[bio] pbmm2/1.13.0 installed on all systems</h1> <article> <h1>[bio] pbmm2/1.13.0 installed on all systems</h1> <p>Sun, 24 Sep 2023 14:09:00 GMT</p> <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> </article> <article> <h1>[apps] Matlab R2023a installed on all systems</h1> <p>Fri, 15 Sep 2023 14:09:00 GMT</p> <p><a href="https://se.mathworks.com/">MATLAB </a>(a proprietary multi-paradigm programming language and numeric computing environment ) version R2023a installed on all systems as module matlab/R2023a.</p> </article> <article> <h1>[bio] paml/4.10.7 installed on all systems</h1> <p>Fri, 25 Aug 2023 14:28:00 GMT</p> <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 /> </p> <p></p> </article> <article> <h1>[bio] phyx/1.3 installed on all systems</h1> <p>Wed, 16 Aug 2023 09:19:00 GMT</p> <p>phyx (phyx performs phylogenetics analyses on trees and sequences) version 1.3 installed on all systems as module phyx/1.3. https://github.com/FePhyFoFum/phyx<br /> </p> </article> <article> <h1>[comp] python/3.11.4 and python3/3.11.4 installed on all systems</h1> <p>Mon, 07 Aug 2023 14:48:00 GMT</p> <p>The Python programming language version 3.11.4 plus a handful of widely used packages.</p> </article> <article> <h1>[bio] HyPhy/2.5.51-mpi installed on all systems</h1> <p>Tue, 27 Jun 2023 15:15:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] HyPhy/2.5.51 installed on all systems</h1> <p>Tue, 27 Jun 2023 15:14:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] InterProScan/5.62-94.0 installed on all systems</h1> <p>Tue, 27 Jun 2023 11:07:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] Multi-CSAR/20180316-8fd582c installed on all systems</h1> <p>Wed, 21 Jun 2023 14:18:00 GMT</p> <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> </article> <article> <h1>[bio] Juicer/2.0 installed on all systems</h1> <p>Tue, 30 May 2023 11:47:00 GMT</p> <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 /> </p> </article> <article> <h1>[apps] python_GIS_packages/3.10.8 installed on all systems</h1> <p>Tue, 30 May 2023 11:32:00 GMT</p> <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> </article> <article> <h1>[apps] Mathematica 13.2 installed on Rackham and Snowy</h1> <p>Mon, 08 May 2023 06:42:00 GMT</p> <p>Mathematica: high-powered computation with thousands of Wolfram Language functions, natural language input, real-world data, mobile support. https://www.wolfram.com/mathematica/</p> </article> <article> <h1>[bio] VarDictJava/1.8.3 installed on all systems</h1> <p>Thu, 04 May 2023 13:45:00 GMT</p> <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 /> </p> </article> <article> <h1>[apps] WPS/4.3.1 installed on Rackham and Snowy</h1> <p>Tue, 11 Apr 2023 09:32:00 GMT</p> <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 /> </p> <p></p> </article> <article> <h1>[apps] WRF/4.3.0-dm-gcc installed on Rackham and Snowy</h1> <p>Tue, 11 Apr 2023 09:30:00 GMT</p> <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 as module WRF/4.3.0-dm-gcc.<br /> </p> <p></p> </article> <article> <h1>[bio] snakemake/7.25.0 installed on all systems</h1> <p>Tue, 11 Apr 2023 09:28:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] IRMA/1.0.3 installed on all systems</h1> <p>Tue, 11 Apr 2023 09:25:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] XP-CLR/1.1.2 installed on all systems</h1> <p>Sat, 11 Mar 2023 11:45:00 GMT</p> <p><a href="https://github.com/hardingnj/xpclr">XP-CLR</a> (Code to compute xp-clr values as per Chen, Patterson & Reich 2010) version 1.1.2 installed on all systems as module XP-CLR/1.1.2.</p> <p></p> </article> <article> <h1>[bio] dentist/4.0.0 installed on all systems</h1> <p>Sat, 11 Mar 2023 11:12:00 GMT</p> <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> </article> <article> <h1>[apps] Moses/4.0 installed on all systems</h1> <p>Mon, 06 Mar 2023 10:10:00 GMT</p> <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> </article> <article> <h1>[bio] MEMEsuite/5.5.1 installed on all systems</h1> <p>Thu, 02 Mar 2023 15:07:00 GMT</p> <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> </article> <article> <h1>[bio] PCAngsd/1.11 installed on all systems</h1> <p>Thu, 02 Mar 2023 15:04:00 GMT</p> <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> </article> <article> <h1>[bio] Cytoscape/3.9.1 installed on all systems</h1> <p>Thu, 02 Mar 2023 14:59:00 GMT</p> <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 /> </p> </article> <article> <h1>[apps] VSCodium/latest installed on all systems</h1> <p>Mon, 27 Feb 2023 08:10:00 GMT</p> <p><a href="https://vscodium.com/">VSCodium</a> is a community-driven, freely-licensed binary distribution of Microsofts editor VS Code.</p> </article> <article> <h1>[bio] SLiM/4.0.1 installed on all systems</h1> <p>Fri, 17 Feb 2023 10:21:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] gcta/1.94.1 installed on all systems</h1> <p>Fri, 03 Feb 2023 12:20:00 GMT</p> <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 /> </p> <p></p> </article> <article> <h1>[comp] julia/1.6.7_LTS installed on all systems</h1> <p>Mon, 30 Jan 2023 12:58:00 GMT</p> <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 /> </p> </article> <article> <h1>[comp] julia/1.8.5 installed on all systems</h1> <p>Mon, 30 Jan 2023 12:54:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] plink2/2.00-alpha-3.7-20221024 installed on all systems</h1> <p>Tue, 24 Jan 2023 08:56:00 GMT</p> <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 /> </p> <p></p> </article> <article> <h1>[libs] PROJ/9.1.1 installed on all systems</h1> <p>Tue, 10 Jan 2023 13:56:00 GMT</p> <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 /> </p> <p></p> </article> <article> <h1>[libs] libtiff/4.5.0 installed on all systems</h1> <p>Tue, 10 Jan 2023 12:34:00 GMT</p> <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 /> </p> <p></p> </article> <article> <h1>[bio] delly/1.1.6 installed on all systems</h1> <p>Tue, 13 Dec 2022 09:33:00 GMT</p> <p> <a href="https://github.com/dellytools/delly">delly</a> (an integrated structural variant (SV) prediction method that can<br /> discover, genotype and visualize deletions, tandem duplications, inversions<br /> and translocations at single-nucleotide resolution in short-read and<br /> long-read massively parallel sequencing data) version 1.1.6 installed on<br /> all systems as module delly/1.1.6.</p> </article> <article> <h1>[bio] MMseqs2/14-7e284 installed on all systems</h1> <p>Fri, 04 Nov 2022 07:14:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] htseq/2.0.2 installed on all systems</h1> <p>Thu, 03 Nov 2022 10:54:00 GMT</p> <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> </article> <article> <h1>[bio] spaln/2.4.13c installed on all systems</h1> <p>Thu, 27 Oct 2022 09:50:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] fastsimcoal/2.7.93 installed on all systems</h1> <p>Wed, 26 Oct 2022 12:50:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] nf-core/2.6 installed on all systems</h1> <p>Tue, 25 Oct 2022 11:31:00 GMT</p> <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> </article> <article> <h1>[bio] Nextflow/22.10.0 installed on all systems</h1> <p>Tue, 25 Oct 2022 10:45:00 GMT</p> <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> </article> <article> <h1>[bio] abricate/1.0.1-20200512-955d402 installed on all systems</h1> <p>Mon, 24 Oct 2022 14:47:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] any2fasta/0.4.2 installed on all systems</h1> <p>Thu, 20 Oct 2022 15:30:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] datamash/1.8 installed on all systems</h1> <p>Mon, 17 Oct 2022 13:52:00 GMT</p> <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> </article> <article> <h1>[bio] KrakenUniq/1.0.1 installed on all systems</h1> <p>Wed, 12 Oct 2022 15:28:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] pathPhynder/1.a-20221011-a407a97 installed on all systems</h1> <p>Mon, 10 Oct 2022 11:41:00 GMT</p> <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> </article> <article> <h1>[data] fastq_screen_data/latest updated on all systems</h1> <p>Tue, 04 Oct 2022 13:57:00 GMT</p> <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> </article> <article> <h1>[libs] gsl/2.7 installed on all systems</h1> <p>Tue, 04 Oct 2022 13:16:00 GMT</p> <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> </article> <article> <h1>[libs] GEOS/3.11.0-gcc10.3.0 installed on all systems</h1> <p>Tue, 04 Oct 2022 12:29:00 GMT</p> <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> </article> <article> <h1>[data] KrakenUniq_data/latest installed on all systems</h1> <p>Tue, 04 Oct 2022 11:29:00 GMT</p> <p>KrakenUniq_data (latest database build for KrakenUniq, plus prebuilt databases available externally) version latest installed on all systems as module KrakenUniq_data/latest. See 'module help KrakenUniq_data/latest' for more information.<br /> </p> </article> <article> <h1>[bio] fastq_screen/0.15.2 installed on all systems</h1> <p>Tue, 04 Oct 2022 08:41:00 GMT</p> <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 /> </p> </article> <article> <h1>[apps] VMD/1.9.3 installed on all systems</h1> <p>Fri, 30 Sep 2022 15:14:00 GMT</p> <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 /> </p> <p></p> </article> <article> <h1>[apps] VMD/1.9.4-alpha-57 installed on all systems</h1> <p>Fri, 30 Sep 2022 15:12:00 GMT</p> <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 /> </p> <p></p> </article> <article> <h1>[bio] KrakenUniq/1.0.0 installed on all systems</h1> <p>Fri, 30 Sep 2022 09:06:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] minimap2/2.24-r1122 installed on all systems</h1> <p>Wed, 28 Sep 2022 06:02:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] vcfstats/0.4.2 installed on all systems</h1> <p>Tue, 27 Sep 2022 13:35:00 GMT</p> <p>[bio] vcfstats/0.4.2 installed on all systems</p> </article> <article> <h1>[bio] GeneMark/4.69-es installed on all systems</h1> <p>Tue, 27 Sep 2022 08:06:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] phast/1.6 installed on all systems</h1> <p>Wed, 21 Sep 2022 13:02:00 GMT</p> <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 /> </p> <p></p> </article> <article> <h1>[bio] satsuma2/37c5f38-20200304 installed on all systems</h1> <p>Wed, 21 Sep 2022 13:01:00 GMT</p> <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 /> </p> <p></p> </article> <article> <h1>[libs] zlib/1.2.12 installed on all systems</h1> <p>Tue, 20 Sep 2022 17:06:00 GMT</p> <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 /> </p> </article> <article> <h1>[libs] bzip2/1.0.8 installed on all system</h1> <p>Tue, 20 Sep 2022 13:10:00 GMT</p> <p><a href="https://sourceware.org/bzip2">bzip2</a> version 1.0.8 installed on all systems as module bzip2/1.0.8.<br /> </p> </article> <article> <h1>[apps] RStudio/2022.07.1-554 installed on all systems</h1> <p>Tue, 20 Sep 2022 10:42:00 GMT</p> <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 /> </p> </article> <article> <h1>[apps] xz/5.2.6 installed on all systems</h1> <p>Tue, 20 Sep 2022 10:12:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] grenedalf/0.2.0-beta installed on all systems</h1> <p>Tue, 20 Sep 2022 06:17:00 GMT</p> <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 /> </p> </article> <article> <h1>[libs] libcurl/7.85.0 installed on all systems</h1> <p>Mon, 19 Sep 2022 16:37:00 GMT</p> <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 /> </p> </article> <article> <h1>[apps] texlive/2022-09-18 installed on all systems</h1> <p>Mon, 19 Sep 2022 15:14:00 GMT</p> <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 /> </p> </article> <article> <h1>[libs] zstd/1.5.2 installed on all systems</h1> <p>Mon, 19 Sep 2022 13:05:00 GMT</p> <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> </article> <article> <h1>[bio] octopus/17a597d-20220708</h1> <p>Fri, 16 Sep 2022 09:10:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] MAGeCK2/20211209-435eacd</h1> <p>Tue, 06 Sep 2022 10:44:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] MAPGD/0.4.40 installed on all systems</h1> <p>Mon, 05 Sep 2022 09:05:00 GMT</p> <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 /> </p> </article> <article> <h1>[build] bubblewrap/0.6.2 installed on all systems</h1> <p>Wed, 10 Aug 2022 11:33:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] ORFfinder/0.4.3 installed on all systems</h1> <p>Tue, 14 Jun 2022 09:21:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] fastsimcoal/2.7.9 installed on all systems</h1> <p>Tue, 31 May 2022 08:56:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] Arlequin/3.5.2.2 installed on all systems</h1> <p>Tue, 31 May 2022 08:54:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] ABCtoolbox/20131120 installed on all systems</h1> <p>Tue, 31 May 2022 08:35:00 GMT</p> <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 /> </p> </article> <article> <h1>[comp] julia/1.7.2 installed on all systems</h1> <p>Tue, 31 May 2022 07:20:00 GMT</p> <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> </article> <article> <h1>[bio] spaln/2.4.9 installed on all systems</h1> <p>Wed, 11 May 2022 08:03:00 GMT</p> <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 /> </p> </article> <article> <h1>[libs] slurm-drmaa/1.1.3-slurm21.08.8 installed on all systems</h1> <p>Tue, 10 May 2022 07:59:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] KrakenUniq/0.6 installed on all systems</h1> <p>Mon, 09 May 2022 12:57:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] bwa-mem2/2.2.1-20211213-edc703f installed on all systems</h1> <p>Thu, 05 May 2022 08:13:00 GMT</p> <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> </article> <article> <h1>[bio] cutadapt/4.0 installed on all systems</h1> <p>Tue, 03 May 2022 21:42:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] SQuIRE/885bf4d-20190301 installed on all systems</h1> <p>Wed, 27 Apr 2022 08:21:00 GMT</p> <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 /> </p> <p></p> </article> <article> <h1>[bio] BioBloomTools/2.3.3-20210218-151b0c0 installed on all systems</h1> <p>Tue, 12 Apr 2022 09:08:00 GMT</p> <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 /> </p> </article> <article> <h1>[comp] LLVM/13.0.1 installed on all systems</h1> <p>Wed, 06 Apr 2022 06:24:00 GMT</p> <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> </article> <article> <h1>[bio] pblat-cluster/1.1 installed on all systems</h1> <p>Tue, 05 Apr 2022 20:45:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] pblat/2.5 installed on all systems</h1> <p>Tue, 05 Apr 2022 20:09:00 GMT</p> <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 /> </p> </article> <article> <h1>[comp] binutils/2.38 installed on all systems</h1> <p>Tue, 05 Apr 2022 16:32:00 GMT</p> <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 /> </p> </article> <article> <h1>[comp] gdb/11.2 installed on all systems</h1> <p>Mon, 04 Apr 2022 15:09:00 GMT</p> <p>gdb version 11.2 installed on all systems as module gdb/11.2.