3.2 https://www.uppmax.uu.se/changelog Fri, 25 Mar 2016 12:16:00 GMT https://www.uppmax.uu.se/changelog 2016-03-25T12:16:00Z RSEM (RNA-seq by expectation maximization) has been updated to version 1.2.29 https://www.uppmax.uu.se/changelog Thu, 24 Mar 2016 12:16:00 GMT https://www.uppmax.uu.se/changelog 2016-03-24T12:16:00Z Openmpi 1.10.2 was installed https://www.uppmax.uu.se/changelog <p>Openmpi 1.10.2 was installed for intel/16.2 and gcc/5.3.0 as module openmpi/1.10.2 on tintin and milou. /agback</p> Wed, 23 Mar 2016 12:15:00 GMT https://www.uppmax.uu.se/changelog 2016-03-23T12:15:00Z Intel Parallel Studio XE 2016 Cluster Edition update 2 installed https://www.uppmax.uu.se/changelog <p>Intel Parallel Studio XE 2016 Cluster Edition update 2 is now installed as intel/16.2 on tintin and milou. /agback</p> Wed, 23 Mar 2016 12:14:00 GMT https://www.uppmax.uu.se/changelog 2016-03-23T12:14:00Z intelmpi 5.1.3 is installed https://www.uppmax.uu.se/changelog <p>intelmpi 5.1.3 is&nbsp;installed as module intelmpi/5.1.3 on tintin and milou. /agback</p> Wed, 23 Mar 2016 12:14:00 GMT https://www.uppmax.uu.se/changelog 2016-03-23T12:14:00Z Intel Advisor XE 2016 updated to update2 https://www.uppmax.uu.se/changelog Wed, 23 Mar 2016 12:12:00 GMT https://www.uppmax.uu.se/changelog 2016-03-23T12:12:00Z canu assembler (a fork of Cabog/Celera Assembler specialised for noisy long reads such as PacBio) updated version 1.1 https://www.uppmax.uu.se/changelog Tue, 22 Mar 2016 12:11:00 GMT https://www.uppmax.uu.se/changelog 2016-03-22T12:11:00Z GEMINI updated to version 0.18.3 https://www.uppmax.uu.se/changelog Tue, 22 Mar 2016 12:09:00 GMT https://www.uppmax.uu.se/changelog 2016-03-22T12:09:00Z MrBayes has been updated to 3.2.6 https://www.uppmax.uu.se/changelog Wed, 16 Mar 2016 12:09:00 GMT https://www.uppmax.uu.se/changelog 2016-03-16T12:09:00Z QualiMap (sequence alignment evaluator) has been updated to version 2.2 https://www.uppmax.uu.se/changelog Tue, 08 Mar 2016 12:07:00 GMT https://www.uppmax.uu.se/changelog 2016-03-08T12:07:00Z iGenomes has been reindexed with the latest version of STAR (2.5.1b) https://www.uppmax.uu.se/changelog Mon, 07 Mar 2016 12:06:00 GMT https://www.uppmax.uu.se/changelog 2016-03-07T12:06:00Z SPAdes 3.7.0 (flexible small-genome assembly) is now installed https://www.uppmax.uu.se/changelog Tue, 01 Mar 2016 12:06:00 GMT https://www.uppmax.uu.se/changelog 2016-03-01T12:06:00Z Matlab R2015b has been installed https://www.uppmax.uu.se/changelog <p>Matlab R2015b has been installed as module matlab/R2015b on milou and tintin. /agback</p> Tue, 01 Mar 2016 12:05:00 GMT https://www.uppmax.uu.se/changelog 2016-03-01T12:05:00Z The ExAC Exome Aggregation Consortium databases releases 0.1, 0.2 and 0.3 downloaded https://www.uppmax.uu.se/changelog Fri, 26 Feb 2016 12:02:00 GMT https://www.uppmax.uu.se/changelog 2016-02-26T12:02:00Z The h5utils 1.12.1 (utilities for working with hdf4/hdf5-format files) are now installed https://www.uppmax.uu.se/changelog Thu, 25 Feb 2016 10:48:00 GMT https://www.uppmax.uu.se/changelog 2016-02-25T10:48:00Z SZIP 2.1 library (high-performance file compression) is now installed https://www.uppmax.uu.se/changelog Wed, 24 Feb 2016 10:42:00 GMT https://www.uppmax.uu.se/changelog 2016-02-24T10:42:00Z HDF4 4.2.11 (libraries and tools supporting a high-performance file format for scientific data) has now been installed https://www.uppmax.uu.se/changelog Wed, 24 Feb 2016 10:40:00 GMT https://www.uppmax.uu.se/changelog 2016-02-24T10:40:00Z BWA 0.7.13 (NGS read alignment) is now installed https://www.uppmax.uu.se/changelog Tue, 23 Feb 2016 10:39:00 GMT https://www.uppmax.uu.se/changelog 2016-02-23T10:39:00Z The Guile programming language version 1.8.8 is now installed https://www.uppmax.uu.se/changelog Tue, 23 Feb 2016 10:39:00 GMT https://www.uppmax.uu.se/changelog 2016-02-23T10:39:00Z snpEff (genetic variant annotation and effect prediction toolbox) has been updated to version 4.2 https://www.uppmax.uu.se/changelog Tue, 23 Feb 2016 10:38:00 GMT https://www.uppmax.uu.se/changelog 2016-02-23T10:38:00Z Delly (structural variant discovery) has been updated to version 0.7.2 https://www.uppmax.uu.se/changelog Mon, 22 Feb 2016 10:37:00 GMT https://www.uppmax.uu.se/changelog 2016-02-22T10:37:00Z MultiQC (aggregate bioinformatics results into single report) has been updated to 0.4 https://www.uppmax.uu.se/changelog Mon, 22 Feb 2016 10:36:00 GMT https://www.uppmax.uu.se/changelog 2016-02-22T10:36:00Z MAKER 2.31.8 (genome annotation pipeline) has been installed https://www.uppmax.uu.se/changelog Wed, 17 Feb 2016 10:35:00 GMT https://www.uppmax.uu.se/changelog 2016-02-17T10:35:00Z GenomeTools 1.5.8 (versatile open source genome analysis software) is now installed https://www.uppmax.uu.se/changelog Tue, 16 Feb 2016 10:35:00 GMT https://www.uppmax.uu.se/changelog 2016-02-16T10:35:00Z seqMINER/1.3.3e (genome mapping data interpretation platform) has been installed https://www.uppmax.uu.se/changelog Mon, 15 Feb 2016 10:34:00 GMT https://www.uppmax.uu.se/changelog 2016-02-15T10:34:00Z ngsplot/2.61 (mining and visualization of NGS data) has been installed https://www.uppmax.uu.se/changelog Mon, 15 Feb 2016 10:34:00 GMT https://www.uppmax.uu.se/changelog 2016-02-15T10:34:00Z freebayes/1.0.2 (bayesian haplotype-based polymorphism discovery and genotyping) has been updated https://www.uppmax.uu.se/changelog Mon, 15 Feb 2016 10:33:00 GMT https://www.uppmax.uu.se/changelog 2016-02-15T10:33:00Z RepeatModeler/1.0.8 (de-novo repeat family identification and modeler) has been installed https://www.uppmax.uu.se/changelog Mon, 15 Feb 2016 10:32:00 GMT https://www.uppmax.uu.se/changelog 2016-02-15T10:32:00Z RepeatMasker/4.0.6 (screens sequences for repeats and low complexity) has been installed https://www.uppmax.uu.se/changelog Mon, 15 Feb 2016 10:31:00 GMT https://www.uppmax.uu.se/changelog 2016-02-15T10:31:00Z ADMIXTURE 1.3.0 (maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets) is now available https://www.uppmax.uu.se/changelog Sat, 13 Feb 2016 10:31:00 GMT https://www.uppmax.uu.se/changelog 2016-02-13T10:31:00Z SOAPdenovo-Trans 1.03 and 1.04 (de novo transcriptome assembly) are now available https://www.uppmax.uu.se/changelog Fri, 12 Feb 2016 10:30:00 GMT https://www.uppmax.uu.se/changelog 2016-02-12T10:30:00Z SGA 0.10.14 (String Graph Assembler) is now available https://www.uppmax.uu.se/changelog Fri, 12 Feb 2016 10:29:00 GMT https://www.uppmax.uu.se/changelog 