</p> </article> <article> <h1>[bio] BlobToolKit/3.1.0 installed on all systems</h1> <p>Mon, 04 Apr 2022 15:09:00 GMT</p> <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> </article> <article> <h1>[bio] Kraken/1.1.1-20210927-375654f installed on all systems</h1> <p>Mon, 04 Apr 2022 11:28:00 GMT</p> <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> </article> <article> <h1>[bio] metaMATE/20220327-3cdacd7 installed on all systems</h1> <p>Mon, 04 Apr 2022 10:19:00 GMT</p> <div>metaMATE version 20220327-3cdacd7 installed on all systems as module metaMATE/20220327-3cdacd7.</div> <div>https://github.com/tjcreedy/metamate</div> </article> <article> <h1>[bio] CROP/1.33 installed on all systems</h1> <p>Mon, 04 Apr 2022 10:18:00 GMT</p> <div>CROP version 1.33 installed on all systems as module CROP/1.33.</div> <div>https://github.com/tingchenlab/CROP</div> </article> <article> <h1>[libs] libicu/5.2-4 installed on all systems</h1> <p>Thu, 31 Mar 2022 10:56:00 GMT</p> <p>The <a href="https://icu.unicode.org/">libicu</a> library on EL8 has been updated to v60 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> </article> <article> <h1>[libs] readline/6.2-11 installed on all systems</h1> <p>Thu, 31 Mar 2022 10:16:00 GMT</p> <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> </article> <article> <h1>[apps] python_ML_packages/3.9.5-cpu installed on all systems</h1> <p>Thu, 31 Mar 2022 07:29:00 GMT</p> <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> </article> <article> <h1>[apps] python_ML_packages/3.9.5-gpu installed on all systems</h1> <p>Thu, 31 Mar 2022 07:28:00 GMT</p> <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> </article> <article> <h1>[bio] ATLAS_aDNA/0.9.9 installed on all systems</h1> <p>Thu, 31 Mar 2022 07:27:00 GMT</p> <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> </article> <article> <h1>[bio] fastq_demux/20200918-1e2c079 installed on all systems</h1> <p>Thu, 31 Mar 2022 07:26:00 GMT</p> <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> </article> <article> <h1>[apps] PsN/5.3.0 installed on all systems</h1> <p>Thu, 31 Mar 2022 07:25:00 GMT</p> <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> </article> <article> <h1>[bio] metaMATE/20220327-3cdacd7 installed on all systems</h1> <p>Thu, 31 Mar 2022 07:23:00 GMT</p> <p>metaMATE version 20220327-3cdacd7 installed on all systems as module metaMATE/20220327-3cdacd7.</p> </article> <article> <h1>[libs] SDSL/2.1.1 installed on all systems</h1> <p>Wed, 30 Mar 2022 15:24:00 GMT</p> <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 /> </p> </article> <article> <h1>[libs] sparsehash/2.0.4 installed on all systems</h1> <p>Wed, 30 Mar 2022 13:30:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] muscle/5.1 installed on all systems</h1> <p>Tue, 29 Mar 2022 13:33:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] tRNAscan-SE/2.0.9 installed on all systems</h1> <p>Mon, 28 Mar 2022 09:33:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] infernal/1.1.4 installed on all systems</h1> <p>Mon, 28 Mar 2022 08:47:00 GMT</p> <p><a href="http://eddylab.org/infernal/">infernal</a> ("INFERence of RNA ALignment" -- 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 /> </p> </article> <article> <h1>[apps] gromacs/4.5.7.th.dp (double precision) is installed on Rackham</h1> <p>Mon, 21 Mar 2022 12:20:00 GMT</p> </article> <article> <h1>[bio] VESPA/1.0.1 installed on all systems</h1> <p>Mon, 21 Mar 2022 08:15:00 GMT</p> <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> </article> <article> <h1>[apps] CPLEXOptimizationStudio/20.10 installed on all systems</h1> <p>Fri, 18 Mar 2022 16:02:00 GMT</p> <p><a href="https://www.ibm.com/se-en/analytics/cplex-optimizer">CPLEX Optimization Studio</a> 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> </article> <article> <h1>[apps] CPLEXOptimizationStudio/12.9.0 installed on all systems</h1> <p>Fri, 18 Mar 2022 15:54:00 GMT</p> <p><a href="https://www.ibm.com/se-en/analytics/cplex-optimizer">CPLEX Optimization Studio</a> 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 /> </p> </article> <article> <h1>[bio] CAMMiQ/20211015-6142150 installed on all systems</h1> <p>Fri, 18 Mar 2022 15:32:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] fastp/0.23.2 installed on all systems</h1> <p>Tue, 15 Mar 2022 16:32:00 GMT</p> <p><a href="https://github.com/OpenGene/fastp">fastp</a> version 0.23.2 installed on all systems as module fastp/0.23.2. fastp is a 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> </article> <article> <h1>[data] Pfam/35.0 installed on all systems</h1> <p>Tue, 15 Mar 2022 12:58:00 GMT</p> <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> </article> <article> <h1>[apps] RStudio/2022.02.0-443 installed on all systems</h1> <p>Mon, 14 Mar 2022 11:05:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] BclConverter/3.9.3 installed on all systems</h1> <p>Wed, 09 Mar 2022 11:32:00 GMT</p> <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 /> </p> </article> <article> <h1>[libs] reinstalled SuperLU/5.2.1 with shared and static libraries</h1> <p>Tue, 08 Mar 2022 13:32:00 GMT</p> <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> </article> <article> <h1>[apps] PsN/5.3.0 installed on all systems</h1> <p>Mon, 07 Mar 2022 15:54:00 GMT</p> <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> </article> <article> <h1>[bio] atlas/0.9.9 installed on all systems</h1> <p>Mon, 07 Mar 2022 06:19:00 GMT</p> <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> </article> <article> <h1>[bio] fastq_demux/20200918-1e2c079 installed on all systems</h1> <p>Mon, 07 Mar 2022 06:19:00 GMT</p> <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> </article> <article> <h1>[bio] GAAS/1.2.0 installed on all systems</h1> <p>Fri, 25 Feb 2022 15:50:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] metaSNV/2.0.1 installed on all systems</h1> <p>Thu, 24 Feb 2022 11:48:00 GMT</p> <p>metaSNV (a metagenomic SNV calling pipeline.) version 2.0.1 installed on all systems as module metaSNV/2.0.1.</p> </article> <article> <h1>[bio] metaSNV/1.0.3 installed on all systems</h1> <p>Thu, 24 Feb 2022 11:47:00 GMT</p> <p>metaSNV (a metagenomic SNV calling pipeline.) version 1.0.3 installed on all systems as module metaSNV/1.0.3.</p> </article> <article> <h1>[apps] pandoc/2.17.1.1 installed on all systems</h1> <p>Thu, 24 Feb 2022 10:08:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] RevBayes/1.1.1-mpi installed on all systems</h1> <p>Mon, 21 Feb 2022 16:43:00 GMT</p> <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> </article> <article> <h1>[bio] RevBayes/1.1.1 installed on all systems</h1> <p>Mon, 21 Feb 2022 16:42:00 GMT</p> <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> </article> <article> <h1>[libs] boost/1.78.0-gcc11.2.0_mpi4.1.2 installed on all systems</h1> <p>Mon, 21 Feb 2022 16:41:00 GMT</p> <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> </article> <article> <h1>[libs] boost/1.78.0_gcc11.2.0 installed on all systems</h1> <p>Mon, 21 Feb 2022 16:41:00 GMT</p> <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> </article> <article> <h1>[comp] Intel OneAPI installed on all systems</h1> <p>Mon, 21 Feb 2022 12:49:00 GMT</p> <p>The package Intel OneAPI with subpackages are installed on all systems</p> </article> <article> <h1>[build] cmake/3.22.2 installed on all systems</h1> <p>Fri, 18 Feb 2022 11:21:00 GMT</p> <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 /> </p> </article> <article> <h1>[apps] gromacs/2021.5.th installed on Rackham and Snowy</h1> <p>Fri, 18 Feb 2022 09:26:00 GMT</p> <p>[apps] gromacs/2021.5.th installed on Rackham and Snowy</p> </article> <article> <h1>[bio] Kraken2/2.1.2-20211210-4f648f5 installed on all systems</h1> <p>Sun, 13 Feb 2022 14:14:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] diamond/2.0.14 installed on all systems</h1> <p>Fri, 11 Feb 2022 14:45:00 GMT</p> <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 2.0.14 installed on all systems as module diamond/2.0.14.<br /> </p> </article> <article> <h1>[data] ncbi_taxonomy/latest installed on all systems</h1> <p>Fri, 11 Feb 2022 13:50:00 GMT</p> <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 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 <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> </article> <article> <h1>[apps] Amber version 20 installed on Rackham and Snowy (GPU)</h1> <p>Thu, 10 Feb 2022 15:05:00 GMT</p> <p>[apps] <a href="https://ambermd.org/GetAmber.php">Amber</a>, a suite of biomolecular simulation programs, version 20 is installed on Rackham and Snowy (GPU) as module Amber/20 for Rackham and Amber/20-GPU for Snowy GPU with CUDA support. </p> </article> <article> <h1>[bio] FusionCatcher/1.33 installed on all systems</h1> <p>Thu, 10 Feb 2022 13:58:00 GMT</p> <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 /> </p> </article> <article> <h1>[apps] ORCA 5.0.2 installed on Rackham and Snowy</h1> <p>Thu, 10 Feb 2022 09:04:00 GMT</p> <p><a href="https://orcaforum.kofo.mpg.de">ORCA</a> version 5.0.2 is installed on Rackham and Snowy as module ORCA/5.0.2. ORCA 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> </article> <article> <h1>[bio] MultiQC/1.12 installed on all systems</h1> <p>Wed, 09 Feb 2022 08:55:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] ngsLD/1.1.1 installed on all systems</h1> <p>Tue, 01 Feb 2022 09:24:00 GMT</p> <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 /> </p> </article> <article> <h1>[libs] slurm-drmaa/1.1.3-slurm19.05.8 installed on all systems</h1> <p>Mon, 31 Jan 2022 15:08:00 GMT</p> <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> </article> <article> <h1>[bio] PEPPER-Margin-DeepVariant/r0.4 installed on all systems</h1> <p>Mon, 31 Jan 2022 09:07:00 GMT</p> <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> </article> <article> <h1>[bio] HUMAnN/3.0.0.a.4 installed on all systems</h1> <p>Mon, 31 Jan 2022 09:06:00 GMT</p> <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> </article> <article> <h1>[bio] Nextflow/21.10.6 installed on all systems</h1> <p>Mon, 31 Jan 2022 09:06:00 GMT</p> <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> </article> <article> <h1>[bio] PEPPER-Margin-DeepVariant/r0.7 installed on all systems</h1> <p>Mon, 31 Jan 2022 09:05:00 GMT</p> <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> </article> <article> <h1>[bio] DeepVariant/1.3.0 installed on all systems</h1> <p>Mon, 31 Jan 2022 09:04:00 GMT</p> <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> </article> <article> <h1>[libs] PROJ/8.1.0 installed on all systems</h1> <p>Fri, 28 Jan 2022 15:51:00 GMT</p> <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 /> </p> <p></p> </article> <article> <h1>[bio] rMATS-turbo/4.1.2 installed on all systems</h1> <p>Fri, 28 Jan 2022 09:28:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] SvABA/1.1.3-20201112-0f60e36 installed on all systems</h1> <p>Thu, 27 Jan 2022 13:57:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] SNP2HLA/1.0.3 installed on all systems</h1> <p>Thu, 27 Jan 2022 12:52:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] CNVnator/0.4.1-20200707-c73786d installed on all systems</h1> <p>Tue, 25 Jan 2022 15:28:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] NextGenMap/0.5.5 installed on all systems</h1> <p>Mon, 24 Jan 2022 15:54:00 GMT</p> <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 /> </p> </article> <article> <h1>[apps] MultiBUGS/2.0 installed on all systems</h1> <p>Fri, 21 Jan 2022 16:16:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] paml/4.9j installed on all systems</h1> <p>Thu, 20 Jan 2022 08:48:00 GMT</p> <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 /> </p> <p></p> </article> <article> <h1>[apps] tesseract/4.1.3 installed on all systems</h1> <p>Wed, 19 Jan 2022 14:44:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] gmap-gsnap/2017-11-15 and gmap-gsnap/2021-12-17 nstalled on all systems</h1> <p>Tue, 18 Jan 2022 11:52:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] TSEBRA/1.0.3-20211126-336c380 installed on all systems</h1> <p>Mon, 17 Jan 2022 06:24:00 GMT</p> <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 /> </p> </article> <article> <h1>[comp] git/2.34.1 installed on all systems</h1> <p>Mon, 10 Jan 2022 14:24:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] RAxML-NG/1.1.0 and RAxML-NG/1.1.0-mpi installed on all systems</h1> <p>Mon, 10 Jan 2022 14:15:00 GMT</p> <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 /> </p> </article> <article> <h1>[apps] paraview/5.9.1 installed on all systems</h1> <p>Wed, 22 Dec 2021 14:29:00 GMT</p> <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 "vgl_paraview".<br /> </p> <p></p> </article> <article> <h1>[comp] julia/1.6.3 installed on all systems</h1> <p>Wed, 22 Dec 2021 11:10:00 GMT</p> <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 /> </p> <p></p> </article> <article> <h1>[comp] julia/1.0.5_LTS installed on all systems</h1> <p>Wed, 22 Dec 2021 11:08:00 GMT</p> <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 /> </p> <p></p> </article> <article> <h1>[bio] Salmon/1.6.0 installed on all systems</h1> <p>Wed, 22 Dec 2021 10:25:00 GMT</p> <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 /> </p> <p></p> </article> <article> <h1>[bio] MetaCRAST/20200310-ed82df4 installed on all systems</h1> <p>Mon, 13 Dec 2021 13:11:00 GMT</p> <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> </article> <article> <h1>[bio] Guppy/5.0.16-gpu and Guppy/5.0.16-cpu nstalled on all systems</h1> <p>Fri, 10 Dec 2021 12:53:00 GMT</p> <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 systems as module Guppy/5.0.16-gpu.</p> <p><a href="https://nanoporetech.com/nanopore-sequencing-data-analysis">Guppy</a> (Oxford Nanopore neural-net basecaller, <strong>CPU only</strong>) version 5.0.16 installed on all systems as module Guppy/5.0.16-cpu.</p> </article> <article> <h1>[bio] bismark/0.23.1 installed on all systems</h1> <p>Wed, 08 Dec 2021 08:00:00 GMT</p> <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> </article> <article> <h1>[apps] RSPt/2021-10-04 installed on Rackham and Snowy</h1> <p>Fri, 03 Dec 2021 12:40:00 GMT</p> <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. Version dated 2021-10-04 installed on all systems as module RSPt/2021-10-04.</p> </article> <article> <h1>[bio] Chromium-cellranger/6.1.2 installed on all systems</h1> <p>Fri, 03 Dec 2021 12:31:00 GMT</p> <p>Chromium-cellranger (Cell line analysis system) version 6.1.2 installed on all systems as module cellranger/6.1.2.