2016-02-12T10:29:00Z The tinyutils 1.1 collection of small utilities for working on columns of numbers is now installed https://www.uppmax.uu.se/changelog Thu, 11 Feb 2016 10:29:00 GMT https://www.uppmax.uu.se/changelog 2016-02-11T10:29:00Z GERP++/20110522 (Genomic Evolutionary Rate Profiling) has been installed https://www.uppmax.uu.se/changelog Wed, 10 Feb 2016 10:27:00 GMT https://www.uppmax.uu.se/changelog 2016-02-10T10:27:00Z CNV-seq 20140812 (detect CNVs using next-generation sequencing data) is now installed https://www.uppmax.uu.se/changelog Tue, 09 Feb 2016 10:26:00 GMT https://www.uppmax.uu.se/changelog 2016-02-09T10:26:00Z MEME Suite 4.11.1 (motif-based sequence analysis tools) has been installed https://www.uppmax.uu.se/changelog Fri, 05 Feb 2016 10:24:00 GMT https://www.uppmax.uu.se/changelog 2016-02-05T10:24:00Z IMPUTE2 2.3.2 (genotype imputation and haplotype phasing program based on ideas from Howie et al. 2009) is now installed https://www.uppmax.uu.se/changelog Tue, 02 Feb 2016 10:24:00 GMT https://www.uppmax.uu.se/changelog 2016-02-02T10:24:00Z GTOOL 0.7.5 (program for transforming sets of genotype data for use with the programs SNPTEST and IMPUTE) is now installed https://www.uppmax.uu.se/changelog Tue, 02 Feb 2016 10:23:00 GMT https://www.uppmax.uu.se/changelog 2016-02-02T10:23:00Z qctool 1.4 (program for the analysis of single SNP association in genome-wide studies) is now installed https://www.uppmax.uu.se/changelog Tue, 02 Feb 2016 10:22:00 GMT https://www.uppmax.uu.se/changelog 2016-02-02T10:22:00Z SNPTEST 2.5.2 (program for the analysis of single SNP association in genome-wide studies) is now installed https://www.uppmax.uu.se/changelog Tue, 02 Feb 2016 10:22:00 GMT https://www.uppmax.uu.se/changelog 2016-02-02T10:22:00Z MEGAHIT (assembler for large/complex metagenomics) has been installed https://www.uppmax.uu.se/changelog Mon, 01 Feb 2016 10:21:00 GMT https://www.uppmax.uu.se/changelog 2016-02-01T10:21:00Z TreeMix 1.12 (a method for inferring the patterns of population splits and mixtures in the history of a set of populations) is now installed https://www.uppmax.uu.se/changelog Sat, 30 Jan 2016 10:21:00 GMT https://www.uppmax.uu.se/changelog 2016-01-30T10:21:00Z The canu assembler version 1.0 (a fork of Cabog/Celera Assembler specialised for noisy long reads such as PacBio) is now installed https://www.uppmax.uu.se/changelog Fri, 29 Jan 2016 10:20:00 GMT https://www.uppmax.uu.se/changelog 2016-01-29T10:20:00Z OPTIMA (alignment of error-prone maps) has been installed https://www.uppmax.uu.se/changelog Fri, 29 Jan 2016 10:19:00 GMT https://www.uppmax.uu.se/changelog 2016-01-29T10:19:00Z OMBlast (alignment of optical mapping data) has been installed https://www.uppmax.uu.se/changelog Fri, 29 Jan 2016 10:19:00 GMT https://www.uppmax.uu.se/changelog 2016-01-29T10:19:00Z Alinea DDT 6.0 is installed https://www.uppmax.uu.se/changelog <p>Alinea DDT 6.0 is installed as module ddt/6.0 on tintin and milou. /agback</p> Wed, 27 Jan 2016 10:18:00 GMT https://www.uppmax.uu.se/changelog 2016-01-27T10:18:00Z FusionCatcher has been upgraded to version 0.99.5a https://www.uppmax.uu.se/changelog Wed, 27 Jan 2016 10:17:00 GMT https://www.uppmax.uu.se/changelog 