</p> </article> <article> <h1>[bio] fastqtk/0.27 installed on all systems</h1> <p>Fri, 03 Dec 2021 10:17:00 GMT</p> <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 /> </p> </article> <article> <h1>[apps] vim/8.2.3701 installed on all systems</h1> <p>Tue, 30 Nov 2021 09:07:00 GMT</p> <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 /> </p> </article> <article> <h1>[apps] QuantumESPRESSO/6.8 installed on Rackham and Snowy</h1> <p>Mon, 29 Nov 2021 16:07:00 GMT</p> <p><a href="http://www.quantum-espresso.org" title="QuantumESPRESSO">QuantumESPRESSO</a> 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. Versions 6.8 installed on Rackham and Snowy as module QuantumESPRESSO/6.8 and QuantumESPRESSO/6.7MaX-Release, respectively.</p> </article> <article> <h1>[bio] trimmomatic/0.39 installed on all systems</h1> <p>Wed, 17 Nov 2021 15:13:00 GMT</p> <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> </article> <article> <h1>[bio] fastp/0.23.1 installed on all systems</h1> <p>Sun, 14 Nov 2021 15:23:00 GMT</p> <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 /> </p> </article> <article> <h1>[comp] nasm/2.15.05 installed on all systems</h1> <p>Sun, 14 Nov 2021 15:05:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] Conterminator/20200601-570993b installed on all systems</h1> <p>Fri, 12 Nov 2021 09:17:00 GMT</p> <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> </article> <article> <h1>[apps] R_packages/4.1.1 installed on all systems</h1> <p>Thu, 11 Nov 2021 15:00:00 GMT</p> <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> </article> <article> <h1>[apps] Cromwell/71 installed on all systems</h1> <p>Wed, 10 Nov 2021 07:49:00 GMT</p> <p>Cromwell (Cromwell is an open-source Workflow Management System for bioinformatics) version 71 installed on all systems as module Cromwell/71.</p> </article> <article> <h1>[bio] vsearch/2.18.0 installed on all systems</h1> <p>Tue, 09 Nov 2021 15:25:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] Bamsurgeon/1.3 installed on all systems</h1> <p>Tue, 09 Nov 2021 11:39:00 GMT</p> <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> </article> <article> <h1>pixy/1.2.5.beta1 installed on all systems</h1> <p>Tue, 09 Nov 2021 08:29:00 GMT</p> <p>pixy (pixy is a command-line tool for painlessly estimating average nucleotide diversity within (π) and between (dxy) populations from a VCF) version 1.2.5.beta1 installed on all systems as module pixy/1.2.5.beta1.</p> </article> <article> <h1>[bio] htslib/1.14 installed on all systems</h1> <p>Mon, 08 Nov 2021 15:53:00 GMT</p> <p>htslib (Tools for working with SAM/BAM/variant files) version 1.14 installed on all systems as module htslib/1.14.</p> </article> <article> <h1>[bio] bcftools/1.14 installed on all systems</h1> <p>Mon, 08 Nov 2021 15:52:00 GMT</p> <p>bcftools (Tools for working with variant files) version 1.14 installed on all systems as module bcftools/1.14.</p> </article> <article> <h1>[bio] NeuSomatic/0.2.1 installed on all systems</h1> <p>Mon, 08 Nov 2021 12:19:00 GMT</p> <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> </article> <article> <h1>[bio] samtools/1.14 installed on all systems</h1> <p>Mon, 08 Nov 2021 12:14:00 GMT</p> <p>samtools (Tools for working with SAM/BAM/variant files) version 1.14 installed on all systems as module samtools/1.14</p> </article> <article> <h1>[bio] pysam/0.17.0-python3.9.5 installed on all systems</h1> <p>Mon, 08 Nov 2021 11:51:00 GMT</p> <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> </article> <article> <h1>[bio] VIBRANT/1.2.1 installed on all systems</h1> <p>Mon, 08 Nov 2021 07:51:00 GMT</p> <p>VIBRANT (Virus Identification By iteRative ANnoTation) version 1.2.1 installed on all systems as module VIBRANT/1.2.1.</p> </article> <article> <h1>[data] WPS-geog/4 installed on all systems</h1> <p>Thu, 28 Oct 2021 12:50:00 GMT</p> <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> </article> <article> <h1>[bio] canu/2.2 installed on all systems</h1> <p>Mon, 25 Oct 2021 14:04:00 GMT</p> <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> </article> <article> <h1>[bio] Flye/2.9 installed on all systems</h1> <p>Mon, 25 Oct 2021 14:03:00 GMT</p> <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> </article> <article> <h1>[bio] SMARTdenovo/20210224-8488de9 installed on all systems</h1> <p>Mon, 25 Oct 2021 13:50:00 GMT</p> <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> </article> <article> <h1>[bio] NextDenovo/2.5.0 installed on all systems</h1> <p>Mon, 25 Oct 2021 13:48:00 GMT</p> <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> </article> <article> <h1>[bio] star/2.7.9a installed on all systems</h1> <p>Wed, 20 Oct 2021 16:10:00 GMT</p> <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 /> </p> </article> <article> <h1>[apps] rclone/1.56.2 installed on all systems</h1> <p>Tue, 19 Oct 2021 10:29:00 GMT</p> <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> </article> <article> <h1>[bio] NextDenovo/2.4.0 installed on all systems</h1> <p>Fri, 15 Oct 2021 04:59:00 GMT</p> <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> </article> <article> <h1>[bio] phaser/20210423-5d4926d installed on all systems</h1> <p>Fri, 15 Oct 2021 04:54:00 GMT</p> <p>phaser (phasing and Allele Specific Expression from RNA-seq) version 20210423-5d4926d installed on all systems as module phaser/20210423-5d4926d</p> </article> <article> <h1>[bio] Racon/1.4.21 installed on all systems</h1> <p>Mon, 11 Oct 2021 15:17:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] ucsc-utilities/v421 installed on all systems</h1> <p>Fri, 08 Oct 2021 15:43:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] snakemake/6.9.1 installed on all systems</h1> <p>Mon, 04 Oct 2021 08:12:00 GMT</p> <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> </article> <article> <h1>[bio] NgsRelate/2.0 installed on all systems</h1> <p>Tue, 21 Sep 2021 15:25:00 GMT</p> <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 /> </p> <p></p> </article> <article> <h1>[bio] maker/3.01.04 installed on all systems</h1> <p>Tue, 21 Sep 2021 15:18:00 GMT</p> <p>maker (Portable and easily configurable genome annotation pipeline) version 3.01.04 installed on all systems as module maker/3.01.04</p> </article> <article> <h1>[bio] nf-core-pipelines/latest installed on all systems</h1> <p>Tue, 21 Sep 2021 15:17:00 GMT</p> <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> </article> <article> <h1>[bio] alphafold/2.0.0 installed on all systems</h1> <p>Tue, 21 Sep 2021 15:16:00 GMT</p> <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> </article> <article> <h1>[bio] MACS/3.0.0a6 installed on all systems</h1> <p>Mon, 20 Sep 2021 06:33:00 GMT</p> <p>MACS (Model-based Analysis of ChIP-Seq) version 3.0.0a6 installed on all systems as module MACS/3.0.0a6.</p> </article> <article> <h1>[bio] IMAP/1.0 installed on all systems</h1> <p>Thu, 09 Sep 2021 08:22:00 GMT</p> <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> </article> <article> <h1>[bio] trinity/2.13.2 installed on all systems</h1> <p>Thu, 09 Sep 2021 07:32:00 GMT</p> <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 /> </p> </article> <article> <h1>[apps] R/4.1.1 installed on all systems</h1> <p>Mon, 06 Sep 2021 13:06:00 GMT</p> <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> </article> <article> <h1>[libs] cairo/1.17.4 installed on all systems</h1> <p>Mon, 06 Sep 2021 09:52:00 GMT</p> <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 /> </p> </article> <article> <h1>[apps] texlive/2021 installed on all systems</h1> <p>Tue, 31 Aug 2021 15:41:00 GMT</p> <p>A full installation of <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> </article> <article> <h1>[apps] SAIGE/0.44.6.5 installed on all systems</h1> <p>Fri, 27 Aug 2021 15:13:00 GMT</p> <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 > 400,000).) version 0.44.6.5 installed on all systems as module SAIGE/0.44.6.5.<br /> </p> </article> <article> <h1>[libs] ARPACK-NG/3.8.0 installed on all systems</h1> <p>Wed, 18 Aug 2021 12:49:00 GMT</p> <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> </article> <article> <h1>[libs] SuperLU/5.2.1 installed on all systems</h1> <p>Tue, 17 Aug 2021 10:07:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] medaka/1.4.3 Installed on all systems</h1> <p>Mon, 16 Aug 2021 07:45:00 GMT</p> <p>[bio] medaka/1.4.3 Installed on all systems</p> </article> <article> <h1>[libs] SymEngine/0.7.0 installed on all systems</h1> <p>Thu, 12 Aug 2021 10:54:00 GMT</p> <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> </article> <article> <h1>[bio] nf-core/2.1 Installed on all systems</h1> <p>Tue, 10 Aug 2021 09:07:00 GMT</p> <p>[bio] nf-core/2.1 Installed on all systems</p> </article> <article> <h1>[bio] InterProScan/5.52-86.0 Installed on all systems</h1> <p>Mon, 09 Aug 2021 10:54:00 GMT</p> <p>[bio] InterProScan/5.52-86.0 Installed on all systems</p> </article> <article> <h1>[bio] Stacks/2.59 installed on all systems</h1> <p>Fri, 06 Aug 2021 10:14:00 GMT</p> <p>Stacks version 2.59 installed on all systems as module Stacks/2.59.</p> </article> <article> <h1>[bio] TSEBRA/1.0.2-20210716-1f167ad installed on all systems</h1> <p>Mon, 19 Jul 2021 09:01:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] braker/2.1.6 installed on all systems</h1> <p>Wed, 07 Jul 2021 19:41:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] ProtHint/2.6.0 installed on all systems</h1> <p>Wed, 07 Jul 2021 19:08:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] GeneMark/4.68-es installed on all systems</h1> <p>Wed, 07 Jul 2021 18:59:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] PathPhynder Installed on all systems</h1> <p>Tue, 06 Jul 2021 12:57:00 GMT</p> <p>A workflow for ancient DNA placement into reference phylogenies.</p> </article> <article> <h1>[bio] Phynder Installed on all systems</h1> <p>Tue, 06 Jul 2021 12:43:00 GMT</p> <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> </article> <article> <h1>[libs] plumed/2.7.1-gcc installed on Rackham</h1> <p>Tue, 06 Jul 2021 12:26:00 GMT</p> <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> </article> <article> <h1>[apps] cp2k/8.1-gcc installed on Rackham</h1> <p>Tue, 06 Jul 2021 08:22:00 GMT</p> <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> </article> <article> <h1>[bio] MultiQC/1.11 installed on all systems</h1> <p>Mon, 05 Jul 2021 10:17:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] IMPUTE5/1.1.5 installed on all systems</h1> <p>Tue, 22 Jun 2021 13:15:00 GMT</p> <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/#impute-5</p> </article> <article> <h1>[comp] julia/1.6.1 installed on all systems</h1> <p>Tue, 22 Jun 2021 09:38:00 GMT</p> <p>julia version 1.6.1 installed on all systems as module julia/1.6.1</p> </article> <article> <h1>[bio] bonito/0.3.7-cpu installed on all systems</h1> <p>Fri, 18 Jun 2021 13:22:00 GMT</p> <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> </article> <article> <h1>[comp] python/3.9.5 installed on all systems</h1> <p>Thu, 03 Jun 2021 13:34:00 GMT</p> <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 'pip3 list' when the module is loaded.</p> </article> <article> <h1>[apps] emacs/27.2 installed on all systems</h1> <p>Thu, 03 Jun 2021 08:07:00 GMT</p> <p>[apps] emacs/27.2 installed on all systems</p> </article> <article> <h1>[bio] pizzly/0.37.3 installed on all systems</h1> <p>Wed, 02 Jun 2021 12:04:00 GMT</p> <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> </article> <article> <h1>[bio] EDirect/15.1 installed on all systems</h1> <p>Mon, 31 May 2021 12:55:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] gffread/0.12.6 installed on all systems</h1> <p>Mon, 31 May 2021 12:18:00 GMT</p> <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 /> </p> </article> <article> <h1>[libs] MPC/1.2.1 installed on all systems</h1> <p>Fri, 28 May 2021 12:51:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] KAT/2.4.2 now based on python/3.7.2</h1> <p>Fri, 28 May 2021 12:02:00 GMT</p> <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> </article> <article> <h1>[bio] annovar/2020.06.08 installed on all systems</h1> <p>Fri, 28 May 2021 11:58:00 GMT</p> <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. The databases have been organised into data modules and the latest are found in the data module annovar_data/2021.05.18.</p> </article> <article> <h1>[bio] FALCON/2018.31.08-03.06 installed on all systems</h1> <p>Tue, 18 May 2021 11:22:00 GMT</p> <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> </article> <article> <h1>[bio] trinotate/3.2.2 installed on all systems</h1> <p>Wed, 12 May 2021 15:11:00 GMT</p> <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 /> </p> </article> <article> <h1>[libs] OpenBLAS 0.3.15 installed in several versions on all clusters</h1> <p>Tue, 11 May 2021 13:06:00 GMT</p> <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. openblas/0.3.15-singlethread does not have multithreading support.</p> </article> <article> <h1>[comp] bison/3.7.6 installed on all systems</h1> <p>Tue, 11 May 2021 09:01:00 GMT</p> <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 /> </p> </article> <article> <h1>[comp] flex/2.6.4 installed on all systems</h1> <p>Tue, 11 May 2021 08:23:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] CheckM/1.1.3 installed on all systems</h1> <p>Wed, 05 May 2021 12:24:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] metaWRAP/1.3.2 installed on all systems</h1> <p>Tue, 04 May 2021 13:18:00 GMT</p> <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> </article> <article> <h1>[bio] SMC++/1.15.2 installed on all systems</h1> <p>Tue, 04 May 2021 10:31:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] ArrowGrid/20191022-9759eb1 installed on all systems</h1> <p>Thu, 29 Apr 2021 15:55:00 GMT</p> <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. 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> </article> <article> <h1>[bio] pbbam/1.6.0 installed on all systems</h1> <p>Thu, 29 Apr 2021 15:24:00 GMT</p> <p><a href="https://github.com/PacificBiosciences/pbbam">pbbam</a> (software package provides components to create, query, & 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 /> </p> </article> <article> <h1>[build] ninja/1.10.0 installed on all systems</h1> <p>Thu, 29 Apr 2021 15:06:00 GMT</p> <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 /> </p> </article> <article> <h1>[build] meson/0.57.2 installed on all systems</h1> <p>Thu, 29 Apr 2021 14:48:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] snippy/4.6.0 installed on all systems</h1> <p>Thu, 29 Apr 2021 14:13:00 GMT</p> <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 /> </p> <p></p> </article> <article> <h1>[bio] HUMAnN/3.0 installed on all systems</h1> <p>Thu, 29 Apr 2021 11:59:00 GMT</p> <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 /> </p> <p></p> </article> <article> <h1>[bio] KneadData/0.10.0 installed on all systems</h1> <p>Thu, 29 Apr 2021 11:58:00 GMT</p> <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 /> </p> <p></p> </article> <article> <h1>[bio] PhyloPhlAn/3.0.2 installed on all systems</h1> <p>Thu, 29 Apr 2021 11:57:00 GMT</p> <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 /> </p> <p></p> </article> <article> <h1>[bio] MetaPhlAn3/3.0.8 installed on all systems</h1> <p>Thu, 29 Apr 2021 11:55:00 GMT</p> <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 /> </p> <p></p> </article> <article> <h1>[bio] BioBakery/3.0 installed on all systems</h1> <p>Thu, 29 Apr 2021 11:50:00 GMT</p> <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 including: HUMAnN/3.0, KneadData/0.10.0, MetaPhlAn3/3.0.8 and<br /> PhyloPhlAn/3.0.2</p> <p></p> <p></p> </article> <article> <h1>[bio] MELT modules have been removed</h1> <p>Tue, 27 Apr 2021 09:51:00 GMT</p> <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. Each user that wishes to use MELT must agree to the MELT license and install the software for themselves. Note that if the software is installed for a research group, each user in the research group must agree to the MELT license as well.</p> </article> <article> <h1>[bio] Salmon/1.4.0 installed on all systems</h1> <p>Fri, 23 Apr 2021 14:15:00 GMT</p> <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> </article> <article> <h1>[bio] bonito/0.3.8 and bonito/0.3.8-cpu installed on all systems</h1> <p>Fri, 23 Apr 2021 08:35:00 GMT</p> <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. 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 /> </p> </article> <article> <h1>[bio] unimap/0.1-r46-dirty installed on all systems</h1> <p>Thu, 22 Apr 2021 15:11:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] minimap2/2.18-r1015 installed on all systems</h1> <p>Thu, 22 Apr 2021 15:02:00 GMT</p> <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> </article> <article> <h1>[comp] k8/0.2.5 installed on all systems</h1> <p>Thu, 22 Apr 2021 14:13:00 GMT</p> <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. k8 is designed for enabling Javascript as a general scripting language, rather than server-side operations. <br /> </p> </article> <article> <h1>[libs] slurm-drmaa/1.1.2-slurm19.05.8 installed on all systems</h1> <p>Wed, 21 Apr 2021 11:19:00 GMT</p> <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> </article> <article> <h1>[bio] NextPolish/1.3.1 installed on all systems</h1> <p>Wed, 21 Apr 2021 11:18:00 GMT</p> <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 /> </p> </article> <article> <h1>[apps] jq/1.6 installed on all systems</h1> <p>Fri, 16 Apr 2021 13:39:00 GMT</p> <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> </article> <article> <h1>[apps] Tcl-Tk/8.6.11 installed on all systems</h1> <p>Fri, 16 Apr 2021 13:38:00 GMT</p> <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> </article> <article> <h1>[apps] FFmpeg/4.4 installed on all systems</h1> <p>Fri, 16 Apr 2021 13:36:00 GMT</p> <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> </article> <article> <h1>[apps] COIN-OR-OptimizationSuite/1.8.0 installed on all systems</h1> <p>Fri, 16 Apr 2021 13:35:00 GMT</p> <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 /> </p> </article> <article> <h1>[apps] R_packages/4.0.4 installed on all systems</h1> <p>Fri, 16 Apr 2021 13:17:00 GMT</p> <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>. There are a total of 20663 CRAN and BioConductor packages installed, out of 20751 packages available. 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> </article> <article> <h1>[comp] yasm/1.3.0 installed on all systems</h1> <p>Tue, 13 Apr 2021 14:30:00 GMT</p> <p><a href="https://yasm.tortall.net/">Yasm</a> (Yasm is a complete rewrite of the NASM assembler under the 'new' BSD License) version 1.3.0 installed on all systems as module yasm/1.3.0.<br /> </p> </article> <article> <h1>[libs] GEOS/3.9.1-gcc9.3.0 installed on all systems</h1> <p>Tue, 13 Apr 2021 13:25:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] BOLT-LMM/2.3.5 installed on all systems</h1> <p>Tue, 13 Apr 2021 13:18:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] HESS/0.5.4-beta installed on all systems</h1> <p>Tue, 13 Apr 2021 10:30:00 GMT</p> <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 /> </p> </article> <article> <h1>[apps] openbabel/3.1.1-gcc9.3.0 installed on all systems</h1> <p>Fri, 09 Apr 2021 16:00:00 GMT</p> <p><a href="https://github.com/openbabel/openbabel">Open Babel</a> (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 /> </p> </article> <article> <h1>[apps] OpenBUGS/3.2.3 installed on all systems</h1> <p>Fri, 09 Apr 2021 14:50:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] MetaPhlAn3/3.0 installed on all systems</h1> <p>Fri, 09 Apr 2021 14:19:00 GMT</p> <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> </article> <article> <h1>[bio] SLiM/3.6 installed on all systems</h1> <p>Thu, 08 Apr 2021 13:40:00 GMT</p> <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> </article> <article> <h1>[apps] ROOT/6.22.08 installed on all systems</h1> <p>Thu, 08 Apr 2021 13:36:00 GMT</p> <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 /> </p> </article> <article> <h1>[apps] ImageMagick/7.0.11-3 installed on all systems</h1> <p>Tue, 06 Apr 2021 12:12:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] MultiQC/1.10.1 installed on all systems</h1> <p>Tue, 06 Apr 2021 07:49:00 GMT</p> <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 /> </p> </article> <article> <h1>[apps] GhostPDL/9.53.3 installed on all systems</h1> <p>Fri, 26 Mar 2021 11:24:00 GMT</p> <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. This includes the well-known Ghostscript interpreter, and also includes header files and the shared library libgs.so.</p> </article> <article> <h1>[data] HaplotypeReferenceConsortium/r1.1 installed on all systems</h1> <p>Wed, 24 Mar 2021 12:28:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] MaSuRCA/4.0.2 installed on all systems</h1> <p>Tue, 23 Mar 2021 17:38:00 GMT</p> <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> </article> <article> <h1>[bio] Pilon/1.24 installed on all systems</h1> <p>Tue, 23 Mar 2021 17:36:00 GMT</p> <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 & Find variation among strains, including large event detection) version 1.24 installed on all systems as module Pilon/1.24.<br /> </p> </article> <article> <h1>[bio] NPStat/1 installed on all systems</h1> <p>Mon, 22 Mar 2021 13:33:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] MELT/2.2.2 installed on all systems</h1> <p>Mon, 22 Mar 2021 08:44:00 GMT</p> <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 /> </p> <p></p> </article> <article> <h1>[bio] DANPOS/3.1.1 and 2.2.2 installed on all systems</h1> <p>Fri, 19 Mar 2021 07:58:00 GMT</p> <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> </article> <article> <h1>[bio] bcftools/1.12, htslib/1.12, samtools/1.12 installed on all systems</h1> <p>Thu, 18 Mar 2021 11:39:00 GMT</p> <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> </article> <article> <h1>[bio] Roary/3.13.0 installed on all systems</h1> <p>Thu, 18 Mar 2021 08:48:00 GMT</p> <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> </article> <article> <h1>[bio] gmap-gsnap/2021-03-08 installed on all systems</h1> <p>Wed, 10 Mar 2021 13:53:00 GMT</p> <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 /> </p> </article> <article> <h1>[libs] protobuf/3.15.5 and protobuf/3.15.5-gcc9.3.0 installed on all systems</h1> <p>Tue, 09 Mar 2021 11:14:00 GMT</p> <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. 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 /> </p> </article> <article> <h1>[bio] Rcorrector/1.0.4 installed on all systems</h1> <p>Mon, 08 Mar 2021 14:31:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] beast2/2.6.3 installed on all systems</h1> <p>Mon, 08 Mar 2021 13:29:00 GMT</p> <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. All packages as available 2021-03-08 are also installed.</p> </article> <article> <h1>[libs] libsodium/1.0.18-stable installed on all systems</h1> <p>Mon, 08 Mar 2021 12:03:00 GMT</p> <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 /> </p> </article> <article> <h1>[libs] libzmq/4.3.4 installed on all systems</h1> <p>Mon, 08 Mar 2021 11:34:00 GMT</p> <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 /> </p> </article> <article> <h1>[libs] libwebp/1.2.0 installed on all systems</h1> <p>Fri, 05 Mar 2021 13:04:00 GMT</p> <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 /> </p> </article> <article> <h1>[apps] RStudio/1.4.1106 installed on all systems</h1> <p>Fri, 05 Mar 2021 12:47:00 GMT</p> <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> </article> <article> <h1>[bio] snpAD/0.3.4 installed on all systems</h1> <p>Tue, 02 Mar 2021 13:53:00 GMT</p> <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> </article> <article> <h1>[apps] gromacs/2021.1.th installed on Rackham and Snowy</h1> <p>Fri, 26 Feb 2021 07:57:00 GMT</p> </article> <article> <h1>[apps] Vapor/3.3.0 installed on all systems</h1> <p>Mon, 22 Feb 2021 10:45:00 GMT</p> <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> </article> <article> <h1>[bio] Shasta/0.7.0 installed on all systems</h1> <p>Thu, 11 Feb 2021 13:16:00 GMT</p> <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 /> </p> <p></p> </article> <article> <h1>[bio] FastML/3.11 installed on all systems</h1> <p>Wed, 10 Feb 2021 15:09:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] FastME/2.1.6.2 installed on all systems</h1> <p>Wed, 10 Feb 2021 14:20:00 GMT</p> <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> </article> <article> <h1>[bio] mrbayes/3.2.7a/-mpi installed on all systems (-gpu on Snowy)</h1> <p>Wed, 10 Feb 2021 09:08:00 GMT</p> <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 installed on all systems <span style="font-size:1em">as mrbayes/3.2.7a-mpi. GPU version is installed on Snowy as mrbayes/3.2.7a-gpu.</span></p> <p></p> </article> <article> <h1>[bio] blast/2.11.0+ installed on all systems</h1> <p>Mon, 08 Feb 2021 11:07:00 GMT</p> <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 /> </p> </article> <article> <h1>[apps] vmtouch/1.3.1-20200309-4b70a9f installed on all systems</h1> <p>Mon, 08 Feb 2021 10:39:00 GMT</p> <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. See 'module help vmtouch/1.3.1-20200309-4b70a9f' for more information.</p> </article> <article> <h1>[comp] python/3.8.7 and python3/3.8.7 installed on all systems</h1> <p>Mon, 01 Feb 2021 12:48:00 GMT</p> <p>Python 3.8.7 is now installed as module python/3.8.7 and python3/3.8.7 on all systems. 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> </article> <article> <h1>[bio] cellranger/5.0.1 and the databases cellranger-data/2020-A and cellranger-VDJ-data/5.0.0 installed on all systems</h1> <p>Fri, 22 Jan 2021 13:08:00 GMT</p> <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 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> </article> <article> <h1>[bio] kallisto/0.46.2 installed on all systems</h1> <p>Mon, 18 Jan 2021 13:39:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] SACRA/1.0.0 installed on all systems</h1> <p>Mon, 18 Jan 2021 12:37:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] SeqKit/0.15.0 installed on all systems</h1> <p>Mon, 18 Jan 2021 12:35:00 GMT</p> <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 /> </p> <p></p> </article> <article> <h1>[bio] last/963 installed on all systems</h1> <p>Mon, 18 Jan 2021 12:33:00 GMT</p> <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 /> </p> <p></p> </article> <article> <h1>[bio] GUSHR/1.0.0 installed on all systems</h1> <p>Mon, 18 Jan 2021 11:08:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] GeneMark/4.62-es installed on all systems</h1> <p>Sun, 17 Jan 2021 15:36:00 GMT</p> <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. The key file is also updated as of today's date, 17-Jan-2021.</p> </article> <article> <h1>[bio] ProtHint/2.5.0 installed on all systems</h1> <p>Thu, 14 Jan 2021 13:44:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] Sniffles/1.0.12-201218-4ff6ecb installed on all systems</h1> <p>Thu, 14 Jan 2021 10:38:00 GMT</p> <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 /> </p> <p></p> </article> <article> <h1>[bio] DelGet/5.4 installed on all systems</h1> <p>Wed, 13 Jan 2021 14:22:00 GMT</p> <p><a href="https://github.com/4ureliek/DelGet">DelGet</a> (finds micro- and midsize deletions (using gaps of 1-30 nt and >30 nt respectively) between orthologous regions of 3 or more species) version 5.4 installed on all systems as module DelGet/5.4.<br /> </p> </article> <article> <h1>[bio] Kalign/1.04 and Kalign/2.04 installed on all systems</h1> <p>Wed, 13 Jan 2021 13:33:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] minimap2/2.17-r941 installed on all systems</h1> <p>Tue, 12 Jan 2021 10:00:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] ANGSD/0.933 installed on all systems</h1> <p>Mon, 04 Jan 2021 15:20:00 GMT</p> <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 /> </p> </article> <article> <h1>[apps] lammps/29Oct2020_gcc_openmpi installed on Rackham</h1> <p>Mon, 04 Jan 2021 13:00:00 GMT</p> <p>lammps (LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel) version 29Oct2020_gcc_openmpi installed on Rackham as module lammps/29Oct2020_gcc_openmpi.<br /> https://lammps.sandia.gov/</p> </article> <article> <h1>[libs] lpsolve/5.5.2.9 installed on all systems</h1> <p>Wed, 16 Dec 2020 15:03:00 GMT</p> <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 /> </p> </article> <article> <h1>[apps] sqlite/3.34.0 installed on all systems</h1> <p>Tue, 15 Dec 2020 14:24:00 GMT</p> <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> </article> <article> <h1>[bio] augustus/3.3.3-CGP installed on all systems</h1> <p>Tue, 15 Dec 2020 11:01:00 GMT</p> <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. This specific module is largely a wrapper around an EasyBuild-built module, with UPPMAX additions for copying the config directory. See 'module help augustus/3.3.3-CGP' for more.</p> </article> <article> <h1>[bio] NeEstimator/2.1 installed on all systems</h1> <p>Fri, 11 Dec 2020 22:13:00 GMT</p> <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> </article> <article> <h1>[bio] RAisD/2.9 installed on all systems</h1> <p>Fri, 11 Dec 2020 22:12:00 GMT</p> <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> </article> <article> <h1>[bio] SNeP/1.1 installed on all systems</h1> <p>Fri, 11 Dec 2020 22:11:00 GMT</p> <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> </article> <article> <h1>[bio] IGV/2.8.13 installed on all systems</h1> <p>Fri, 11 Dec 2020 14:29:00 GMT</p> <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. The corresponding IGVtools are available in IGVtools/2.8.13.</p> </article> <article> <h1>[bio] IGVtools/2.8.13 installed on all systems</h1> <p>Fri, 11 Dec 2020 10:55:00 GMT</p> <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> </article> <article> <h1>[bio] SHAPEIT/v4.1.3 installed on all systems</h1> <p>Wed, 09 Dec 2020 09:39:00 GMT</p> <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 /> </p> </article> <article> <h1>[apps] ORCA/4.2.1 installed on all systems</h1> <p>Tue, 08 Dec 2020 18:17:00 GMT</p> <p>ORCA version 4.2.1 installed on all systems as module ORCA/4.2.1.