2016-01-27T10:17:00Z Subversion version 1.9.3 (source control system) has been installed https://www.uppmax.uu.se/changelog Tue, 26 Jan 2016 10:17:00 GMT https://www.uppmax.uu.se/changelog 2016-01-26T10:17:00Z The Tablet genome viewer version 1.15.09.01 is now installed https://www.uppmax.uu.se/changelog Tue, 26 Jan 2016 10:17:00 GMT https://www.uppmax.uu.se/changelog 2016-01-26T10:17:00Z STAR has been upgraded to version 2.5.1b https://www.uppmax.uu.se/changelog Tue, 26 Jan 2016 10:16:00 GMT https://www.uppmax.uu.se/changelog 2016-01-26T10:16:00Z sratools (SRA Toolkit) has been upgraded to version 2.5.7 https://www.uppmax.uu.se/changelog Tue, 26 Jan 2016 10:15:00 GMT https://www.uppmax.uu.se/changelog 2016-01-26T10:15:00Z The deepTools package version 2.0.1 (user-friendly tools for the normalization and visualization of deep-sequencing data) is now installed https://www.uppmax.uu.se/changelog Tue, 26 Jan 2016 10:14:00 GMT https://www.uppmax.uu.se/changelog 2016-01-26T10:14:00Z Texinfo 6.0 is available https://www.uppmax.uu.se/changelog Thu, 21 Jan 2016 10:14:00 GMT https://www.uppmax.uu.se/changelog 2016-01-21T10:14:00Z Additional modules for Intel Parallel Studio XE 2016 CE https://www.uppmax.uu.se/changelog Tue, 19 Jan 2016 10:11:00 GMT https://www.uppmax.uu.se/changelog 2016-01-19T10:11:00Z Corset 1.04 (transcript quantification) is now available https://www.uppmax.uu.se/changelog Tue, 19 Jan 2016 10:11:00 GMT https://www.uppmax.uu.se/changelog 2016-01-19T10:11:00Z The pblat-cluster aligner (MPI-enabled blat aligner) version 0.1 is now installed https://www.uppmax.uu.se/changelog Fri, 15 Jan 2016 10:10:00 GMT https://www.uppmax.uu.se/changelog 2016-01-15T10:10:00Z The pblat aligner (pthread-enabled blat aligner) version 1.6 is now installed https://www.uppmax.uu.se/changelog Fri, 15 Jan 2016 10:09:00 GMT https://www.uppmax.uu.se/changelog 2016-01-15T10:09:00Z intelmpi 5.1.2 is installed https://www.uppmax.uu.se/changelog <p>intelmpi 5.1.2 is&nbsp;installed as module intelmpi/5.1.2 on tintin and milou. /agback</p> Fri, 15 Jan 2016 10:08:00 GMT https://www.uppmax.uu.se/changelog 2016-01-15T10:08:00Z Intel Parallel Studio XE 2016 Cluster Edition is now installed https://www.uppmax.uu.se/changelog <p>Intel Parallel Studio XE 2016 Cluster Edition is now installed as intel/16.1 on tintin and milou. /agback</p> Fri, 15 Jan 2016 10:08:00 GMT https://www.uppmax.uu.se/changelog 2016-01-15T10:08:00Z Openmpi 1.10.1 was installed https://www.uppmax.uu.se/changelog <p>Openmpi 1.10.1 was installed for gcc/5.3.0, intel/15.3 and pgi/15.10 as module openmpi/1.10.1 on tintin and milou. /agback</p> Mon, 11 Jan 2016 10:07:00 GMT https://www.uppmax.uu.se/changelog 2016-01-11T10:07:00Z pgi 15.10 was installed https://www.uppmax.uu.se/changelog <p>pgi 15.10 was installed as module pgi/15.10 on milou and tintin. /agback</p> Mon, 11 Jan 2016 10:07:00 GMT https://www.uppmax.uu.se/changelog 2016-01-11T10:07:00Z gcc 5.3.0 was installed https://www.uppmax.uu.se/changelog <p>gcc 5.3.0 was installed as module gcc/5.3.0 on milou and tintin. /agback</p> Mon, 11 Jan 2016 10:06:00 GMT https://www.uppmax.uu.se/changelog 2016-01-11T10:06:00Z HISAT2 2.0.1-beta (graph-based alignment of next generation