</p> </article> <article> <h1>[bio] cyvcf2/0.30.1 installed on all systems</h1> <p>Tue, 08 Dec 2020 13:15:00 GMT</p> <p>cyvcf2 version 0.30.1 installed on all systems as module cyvcf2/0.30.1.</p> <p>https://github.com/brentp/cyvcf2</p> </article> <article> <h1>[apps] wrf-python/1.3.1 installed on Rackham and Snowy</h1> <p>Mon, 07 Dec 2020 20:53:00 GMT</p> <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 Rackham and Snowy as module wrf-python/1.3.1.<br /> </p> </article> <article> <h1>[bio] IntaRNA/3.2.1 installed on all systems</h1> <p>Mon, 07 Dec 2020 16:06:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] RNAfold/2.4.17 aka ViennaRNA/2.4.17 installed on all systems</h1> <p>Mon, 07 Dec 2020 15:02:00 GMT</p> <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. These are different names for the same module.<br /> </p> </article> <article> <h1>[bio] MEGAN/6.20.17 installed on all systems</h1> <p>Mon, 07 Dec 2020 14:45:00 GMT</p> <p>MEGAN version 6.20.17 installed on all systems as module MEGAN/6.20.17.</p> </article> <article> <h1>[bio] cutadapt/3.1 installed on all systems</h1> <p>Mon, 07 Dec 2020 14:04:00 GMT</p> <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> </article> <article> <h1>[bio] HISAT2/2.2.1 installed on all systems</h1> <p>Thu, 03 Dec 2020 15:43:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] Unicycler/0.4.8 installed on all clusters</h1> <p>Wed, 02 Dec 2020 12:54:00 GMT</p> <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. This is an alias module for the EasyBuild module Unicycler/0.4.8-gompi-2020a-Python-3.8.2.</p> </article> <article> <h1>[bio] SHAPEIT/v3.r884.2 installed on all systems</h1> <p>Wed, 02 Dec 2020 11:19:00 GMT</p> <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> </article> <article> <h1>[apps] NCO/4.9.3 installed on all systems</h1> <p>Tue, 01 Dec 2020 13:47:00 GMT</p> <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 /> </p> <p></p> </article> <article> <h1>[bio] quast/5.0.2 installed on all systems</h1> <p>Mon, 30 Nov 2020 13:07:00 GMT</p> <p>quast (Quality Assessment Tool for Genome Assemblies) version 5.0.2 installed on all systems as module quast/5.0.2.</p> </article> <article> <h1>[apps] ncview/2.1.7 installed on all systems</h1> <p>Thu, 26 Nov 2020 20:28:00 GMT</p> <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> </article> <article> <h1>[bio] MaSuRCA/3.4.2 installed on all systems</h1> <p>Wed, 25 Nov 2020 11:07:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] MUMmer/4.0.0rc1 installed on all systems</h1> <p>Wed, 25 Nov 2020 09:15:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] schmutzi/20200706-597c6bc installed on all systems</h1> <p>Wed, 25 Nov 2020 08:59:00 GMT</p> <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. The previously installed older version schmutzi/20160424 is also enabled.</p> </article> <article> <h1>[bio] gcta/1.93.2beta installed on all systems</h1> <p>Tue, 24 Nov 2020 10:18:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] trinity/2.11.0 installed on all systems</h1> <p>Mon, 23 Nov 2020 14:18:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] TargetP/2.0 installed on all systems</h1> <p>Mon, 23 Nov 2020 12:48:00 GMT</p> <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> </article> <article> <h1>[bio] TransDecoder/5.5.0 installed on all systems</h1> <p>Mon, 23 Nov 2020 11:51:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] MAGeCK/0.5.9.4 installed on all systems</h1> <p>Thu, 19 Nov 2020 17:18:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] selscan/1.3.0 installed on all systems</h1> <p>Wed, 18 Nov 2020 12:07:00 GMT</p> <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> </article> <article> <h1>[bio] SweeD/4.0.0 installed on all systems</h1> <p>Wed, 18 Nov 2020 12:06:00 GMT</p> <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> </article> <article> <h1>[bio] cellranger-ARC/1.0.0 and cellranger-ARC-data/2020-A installed on all systems</h1> <p>Mon, 16 Nov 2020 15:06:00 GMT</p> <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. Also installed are Cellranger ARC reference data in cellranger-ARC-data/2020-A.</p> </article> <article> <h1>[bio] cellranger-DNA/1.1.0 and cellranger-DNA-data/1.0.0 installed on all systems</h1> <p>Mon, 16 Nov 2020 14:57:00 GMT</p> <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. Also installed are reference data as cellranger-DNA-data/1.0.0.</p> </article> <article> <h1>[bio] cellranger/4.0.0 and cellranger-data/4.0.0 installed on all systems</h1> <p>Mon, 16 Nov 2020 14:53:00 GMT</p> <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. Also installed is Cellranger reference data as cellranger-data/4.0.0.<br /> </p> </article> <article> <h1>[bio] spaceranger/1.2.0 installed on all systems</h1> <p>Mon, 16 Nov 2020 14:49:00 GMT</p> <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> </article> <article> <h1>[bio] NanoPlot/1.33.1 installed on all systems</h1> <p>Mon, 16 Nov 2020 12:19:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] megahit/1.2.9 installed on all systems</h1> <p>Thu, 12 Nov 2020 20:34:00 GMT</p> <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> </article> <article> <h1>[bio] diamond/2.0.4 installed on all systems</h1> <p>Thu, 12 Nov 2020 14:05:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] mafTools/20170914-82077ac installed on all systems</h1> <p>Thu, 12 Nov 2020 14:05:00 GMT</p> <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 /> </p> </article> <article> <h1>[apps] QGIS/3.4.12 installed on all systems</h1> <p>Tue, 10 Nov 2020 14:33:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] Beagle/5.1 installed on all systems</h1> <p>Mon, 09 Nov 2020 10:33:00 GMT</p> <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> </article> <article> <h1>[bio] FastQC/0.11.9 installed on all systems</h1> <p>Mon, 09 Nov 2020 10:23:00 GMT</p> <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> </article> <article> <h1>[bio] spades/3.14.1 installed on all systems</h1> <p>Thu, 29 Oct 2020 10:47:00 GMT</p> <p>spades (SPAdes -- 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> </article> <article> <h1>[bio] cactus/1.2.3 installed on all systems</h1> <p>Wed, 28 Oct 2020 15:12:00 GMT</p> <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. Both the prebuilt Singularity image and locally-built binaries are available.</p> <p>This is a complicated tool to run. Please contact support@uppmax.uu.se for additional help.</p> </article> <article> <h1>[apps] SAIGE/0.42.1 installed on all systems</h1> <p>Wed, 28 Oct 2020 15:10:00 GMT</p> <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 > 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> </article> <article> <h1>[bio] jellyfish/2.3.0 installed on all systems</h1> <p>Wed, 28 Oct 2020 15:03:00 GMT</p> <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> </article> <article> <h1>[bio] jellyfish/1.1.12 installed on all systems</h1> <p>Wed, 28 Oct 2020 15:02:00 GMT</p> <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> </article> <article> <h1>[apps] PRISMS-PF/2.1.1 installed on Rackham and Snowy</h1> <p>Fri, 23 Oct 2020 09:05:00 GMT</p> <p>PRISMS-PF (PRedictive Integrated Structural Materials Science–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> </article> <article> <h1>[apps] NCL/6.6.2 installed on Rackham</h1> <p>Tue, 06 Oct 2020 12:37:00 GMT</p> <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> </article> <article> <h1>[bio] StringTie/2.1.4 installed on all systems</h1> <p>Thu, 01 Oct 2020 12:52:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] segemehl/0.3.4 installed on all systems</h1> <p>Mon, 28 Sep 2020 09:18:00 GMT</p> <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> </article> <article> <h1>[apps] WRF/WPS-4.1.3 installed on Rackham and Snowy</h1> <p>Fri, 25 Sep 2020 11:50:00 GMT</p> <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> </article> <article> <h1>[bio] vcflib/1.0.1 installed on all systems</h1> <p>Wed, 16 Sep 2020 13:38:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] plink2/2.00-alpha-2.3-20200124 installed on all systems</h1> <p>Wed, 16 Sep 2020 09:42:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] picard/2.23.4 installed on all systems</h1> <p>Wed, 16 Sep 2020 08:49:00 GMT</p> <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> </article> <article> <h1>[bio] AdmixTools/7.0.1 installed on all systems</h1> <p>Tue, 15 Sep 2020 13:06:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] msmc/1.1.0 installed on all systems</h1> <p>Thu, 10 Sep 2020 11:40:00 GMT</p> <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> </article> <article> <h1>[apps] SPRKKR versions 7.7.1 and 7.7.3 installed on Rackham and Snowy</h1> <p>Thu, 10 Sep 2020 10:38:00 GMT</p> <p><a href="https://www.ebert.cup.uni-muenchen.de/index.php/en/software-en/13-sprkkr" title="SPRKKR">SPRKKR</a> - a spin polarized relativistic Korringa-Kohn-Rostoker (SPR-KKR) code for calculating solid state properties - versions 7.7.1 and 7.7.3 are installed on Rackham and Snowy as modules SPRKKR/7.7.1 and SPRKKR/7.7.3.</p> </article> <article> <h1>[bio] ms/20071014 installed on all systems</h1> <p>Wed, 09 Sep 2020 13:58:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] METAL/2011-03-25 installed on all systems</h1> <p>Tue, 08 Sep 2020 08:49:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] GenomeTools/1.6.1 installed on all systems</h1> <p>Thu, 27 Aug 2020 11:11:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] RECON/1.08 installed on all systems</h1> <p>Mon, 24 Aug 2020 12:06:00 GMT</p> <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. This version uses an <a href="http://www.repeatmasker.org/RepeatModeler/RECON-1.08.tar.gz">updated version of the source</a>.</p> </article> <article> <h1>[bio] RepeatScout/1.0.6 installed on all systems</h1> <p>Mon, 24 Aug 2020 11:41:00 GMT</p> <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. This version is <a href="http://www.repeatmasker.org/RepeatScout-1.0.6.tar.gz">specially modified</a> to handle multiple sequences.</p> </article> <article> <h1>[bio] RepeatScout/1.0.5 installed on all systems</h1> <p>Mon, 24 Aug 2020 11:08:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] nseg/1.0.1 installed on all systems</h1> <p>Mon, 24 Aug 2020 10:59:00 GMT</p> <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. 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 /> </p> </article> <article> <h1>[bio] trf/4.09.1 installed on all system</h1> <p>Mon, 24 Aug 2020 10:26:00 GMT</p> <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> </article> <article> <h1>[apps] tmux/3.1b installed on all systems</h1> <p>Fri, 21 Aug 2020 12:53:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] ont_fast5_api/3.1.6 installed on all systems</h1> <p>Fri, 21 Aug 2020 08:56:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] MethPipe/4.1.1 installed on all systems</h1> <p>Thu, 20 Aug 2020 10:52:00 GMT</p> <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. <a href="http://smithlabresearch.org/software/radmeth/">RADmeth</a> is now included in MethPipe.</p> </article> <article> <h1>[apps] nonmem/7.4.4 and nonmem/7.4.4-intel installed on all systems</h1> <p>Thu, 20 Aug 2020 10:43:00 GMT</p> <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. The '-intel' module cannot be used on Bianca.</p> </article> <article> <h1>[apps] PsN/5.0.0 installed on all systems</h1> <p>Tue, 18 Aug 2020 15:18:00 GMT</p> <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. 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 nonmem/7.4.4-intel (PsN name is 7_4_4_intel). 7_4_4 is the default. 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> </article> <article> <h1>[apps] pandoc/2.10.1 installed on all systems</h1> <p>Mon, 17 Aug 2020 12:32:00 GMT</p> <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 /> </p> </article> <article> <h1>[comp] git/2.28.0 installed on all systems</h1> <p>Mon, 17 Aug 2020 11:23:00 GMT</p> <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> </article> <article> <h1>[comp] git/2.24.0 installed on all systems</h1> <p>Mon, 17 Aug 2020 11:16:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] Tombo/1.5.1 installed on all systems</h1> <p>Wed, 12 Aug 2020 11:01:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] freebayes/1.3.2 installed on all systems</h1> <p>Wed, 12 Aug 2020 11:00:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] Redundans/0.14a-20190509-ffae69e installed on all systems</h1> <p>Wed, 12 Aug 2020 10:57:00 GMT</p> <p><a href="https://github.com/lpryszcz/redundans">Redundans</a> version 0.14a including commits through ffae69e dated 2019 May 09 is now installed on all systems as module Redundans/0.14a-20190509-ffae69e.</p> </article> <article> <h1>[bio] blast/2.10.1+ installed on all systems</h1> <p>Mon, 10 Aug 2020 08:33:00 GMT</p> <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 " 1>&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> </article> <article> <h1>[bio] EnsEMBL-API/94 installed on all systems</h1> <p>Tue, 28 Jul 2020 08:39:00 GMT</p> <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> </article> <article> <h1>[bio] LDpred/1.0.10 installed on all systems</h1> <p>Tue, 21 Jul 2020 10:33:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] CITE-seq-Count/1.4.3 installed on all systems</h1> <p>Mon, 20 Jul 2020 13:23:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] htseq/0.12.4 installed on all systems</h1> <p>Mon, 20 Jul 2020 11:47:00 GMT</p> <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 /> </p> </article> <article> <h1>[build] cmake/3.17.3 installed on all systems</h1> <p>Mon, 13 Jul 2020 12:21:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] vawk/0.0.1 installed on all systems</h1> <p>Tue, 30 Jun 2020 14:34:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] RepeatMasker/4.1.0 installed on all systems</h1> <p>Tue, 30 Jun 2020 14:32:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] bwa-meth/0.2.2 installed on all systems</h1> <p>Thu, 18 Jun 2020 13:01:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] MethylDackel/0.5.1 installed on all systems</h1> <p>Thu, 18 Jun 2020 12:34:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] libBigWig/0.4.4 installed on all systems</h1> <p>Thu, 18 Jun 2020 12:12:00 GMT</p> </article> <article> <h1>[bio] BEDTools/2.29.2 installed on all systems</h1> <p>Thu, 04 Jun 2020 13:42:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] braker/2.1.5 installed on all systems</h1> <p>Thu, 04 Jun 2020 12:53:00 GMT</p> <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 help braker/2.1.5'.</p> </article> <article> <h1>[bio] MaxBin/2.2.7 installed on all systems</h1> <p>Tue, 02 Jun 2020 18:23:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] CONCOCT/1.1.0 installed on all systems</h1> <p>Tue, 02 Jun 2020 16:35:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] CheckM/1.1.2 installed on all systems</h1> <p>Tue, 02 Jun 2020 08:47:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] MultiQC/1.9 installed on all systems</h1> <p>Mon, 01 Jun 2020 09:31:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] MakeHub/1.0.5-1ecd6bb installed on all systems</h1> <p>Fri, 29 May 2020 16:10:00 GMT</p> <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> </article> <article> <h1>[bio] ucsc-utilities/v398 installed on all systems</h1> <p>Fri, 29 May 2020 15:51:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] GenomeThreader/1.7.1 installed on all systems</h1> <p>Thu, 28 May 2020 13:54:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] cdbfasta/1.00 installed on all systems</h1> <p>Thu, 28 May 2020 13:07:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] ProtHint/2.4.0 installed on all systems</h1> <p>Thu, 28 May 2020 11:08:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] spaln/2.4.0 installed on all systems</h1> <p>Wed, 27 May 2020 15:43:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] HOMER/4.11 with all data installed on all systems</h1> <p>Mon, 25 May 2020 14:27:00 GMT</p> <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. All available data sources are also installed.</p> </article> <article> <h1>[apps] RStudio/1.2.5042 installed on all systems</h1> <p>Wed, 20 May 2020 08:20:00 GMT</p> <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 /> </p> </article> <article> <h1>[apps] GDAL/3.1.0 installed on all systems</h1> <p>Tue, 19 May 2020 12:05:00 GMT</p> <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 /> </p> </article> <article> <h1>[apps] ROOT/6.20.04 installed on all systems</h1> <p>Tue, 19 May 2020 12:04:00 GMT</p> <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> </article> <article> <h1>[libs] PROJ/6.3.2 installed on all systems</h1> <p>Mon, 18 May 2020 14:49:00 GMT</p> <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> </article> <article> <h1>[bio] rsem/1.3.3 installed on all systems</h1> <p>Mon, 18 May 2020 09:19:00 GMT</p> <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> </article> <article> <h1>[bio] Stacks/2.53 installed on all systems</h1> <p>Mon, 11 May 2020 12:49:00 GMT</p> <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> </article> <article> <h1>[comp] rust/1.43.1 installed on all systems</h1> <p>Fri, 08 May 2020 08:46:00 GMT</p> <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> </article> <article> <h1>[apps] Armadillo/9.700.2 installed on all systems</h1> <p>Fri, 24 Apr 2020 15:24:00 GMT</p> <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> </article> <article> <h1>[apps] Singular/4.1.2 installed on all systems</h1> <p>Fri, 24 Apr 2020 14:51:00 GMT</p> <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>. <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> </article> <article> <h1>[apps] gromacs/2020-GPU installed on Snowy hybrid nodes</h1> <p>Thu, 23 Apr 2020 19:57:00 GMT</p> <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> </article> <article> <h1>[bio] phylobayesmpi/1.8b installed on all systems</h1> <p>Wed, 22 Apr 2020 16:28:00 GMT</p> <p><a href="https://github.com/bayesiancook/pbmpi">PhyloBayes MPI</a> (PhyloBayes with MPI support) version 1.8b installed on all systems as module phylobayesmpi/1.8b. This module loads gcc/9.2.0 and openmpi/3.1.4 and should work equally well on all clusters.<br /> </p> </article> <article> <h1>[apps] Ansys/2020R1 installed on Rackham</h1> <p>Wed, 22 Apr 2020 15:24:00 GMT</p> <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, 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> </article> <article> <h1>[bio] biopython/1.76-py3 installed on all systems</h1> <p>Mon, 20 Apr 2020 16:22:00 GMT</p> <p><a href="https://biopython.org">BioPython</a> (Python packages for doing bioinformatics tasks) version 1.76-py3 installed on all systems as module biopython/1.76-py3. This module loads python/3.7.2 as a prerequisite.</p> </article> <article> <h1>[comp] fpc/3.0.4 installed on all systems</h1> <p>Mon, 20 Apr 2020 16:20:00 GMT</p> <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> </article> <article> <h1>[apps] OpenFOAM version v1912 installed on all systems</h1> <p>Mon, 20 Apr 2020 15:41:00 GMT</p> <p style="margin-left:0px"><strong>OpenFOAM</strong> (a free, open source computational fluid 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> </article> <article> <h1>[apps] OpenFOAM versions 6 and 7 installed on all systems</h1> <p>Mon, 20 Apr 2020 15:37:00 GMT</p> <p style="margin-left:0px"><strong>OpenFOAM</strong> (a free, open source computational fluid 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> </article> <article> <h1>[bio] Genepop/4.7 installed on all systems</h1> <p>Mon, 20 Apr 2020 15:19:00 GMT</p> <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> </article> <article> <h1>[apps] XCrySDen versions 1.5.60 and 1.6.2 installed on Rackham</h1> <p>Fri, 17 Apr 2020 08:38:00 GMT</p> <p>XCrySDen (a crystalline and molecular structure visualisation program) 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>. <a href="http://www.xcrysden.org" title="http://www.xcrysden.org">http://www.xcrysden.org</a></p> <p></p> </article> <article> <h1>[apps] Siesta version 4.1-MaX-1.0 installed on all systems</h1> <p>Thu, 16 Apr 2020 10:20:00 GMT</p> <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>. <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> </article> <article> <h1>[apps] Siesta version 4.1-b4 installed on all systems</h1> <p>Thu, 16 Apr 2020 10:10:00 GMT</p> <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>. <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> </article> <article> <h1>[bio] diamond/0.931 is installed on all systems</h1> <p>Fri, 10 Apr 2020 08:25:00 GMT</p> <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> </article> <article> <h1>[bio] canu/2.0 installed on all systems</h1> <p>Thu, 09 Apr 2020 13:10:00 GMT</p> <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. Note that assemblies begun with previous version of Canu (canu/1.x) cannot be continued by canu/2.0.</p> </article> <article> <h1>[bio] SpeedSeq/0.1.2-20180208-4e60002 installed on all systems</h1> <p>Mon, 06 Apr 2020 09:20:00 GMT</p> <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> </article> <article> <h1>[bio] raxml/8.2.12-gcc iand raxml/8.2.12-gcc-mpi nstalled on all systems</h1> <p>Wed, 01 Apr 2020 09:47:00 GMT</p> <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> </article> <article> <h1>[bio] DATES/753 installed on all systems</h1> <p>Tue, 31 Mar 2020 14:46:00 GMT</p> <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> </article> <article> <h1>[libs] gsl/2.5 installed on all systems</h1> <p>Tue, 31 Mar 2020 13:37:00 GMT</p> <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> </article> <article> <h1>[libs] openblas/0.2.20 and openblas/0.2.20-singlethread installed on all systems</h1> <p>Tue, 31 Mar 2020 13:33:00 GMT</p> <p><a href="https://github.com/xianyi/OpenBLAS">OpenBLAS</a> ( an optimized Basic Linear Algebra Subprograms [BLAS] library based on <a href="https://www.tacc.utexas.edu/research-development/tacc-software/gotoblas2">GotoBLAS2</a> 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, on all systems.</p> </article> <article> <h1>[libs] fftw/3.3.8 installed on all systems</h1> <p>Tue, 31 Mar 2020 13:27:00 GMT</p> <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> </article> <article> <h1>[bio] iqtree/2.0-rc2-omp-mpi installed on all systems</h1> <p>Thu, 26 Mar 2020 13:43:00 GMT</p> <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> </article> <article> <h1>[bio] barrnap/0.9 installed on all systems</h1> <p>Mon, 23 Mar 2020 12:16:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] LUMPY/0.3.0 installed on all systems</h1> <p>Fri, 13 Mar 2020 16:18:00 GMT</p> <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> </article> <article> <h1>[bio] sambamba/0.7.1 installed on all systems</h1> <p>Fri, 13 Mar 2020 15:08:00 GMT</p> <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> </article> <article> <h1>[bio] fastp/0.20.0 installed on all systems</h1> <p>Tue, 10 Mar 2020 10:52:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] LINKS/1.8.7 installed on all systems</h1> <p>Fri, 06 Mar 2020 10:29:00 GMT</p> <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> </article> <article> <h1>[bio] ARCS/1.1.1 installed on all systems</h1> <p>Fri, 06 Mar 2020 10:26:00 GMT</p> <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. This module also loads LINKS/1.8.7 and tigmint/1.1.2.</p> </article> <article> <h1>[apps] swig/3.0.12 installed on all systems</h1> <p>Thu, 05 Mar 2020 13:13:00 GMT</p> <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> </article> <article> <h1>[bio] GAA/1.1 installed on all systems</h1> <p>Thu, 05 Mar 2020 12:33:00 GMT</p> <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> </article> <article> <h1>[apps] NCO/4.8.1 and NCO/4.9.2 installed on all systems</h1> <p>Thu, 05 Mar 2020 09:59:00 GMT</p> <p><a href="http://nco.sourceforge.net/">NCO</a> (toolkit manipulates and analyzes data stored in <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> </article> <article> <h1>[apps] ABINIT/8.10.3 installed on all systems</h1> <p>Thu, 27 Feb 2020 15:54:00 GMT</p> <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> </article> <article> <h1>[libs] NLopt/2.6.1 installed on all systems</h1> <p>Tue, 25 Feb 2020 14:38:00 GMT</p> <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> </article> <article> <h1>[bio] deepTools/3.3.2 installed on all systems</h1> <p>Mon, 24 Feb 2020 15:16:00 GMT</p> <p><a href="https://github.com/deeptools/deepTools">deepTools</a> (tools to process and analyze deep sequencing data) version 3.3.2 installed on all systems as module deepTools/3.3.2.</p> </article> <article> <h1>[bio] MACS/2.2.6 installed on all systems</h1> <p>Mon, 24 Feb 2020 15:00:00 GMT</p> <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> </article> <article> <h1>[bio] PCAngsd/0.982 installed on all systems</h1> <p>Thu, 20 Feb 2020 13:11:00 GMT</p> <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> </article> <article> <h1>[bio] SLiM/3.3.2 installed on all systems</h1> <p>Tue, 11 Feb 2020 19:20:00 GMT</p> <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> </article> <article> <h1>[bio] SLiM/2.6 installed on all systems</h1> <p>Tue, 11 Feb 2020 19:06:00 GMT</p> <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> </article> <article> <h1>[bio] beagle/3.1.2 installed on all systems</h1> <p>Tue, 11 Feb 2020 16:28:00 GMT</p> <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> </article> <article> <h1>[bio] beast2/2.6.2pre installed on all systems</h1> <p>Tue, 11 Feb 2020 10:37:00 GMT</p> <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> </article> <article> <h1>[bio] PRSice version 2.2.11.b installed on all systems</h1> <p>Mon, 10 Feb 2020 15:07:00 GMT</p> <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> </article> <article> <h1>[bio] cd-hit/4.8.1 installed on all systems</h1> <p>Tue, 04 Feb 2020 10:31:00 GMT</p> <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> </article> <article> <h1>[bio] MaSuRCA/3.3.5 installed on all systems</h1> <p>Thu, 30 Jan 2020 12:24:00 GMT</p> <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> </article> <article> <h1>[bio] quickmerge/0.3-9233726 installed on all systems</h1> <p>Thu, 30 Jan 2020 12:22:00 GMT</p> <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. By default, the module loads MUMmer74.0.0beta2 for alignment, to enable multithreading. If an earlier, nonmultithreaded MUMmer is desired, load the appropriate MUMmer module after loading this module.</p> </article> <article> <h1>[bio] bam2fastx/1.3.0-80dbf79 installed on all systems</h1> <p>Wed, 29 Jan 2020 11:35:00 GMT</p> <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) 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> </article> <article> <h1>[bio] augustus/3.3.3 installed on all systems</h1> <p>Mon, 27 Jan 2020 18:25:00 GMT</p> <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> </article> <article> <h1>[bio] Salmon/1.1.0 installed on all systems</h1> <p>Fri, 24 Jan 2020 11:40:00 GMT</p> <p><a href="https://salmon.readthedocs.io/en/latest/salmon.html">Salmon</a> version 1.1.0, a tool for transcript quantification from RNA-seq data, has been installed on all systems as module Salmon/1.1.0 . </p> </article> <article> <h1>[bio] subread/2.0.0 installed on all systems</h1> <p>Fri, 17 Jan 2020 14:55:00 GMT</p> <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> </article> <article> <h1>[bio] bambam/1.4 installed on all systems</h1> <p>Wed, 15 Jan 2020 15:08:00 GMT</p> <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> </article> <article> <h1>[bio] LDpred/1.0.11 installed on all systems</h1> <p>Thu, 19 Dec 2019 15:02:00 GMT</p> <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> </article> <article> <h1>[bio] samtools/1.10, bcftools/1.10 and htslib/1.10 installed on all systems</h1> <p>Fri, 13 Dec 2019 17:14:00 GMT</p> <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. These have all been compiled with libcurl, AWS S3, GCS and HTSlib plugins enabled. BCFtools has been compiled with Perl filters enabled and GSL support, which adds the +polysomy plugin.</p> </article> <article> <h1>[bio] spaceranger/1.0.0 and spaceranger-data/1.0.0 installed on all systems</h1> <p>Thu, 12 Dec 2019 14:27:00 GMT</p> <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. Also installed is the data module spaceranger-data/1.0.0, which provides Visium Dual Index sets. Reference data for this module is provided by the cellranger-data/3.0.0 module.</p> </article> <article> <h1>[libs] PLplot/5.15.0 and PLplot/5.15.0-old_wxWidgets installed on all systems</h1> <p>Wed, 11 Dec 2019 14:52:00 GMT</p> <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 -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> </article> <article> <h1>[libs] hdf4/4.2.14-gcc6.3.0 installed on all systems</h1> <p>Wed, 11 Dec 2019 14:41:00 GMT</p> <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> </article> <article> <h1>[libs] pslib/0.4.6 installed on all systems</h1> <p>Wed, 11 Dec 2019 14:02:00 GMT</p> <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> </article> <article> <h1>[libs] wxWidgets/3.1.3-{gtk2,gtk3,qt5} are now installed on all systems</h1> <p>Wed, 11 Dec 2019 13:59:00 GMT</p> <p><a href="https://www.wxwidgets.org/">WxWidgets</a> (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. 