sequencing reads to a population of genomes) is now installed https://www.uppmax.uu.se/changelog Tue, 05 Jan 2016 10:03:00 GMT https://www.uppmax.uu.se/changelog 2016-01-05T10:03:00Z StringTie 1.2.0 (Transcript assembly and quantification for RNA-Seq) is now available https://www.uppmax.uu.se/changelog Tue, 05 Jan 2016 10:02:00 GMT https://www.uppmax.uu.se/changelog 2016-01-05T10:02:00Z Salmon 0.6.0 (fast transcript quantification from RNA-Seq data) is now available https://www.uppmax.uu.se/changelog Fri, 01 Jan 2016 10:01:00 GMT https://www.uppmax.uu.se/changelog 2016-01-01T10:01:00Z Jellyfish 2.2.4 (k-mer counting) is now available https://www.uppmax.uu.se/changelog Fri, 01 Jan 2016 09:59:00 GMT https://www.uppmax.uu.se/changelog 2016-01-01T09:59:00Z [comp] gcc/5.4.0 installed https://www.uppmax.uu.se/changelog <p>gcc-5.4.0 has been installed on Irma, Milou and Tintin as gcc/5.4.0. /agback</p> Fri, 10 Jun 2016 07:18:00 GMT https://www.uppmax.uu.se/changelog 2016-06-10T07:18:00Z [bio] canu/1.3 assembler installed https://www.uppmax.uu.se/changelog <p><a href="http://canu.readthedocs.io/en/stable/">The canu assembler</a>&nbsp;assembler (a fork of Celera Assembler specialised for PacBio reads) version 1.3 is now installed as module&nbsp;canu/1.3&nbsp;as part of the assembly subgroup of bioinfo-tools on milou and tintin. &nbsp;This is an update for both systems. &nbsp;/douglas</p> Thu, 09 Jun 2016 17:55:00 GMT https://www.uppmax.uu.se/changelog 2016-06-09T17:55:00Z [bio] GATK updated https://www.uppmax.uu.se/changelog <p>Genome Analysis Toolkit</p> Tue, 07 Jun 2016 12:50:00 GMT https://www.uppmax.uu.se/changelog 2016-06-07T12:50:00Z Pilon 1.17 installed https://www.uppmax.uu.se/changelog Mon, 16 May 2016 11:58:00 GMT https://www.uppmax.uu.se/changelog 2016-05-16T11:58:00Z Micca 1.4.0 installed https://www.uppmax.uu.se/changelog Mon, 16 May 2016 11:57:00 GMT https://www.uppmax.uu.se/changelog 2016-05-16T11:57:00Z Matlab r2016a installed https://www.uppmax.uu.se/changelog Mon, 16 May 2016 11:56:00 GMT https://www.uppmax.uu.se/changelog 2016-05-16T11:56:00Z Stacks 1.40 installed https://www.uppmax.uu.se/changelog Mon, 16 May 2016 11:55:00 GMT https://www.uppmax.uu.se/changelog 2016-05-16T11:55:00Z GMAP/GSNAP modules installed on Milou and Tintin https://www.uppmax.uu.se/changelog Mon, 16 May 2016 11:54:00 GMT https://www.uppmax.uu.se/changelog 2016-05-16T11:54:00Z Blast databases were updated https://www.uppmax.uu.se/changelog Mon, 16 May 2016 11:52:00 GMT https://www.uppmax.uu.se/changelog 2016-05-16T11:52:00Z AdapterRemoval installed https://www.uppmax.uu.se/changelog Mon, 16 May 2016 11:51:00 GMT https://www.uppmax.uu.se/changelog 2016-05-16T11:51:00Z Blast has been upgraded to version 2.2.31+ on Milou and Tintin. https://www.uppmax.uu.se/changelog Mon, 07 Dec 2015 09:34:00 GMT https://www.uppmax.uu.se/changelog 2015-12-07T09:34:00Z GATK has been upgraded to version 3.5.0 on Milou and Tintin. https://www.uppmax.uu.se/changelog Mon, 07 Dec 2015 09:33:00 GMT https://www.uppmax.uu.se/changelog 2015-12-07T09:33:00Z We have installed many Perl modules/packages https://www.uppmax.uu.se/changelog Tue, 08 Dec 2015 09:31:00 GMT https://www.uppmax.uu.se/changelog 2015-12-08T09:31:00Z