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> </article> <article> <h1>[comp] patchelf/0.10 installed on all systems</h1> <p>Wed, 11 Dec 2019 13:56:00 GMT</p> <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> </article> <article> <h1>[apps] gdl/1.0.0-rc.1 installed on all systems</h1> <p>Wed, 11 Dec 2019 13:54:00 GMT</p> <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> </article> <article> <h1>[comp] git-lfs/2.9.1 installed on all systems</h1> <p>Fri, 06 Dec 2019 13:37:00 GMT</p> <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> </article> <article> <h1>[comp] git/2.24.0 installed on all systems</h1> <p>Fri, 06 Dec 2019 13:07:00 GMT</p> <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> </article> <article> <h1>[libs] SHAPELIB/1.5.0 installed on all systems</h1> <p>Fri, 06 Dec 2019 09:41:00 GMT</p> <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> </article> <article> <h1>[libs] Qhull/2019.1 installed on all systems</h1> <p>Thu, 05 Dec 2019 16:56:00 GMT</p> <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> </article> <article> <h1>[bio] SignalP/5.0b installed on all systems</h1> <p>Thu, 05 Dec 2019 15:57:00 GMT</p> <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> </article> <article> <h1>[bio] cellranger-ATAC/1.2.0 installed on all systems</h1> <p>Tue, 03 Dec 2019 15:57:00 GMT</p> <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. This module is loaded with the cellranger-ATAC/1.2.0 module.</p> </article> <article> <h1>[bio] diamond/0.9.29 installed on all systems</h1> <p>Thu, 28 Nov 2019 12:14:00 GMT</p> <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> </article> <article> <h1>[libs] deal.II/9.1.1-gcc and deal.II/9.1.1-intel installed on all systems</h1> <p>Wed, 27 Nov 2019 16:06:00 GMT</p> <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 2019.1.144, Intel MPI 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. For more information, see 'module help deal.II/9.1.1-gcc and 'module help deal.II/9.1.1-intel'.</p> </article> <article> <h1>[bio] NanoComp/1.9.2 installed on all systems</h1> <p>Thu, 21 Nov 2019 13:59:00 GMT</p> <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> </article> <article> <h1>[bio] MultiQC/1.8 installed on all systems</h1> <p>Thu, 21 Nov 2019 12:57:00 GMT</p> <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> </article> <article> <h1>[bio] FastANI/1.2 installed on all systems</h1> <p>Wed, 13 Nov 2019 09:43:00 GMT</p> <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> </article> <article> <h1>[bio] LDpred/1.0.8 installed on all systems</h1> <p>Tue, 05 Nov 2019 13:22:00 GMT</p> <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> </article> <article> <h1>[bio] Stacks/2.41 installed on all systems</h1> <p>Sat, 26 Oct 2019 15:48:00 GMT</p> <p><a href="http://catchenlab.life.illinois.edu/stacks/">Stacks</a> (Software pipeline for building loci from short-read sequences) version 2.41 installed on all systems as module Stacks/2.41.</p> </article> <article> <h1>[bio] qctool/2.0.6 installed on all systems</h1> <p>Fri, 25 Oct 2019 20:05:00 GMT</p> <p><a href="https://www.well.ox.ac.uk/~gav/qctool/#overview">QCTOOL</a> (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> </article> <article> <h1>[bio] Metaxa2/2.2 and Metaxa2/2.1.3 installed on all systems</h1> <p>Fri, 25 Oct 2019 10:15:00 GMT</p> <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> </article> <article> <h1>[apps] GOTM/5.3-221-gac7ec88d installed on all ssytems</h1> <p>Fri, 25 Oct 2019 10:13:00 GMT</p> <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> </article> <article> <h1>[apps] CDO/1.9.5 installed on all systems</h1> <p>Fri, 25 Oct 2019 10:11:00 GMT</p> <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> </article> <article> <h1>[bio] usearch/11.0.667 installed on all systems</h1> <p>Mon, 21 Oct 2019 15:36:00 GMT</p> <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> </article> <article> <h1>[bio] vsearch/2.14.1 installed on all systems</h1> <p>Mon, 21 Oct 2019 15:00:00 GMT</p> <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> </article> <article> <h1>[bio] bcftools/1.9-develop installed on all systems</h1> <p>Thu, 17 Oct 2019 16:09:00 GMT</p> <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. This also uses the <a href="https://github.com/samtools/htslib">latest development version of HTSlib</a>. 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. Use with these cautions in mind.</p> </article> <article> <h1>[bio] htslib/1.9 installed on all systems</h1> <p>Thu, 17 Oct 2019 15:27:00 GMT</p> </article> <article> <h1>[bio] bcftools/1.9 installed on all systems</h1> <p>Thu, 17 Oct 2019 15:27:00 GMT</p> </article> <article> <h1>[apps] ALPS/2.3.0 installed on all systems</h1> <p>Tue, 15 Oct 2019 13:13:00 GMT</p> <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. Version 2.3.0 has been installed as module ALPS/2.3.0 on all systems. When loading the module the ALPS system will be available to use 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> </article> <article> <h1>[bio] diamond/0.9.26 installed on all systems</h1> <p>Tue, 15 Oct 2019 13:11:00 GMT</p> <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> </article> <article> <h1>[apps] Graphviz version 2.40.1 installed on all systems</h1> <p>Thu, 10 Oct 2019 12:22:00 GMT</p> <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> </article> <article> <h1>[bio] maker/2.31.10 installed on all systems</h1> <p>Wed, 09 Oct 2019 17:16:00 GMT</p> <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. This is built with MPI support by default.</p> </article> <article> <h1>[bio] pysam/0.15.3-python3.6.8 and pysam/0.15.3-python3.7.2 now available on all systems</h1> <p>Tue, 08 Oct 2019 09:05:00 GMT</p> <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> </article> <article> <h1>[bio] fcGENE version 1.0.7 installed on all systems</h1> <p>Mon, 07 Oct 2019 07:05:00 GMT</p> <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> </article> <article> <h1>[bio] kaiju/1.7.2 has bee installed on all systems</h1> <p>Sat, 05 Oct 2019 10:54:00 GMT</p> <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> </article> <article> <h1>Slurm updated to 19.05</h1> <p>Thu, 03 Oct 2019 09:28:00 GMT</p> <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> </article> <article> <h1>[bio] BraCeR version 2019_10_03_22e49cb installed on all systems</h1> <p>Thu, 03 Oct 2019 09:01:00 GMT</p> <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 /> </p> </article> <article> <h1>[bio] blast/2.9.0+ installed on all systems</h1> <p>Tue, 01 Oct 2019 13:43:00 GMT</p> <p>UPPMAX-local <a href="https://blast.ncbi.nlm.nih.gov/Blast.cgi">Blast</a> (canonical sequence search tool) version 2.9.0+ is now installed as module blast/2.9.0+ on all Uppmax systems. This is the first blast module version to support the V5 databases now provided by NCBI. Currently available are nr_v5, nt_v5, refseq_protein_v5 and refseq_rna_v5. These databases include taxonomy information and other features. NCBI will discontinue updating the older database versions at the end of September 2019.</p> </article> <article> <h1>[bio] velocyto/0.17.17 installed on all systems</h1> <p>Mon, 30 Sep 2019 07:49:00 GMT</p> <p><a href="http://velocyto.org/velocyto.py/index.html">Velocyto</a> (library for the analysis of RNA velocity) version 0.17.17 is now installed as module velocyto/0.17.17 on all systems.</p> </article> <article> <h1>[bio] pblat/2.1 and pblat-cluster/1.0 installed on all systems</h1> <p>Tue, 24 Sep 2019 09:30:00 GMT</p> <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. Each is updated to blat v36x2 (jksrc.v376).</p> </article> <article> <h1>[bio] fasta/36.3.8h and three older versions installed on all systems</h1> <p>Wed, 18 Sep 2019 14:23:00 GMT</p> <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> </article> <article> <h1>[apps] R/3.6.1 and R_packages/3.6.1 installed on all systems</h1> <p>Wed, 18 Sep 2019 14:12:00 GMT</p> <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> module are now installed on all systems. The R_packages/3.6.1 module contains a total of <span style="font-size:1em">17657 CRAN and BioConductor packages installed, out of 17992 packages available. Of these, </span>14579 CRAN packages are installed, out of 14913 available, and 3054 BioConductor-specific packages are installed, out of 3079 available.</p> </article> <article> <h1>[bio] star-fusion/1.7.0 and genome resource libraries installed on all systems</h1> <p>Wed, 18 Sep 2019 09:53:00 GMT</p> <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. 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. 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> </article> <article> <h1>[apps] CDO/1.9.7.1 and CDO/1.9.7.1-intel18.3 now installed on all systems</h1> <p>Tue, 17 Sep 2019 16:02:00 GMT</p> <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> </article> <article> <h1>[libs] Magics/3.3.1 and Magics/3.3.1-intel18.3 installed on all systems</h1> <p>Tue, 17 Sep 2019 15:59:00 GMT</p> <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> </article> <article> <h1>[libs] ecCodes/2.13.1 installed on all systems</h1> <p>Tue, 17 Sep 2019 15:50:00 GMT</p> <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> </article> <article> <h1>[libs] PROJ.4/4.9.3 and PROJ.4/4.9.3-intel18.3 installed on all systems</h1> <p>Tue, 17 Sep 2019 15:45:00 GMT</p> <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> </article> <article> <h1>[libs] hdf5/1.10.5 and hdf5/1.10.5-intel18.3 installed on all systems</h1> <p>Tue, 17 Sep 2019 15:42:00 GMT</p> <p>The <a href="https://www.hdfgroup.org/solutions/hdf5/">HDF5</a> 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. These modules make use of compression provided by szip/2.1.1 and zlib/1.2.11, which are loaded as prerequisites.</p> </article> <article> <h1>[bio] star/2.7.2b installed on all systems</h1> <p>Mon, 16 Sep 2019 09:24:00 GMT</p> <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> </article> <article> <h1>[bio] GEM-Tools/1.7.1 installed on all systems</h1> <p>Tue, 10 Sep 2019 09:25:00 GMT</p> <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> </article> <article> <h1>[bio] GEM/3.4 and GEM/2.7 installed on all systems</h1> <p>Tue, 10 Sep 2019 08:29:00 GMT</p> <p><a href="https://groups.csail.mit.edu/cgs/gem/">GEM</a> (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> </article> <article> <h1>[bio] ExaBayes/1.5 and ExaBayes/1.5-mpi installed on all systems</h1> <p>Mon, 09 Sep 2019 14:48:00 GMT</p> <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. Refer to 'module help ExaBayes' for assistance on using ExaBayes.</p> </article> <article> <h1>[bio] spades/3.13.1 installed on all systems</h1> <p>Thu, 05 Sep 2019 14:23:00 GMT</p> <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> </article> <article> <h1>[libs] netcdf/4.7.1 and netcdf/4.7.1-intel18.3 installed on all systems</h1> <p>Tue, 03 Sep 2019 09:57:00 GMT</p> <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. This makes use of the hdf5/1.10.5 and hdf5/1.10.5-intel18.3 libraries, respectively.</p> </article> <article> <h1>[libs] freetype/2.10.1 installed on all systems</h1> <p>Tue, 03 Sep 2019 09:55:00 GMT</p> <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> </article> <article> <h1>[bio] rtgtools version 3.10.1 installed on all systems</h1> <p>Fri, 30 Aug 2019 09:57:00 GMT</p> <p>rtgtools version 3.10.1 installed on all systems, 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> </article> <article> <h1>[bio] ART version 2016-06-05 installed on all systems</h1> <p>Fri, 30 Aug 2019 08:40:00 GMT</p> <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> </article> <article> <h1>[bio] VerifyBamID2/1.0.6 installed on all systems</h1> <p>Wed, 28 Aug 2019 15:05:00 GMT</p> <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> </article> <article> <h1>[bio] verifyBamID/1.1.3 installed on all systems</h1> <p>Wed, 28 Aug 2019 14:02:00 GMT</p> <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> </article> <article> <h1>[apps] awscli/1.16.225 installed on all systems</h1> <p>Mon, 26 Aug 2019 11:56:00 GMT</p> <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> </article> <article> <h1>[bio] blobtools/1.1.1 installed on all systems</h1> <p>Mon, 26 Aug 2019 11:28:00 GMT</p> <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. See 'module help blobtools/1.1.1' for advice on building your own taxonomy database.</p> </article> <article> <h1>[apps] circos/0.69-9 installed on all systems</h1> <p>Fri, 23 Aug 2019 15:15:00 GMT</p> <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> </article> <article> <h1>[bio] iqtree/1.6.12-omp-mpi installed on all systems</h1> <p>Fri, 23 Aug 2019 13:53:00 GMT</p> <p>The latest version of <a href="http://www.iqtree.org/">IQ-TREE</a> (efficient phylogeny estimation) has been installed as module iqtree/1.6.12-omp-mpi on all systems. 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 iqtree/1.6.12-omp-mpi' for more information.</p> </article> <article> <h1>[bio] longranger/2.2.2 fixed</h1> <p>Fri, 23 Aug 2019 13:02:00 GMT</p> <p>An error in a module file prevented the longranger/2.2.2 module from working correctly. This is now fixed.</p> </article> <article> <h1>[libs] Various versions of Boost 1.70.0 installed</h1> <p>Mon, 19 Aug 2019 14:20:00 GMT</p> <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. 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. 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, boost/1.70.0_intel18.3, and boost/1.70.0_intel18.3_mpi3.1.3.</p> </article> <article> <h1>[bio] bgen/1.1.4 installed on all systems</h1> <p>Mon, 19 Aug 2019 13:47:00 GMT</p> <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> </article> <article> <h1>[apps] DOCK version 3.7 installed on all systems</h1> <p>Tue, 13 Aug 2019 08:53:00 GMT</p> <p>DOCK version 3.7 installed on all systems as module DOCK/3.7.<br /> http://dock.compbio.ucsf.edu/DOCK_3.7/</p> </article> <article> <h1>[bio] HiCUP/0.7.2 installed on all systems</h1> <p>Thu, 08 Aug 2019 13:01:00 GMT</p> <p><a href="https://www.bioinformatics.babraham.ac.uk/projects/hicup/">HiCUP</a> (a 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> </article> <article> <h1>[bio] transrate/1.0.1 and transrate/1.0.2 installed on all systems</h1> <p>Wed, 07 Aug 2019 14:06:00 GMT</p> <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. <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> </article> <article> <h1>[bio] HyPhy/2.5.0 and HyPhy/2.5.0-mpi installed on all systems</h1> <p>Wed, 07 Aug 2019 13:24:00 GMT</p> <p><a href="http://www.hyphy.org/">HyPhy</a> (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> </article> <article> <h1>[bio] star/2.7.1a installed on all systems</h1> <p>Tue, 06 Aug 2019 14:29:00 GMT</p> <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> </article> <article> <h1>[bio] FusionCatcher/1.10 installed on all systems</h1> <p>Tue, 06 Aug 2019 14:17:00 GMT</p> <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. See 'module help FusionCatcher/1.10' for more information.</p> </article> <article> <h1>[bio] bowtie/1.2.2 and bowtie/1.2.3 installed on all systems</h1> <p>Mon, 05 Aug 2019 15:00:00 GMT</p> <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> </article> <article> <h1>[bio] picard/2.19.2 and picard/2.20.4 installed on all systems</h1> <p>Mon, 05 Aug 2019 14:35:00 GMT</p> <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> </article> <article> <h1>[bio] bbmap/38.61b installed on all systems</h1> <p>Mon, 05 Aug 2019 12:43:00 GMT</p> <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> </article> <article> <h1>[bio] star/2.7.0f installed on all systems</h1> <p>Mon, 05 Aug 2019 09:42:00 GMT</p> <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> </article> <article> <h1>[bio] blat/36 available on all systems</h1> <p>Thu, 01 Aug 2019 13:12:00 GMT</p> <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> </article> <article> <h1>[bio] older bwa versions now available on all systems</h1> <p>Thu, 01 Aug 2019 13:09:00 GMT</p> <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 on all systems: bwa/0.5.8a, bwa/0.5.9, bwa/0.6.1, bwa/0.6.2</p> </article> <article> <h1>[bio] SortMeRNA/3.0.3 is now installed on all systems</h1> <p>Thu, 01 Aug 2019 09:28:00 GMT</p> <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. 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> </article> <article> <h1>[bio] DosageConvertor version 1.0.4 installed on all systems</h1> <p>Fri, 05 Jul 2019 15:34:00 GMT</p> <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> </article> <article> <h1>[bio] SiBELia/3.0.7 installed on all systems</h1> <p>Fri, 28 Jun 2019 15:09:00 GMT</p> <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> </article> <article> <h1>[bio] SMARTdenovo/20180219-5cc1356 installed on all systems</h1> <p>Wed, 19 Jun 2019 14:52:00 GMT</p> <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 SMARTdenovo/20180219-5cc1356 on all systems.</p> </article> <article> <h1>[bio] wtdbg2/2.4 installed on all systems</h1> <p>Tue, 18 Jun 2019 15:53:00 GMT</p> <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> </article> <article> <h1>[bio] Flye/2.4.2 installed on all systems</h1> <p>Tue, 18 Jun 2019 14:12:00 GMT</p> <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> </article> <article> <h1>[bio] Filtlong/0.2.0-20190515-13504b7 installed on all systems</h1> <p>Tue, 18 Jun 2019 10:41:00 GMT</p> <p><a href="https://github.com/rrwick/Filtlong">Filtlong</a> (tool for filtering long reads by quality) version 0.2.0 through commit 13504b7 on 15 May 2019 is now installed as module Filtlong/0.2.0-20190515-13504b7 on all systems.</p> </article> <article> <h1>[bio] Porechop/0.2.4 has been installed on all systems</h1> <p>Tue, 18 Jun 2019 10:15:00 GMT</p> <p><a href="https://github.com/rrwick/Porechop">Porechop</a> (tool for finding and removing adapters from <a href="https://nanoporetech.com/">Oxford Nanopore</a> reads) is now installed as module Porechop/0.2.4 on all systems.</p> </article> <article> <h1>[bio] sratools/2.9.6-1 installed on all systems</h1> <p>Tue, 18 Jun 2019 10:13:00 GMT</p> <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> </article> <article> <h1>[bio] canu/1.8 installed on all systems</h1> <p>Mon, 17 Jun 2019 11:04:00 GMT</p> <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> </article> <article> <h1>[apps] gnuplot/5.2.7 installed on all systems</h1> <p>Mon, 17 Jun 2019 10:39:00 GMT</p> <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> </article> <article> <h1>[bio] BioPerl/1.7.2_Perl5.26.2 installed on all systems</h1> <p>Mon, 17 Jun 2019 07:40:00 GMT</p> <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> </article> <article> <h1>[bio] PhyML/3.3.20190321 installed on all systems</h1> <p>Fri, 14 Jun 2019 13:07:00 GMT</p> <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. The tools phyml, phyrex and phytime are available.</p> </article> <article> <h1>[bio] several bioinformatics modules enabled on all systems</h1> <p>Thu, 13 Jun 2019 09:33:00 GMT</p> <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. If you require any other modules not currently available on active systems that were previously available on Milou, please let us know.</p> </article> <article> <h1>[bio] RegScan/0.5 installed on all systems</h1> <p>Thu, 13 Jun 2019 09:12:00 GMT</p> <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. 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> </article> <article> <h1>[comp] perl6/rakudo-star-2019.03 installed on all systems</h1> <p>Sat, 08 Jun 2019 14:01:00 GMT</p> <p><a href="https://perl6.org/">Perl 6</a> (advanced scripting language) version Rakudo Star 2019.03 is now installed as module perl6/rakudo-star-2019.03 on all systems.</p> </article> <article> <h1>[comp] julia/1.1.1 installed on all systems</h1> <p>Sat, 08 Jun 2019 13:51:00 GMT</p> <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> </article> <article> <h1>[bio] SMRT/7.0.1 installed on all systems</h1> <p>Fri, 07 Jun 2019 14:19:00 GMT</p> <p><a href="https://www.pacb.com">SMRT Link</a> (analysis software for PacBio long-read technology) version 7.0.1 has been installed on all systems as module SMRT/7.0.1.</p> </article> <article> <h1>[comp] git/2.21.0 installed on all systems</h1> <p>Tue, 04 Jun 2019 08:38:00 GMT</p> <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> </article> <article> <h1>[bio] bowtie2/2.3.5.1 installed on all systems</h1> <p>Mon, 03 Jun 2019 12:46:00 GMT</p> <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> </article> <article> <h1>[bio] bismark/0.22.1 installed on all systems</h1> <p>Mon, 03 Jun 2019 12:45:00 GMT</p> <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> </article> <article> <h1>[bio] Chromium Long Ranger version 2.2.2 is now installed as module longranger/2.2.2 on all systems.</h1> <p>Wed, 29 May 2019 12:41:00 GMT</p> <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> </article> <article> <h1>[bio] RAxML-NG/0.9.0 and RAxML-NG/0.9.0-mpi installed on all systems</h1> <p>Wed, 29 May 2019 10:06:00 GMT</p> <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> </article> <article> <h1>[bio] Yleaf/2.0 installed on all systems</h1> <p>Tue, 28 May 2019 13:59:00 GMT</p> <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. Indices for both hg19 and hg38 are available.</p> </article> <article> <h1>[bio] medaka version 0.7.1 installed on all systems</h1> <p>Tue, 28 May 2019 08:22:00 GMT</p> <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 /> </p> <p></p> </article> <article> <h1>[bio] oncotator version 1.9.9.0 installed on all systems</h1> <p>Mon, 27 May 2019 13:00:00 GMT</p> <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> </article> <article> <h1>[bio] Kraken2/2.0.8-beta installed on all systems</h1> <p>Mon, 27 May 2019 09:47:00 GMT</p> <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> </article> <article> <h1>[bio] psmc/0.6.5-r67-e5f7df5 installed on all systems</h1> <p>Thu, 23 May 2019 13:34:00 GMT</p> <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> </article> <article> <h1>[bio] GEMMA version 0.98.1 installed on all systems</h1> <p>Thu, 23 May 2019 10:30:00 GMT</p> <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> </article> <article> <h1>[bio] kallisto/0.45.1 installed on all systems</h1> <p>Thu, 16 May 2019 10:35:00 GMT</p> <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> </article> <article> <h1>[bio] exonerate/2.4.0 installed on all systems</h1> <p>Tue, 14 May 2019 16:25:00 GMT</p> <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> </article> <article> <h1>[apps] R/3.6.0 and R_packages/3.6.0 installed on all systems</h1> <p>Tue, 14 May 2019 13:27:00 GMT</p> <p><a href="https://www.r-project.org/">R</a> (statistical language and environment) version 3.6.0 "Planting of a Tree" is now installed as module R/3.6.0 on all systems. 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 16800 CRAN and BioConductor packages.</p> </article> <article> <h1>[bio] DeepVariant version 0.8.0 installed on all systems</h1> <p>Mon, 13 May 2019 12:34:00 GMT</p> <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> </article> <article> <h1>[bio] diamond/0.9.24 installed on all systems</h1> <p>Mon, 13 May 2019 12:27:00 GMT</p> <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> </article> <article> <h1>[bio] snakemake version 5.4.5 installed on all systems</h1> <p>Mon, 06 May 2019 12:12:00 GMT</p> <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> </article> <article> <h1>[bio] TrimGalore/0.6.1 now installed on all systems</h1> <p>Fri, 03 May 2019 09:29:00 GMT</p> <p><a href="http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/">Trim Galore!</a> (wrapper tool around Cutadapt and FastQC 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> </article> <article> <h1>[bio] FastQC/0.11.8 now installed on all systems</h1> <p>Fri, 03 May 2019 09:28:00 GMT</p> <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> </article> <article> <h1>[bio] cutadapt/2.3 installed on all systems</h1> <p>Fri, 03 May 2019 09:26:00 GMT</p> <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> </article> <article> <h1>[bio] Redundans/0.14a-de_novo-42e8edf-20190314 installed on all systems</h1> <p>Thu, 02 May 2019 15:18:00 GMT</p> <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) 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 on all systems. <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. See 'module help Redundans/0.14a-de_novo-42e8edf-20190314' for more information.</p> </article> <article> <h1>[bio] Redundans/0.14a-d11d32b-20190313 installed on all systems</h1> <p>Thu, 02 May 2019 15:09:00 GMT</p> <p><a href="https://github.com/lpryszcz/redundans">Redundans</a> (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 Redundans/0.14a-d11d32b-20190313 on all systems.</p> </article> <article> <h1>[bio] Platanus-allee/2.0.2 now installed on all systems</h1> <p>Thu, 02 May 2019 15:07:00 GMT</p> <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> </article> <article> <h1>[bio] Platanus/1.2.4 now installed on all systems</h1> <p>Thu, 02 May 2019 11:00:00 GMT</p> <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. The version 1.2.1 previously available on milou is also now installed for all current clusters.</p> </article> <article> <h1>[bio] minimap2/2.16 installed on all systems</h1> <p>Thu, 02 May 2019 10:57:00 GMT</p> <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> </article> <article> <h1>[bio] Stargazer version 1.0.4 installed on all systems</h1> <p>Tue, 23 Apr 2019 13:31:00 GMT</p> <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> </article> <article> <h1>[bio] LTR_Finder/1.0.7 installed on all systems</h1> <p>Mon, 15 Apr 2019 12:47:00 GMT</p> <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. GtRNAdb databases are available, see 'module help LTR_Finder/1.0.7' for more information. When on milou, this module was named 'ltr-finder'.</p> </article> <article> <h1>[apps] gromacs 2019.1 with threads</h1> <p>Sat, 13 Apr 2019 13:24:00 GMT</p> <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> </article> <article> <h1>[bio] GATK/4.1.0.0 and GATK/4.1.1.0 installed on all systems</h1> <p>Fri, 12 Apr 2019 15:57:00 GMT</p> <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. The <strong>gatk</strong> wrapper available for each makes it easy to run each; see 'module help GATK/4.1.1.0' for more information.</p> </article> <article> <h1>[apps] p7zip/16.02 module repaired</h1> <p>Fri, 12 Apr 2019 15:56:00 GMT</p> <p>The p7zip/16.02 module has been repaired, by adding additional executables 7z and 7zr.</p> </article> <article> <h1>[apps] Octave 5.1.0 installed on all systems</h1> <p>Fri, 12 Apr 2019 13:31:00 GMT</p> <p>Version 5.1.0 of GNU Octave, a Matlab-compatible programming language for scientific computing, is now available on all systems as module octave/5.1.0.</p> </article> <article> <h1>[bio] umi_tools/1.0.0 installed on all systems</h1> <p>Wed, 03 Apr 2019 12:34:00 GMT</p> <p><a href="https://github.com/CGATOxford/UMI-tools">UMI-tools</a> (tools for dealing with Unique Molecular Identifiers) version 1.0.0 was published as module umi_tools/1.0.0.</p> </article> <article> <h1>[bio] star-fusion/1.5.0 and genome resource libraries installed on all systems</h1> <p>Wed, 03 Apr 2019 11:14:00 GMT</p> <p><a href="https://github.com/STAR-Fusion/STAR-Fusion/wiki">STAR-fusion</a> (use the <a href="https://github.com/alexdobin/STAR">STAR</a> 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. Also installed and newly available are the genome resource libraries both for version 1.5.0 and earlier versions of star-fusion. See 'module help star-fusion/1.5.0' for more information.</p> </article> <article> <h1>[bio] prinseq/0.20.4 installed on all systems</h1> <p>Tue, 02 Apr 2019 15:52:00 GMT</p> <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> </article> <article> <h1>[apps] OpenFOAM v4.1 installed on Rackham</h1> <p>Tue, 02 Apr 2019 09:21:00 GMT</p> <p>OpenFOAM 4.1 is now installed on Rackham.</p> <p><strong>module load OpenFOAM/4.1</strong></p> <p><strong>source $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 $FOAM_BASHRC</strong></p> <p>Please unload all modules (except for the <em>uppmax</em> one) prior to loading OpenFOAM.</p> </article> <article> <h1>[apps] gromacs/2019.1 installed on Rackham</h1> <p>Wed, 27 Mar 2019 13:50:00 GMT</p> <p>Gromacs versions 2019.1, 2018.6, and 2016.6 are available as modules on Rackham: </p> <ul> <li>gromacs/2019.1</li> <li>gromacs/2018.6</li> <li>gromacs/2016.6</li> </ul> </article> <article> <h1>[libs] cairo/1.17.2 installed on all systems</h1> <p>Tue, 26 Mar 2019 15:49:00 GMT</p> <p>The <a href="https://www.cairographics.org/">cairo</a> libraries (2D graphics plotting) version 1.17.2 are now installed as module cairo/1.17.2 on all systems.</p> </article> <article> <h1>[apps] vim/8.1-1053 installed on all systems</h1> <p>Tue, 26 Mar 2019 15:47:00 GMT</p> <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. Included is scripting support for python/2.7.15, python3/3.7.2, ruby/2.6.2, perl, and tcl.</p> </article> <article> <h1>[comp] ruby/2.6.2 installed on all systems</h1> <p>Tue, 26 Mar 2019 15:42:00 GMT</p> <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. Both shared and static versions of libruby are also provided.</p> </article> <article> <h1>[bio] star/2.7.0e installed on all systems</h1> <p>Mon, 25 Mar 2019 14:59:00 GMT</p> <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. The 2.7.0 released include support for STARsolo, single-cell alignments that are said to be ~10x faster than CellRanger.</p> </article> <article> <h1>[bio] phast/1.5 installed on all systems</h1> <p>Mon, 25 Mar 2019 11:53:00 GMT</p> <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> </article> <article> <h1>[build] maven/3.6.0 installed on all systems</h1> <p>Thu, 21 Mar 2019 15:43:00 GMT</p> <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> </article> <article> <h1>[build] automake/1.16.1 installed on all systems</h1> <p>Tue, 19 Mar 2019 16:15:00 GMT</p> <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> </article> <article> <h1>[apps] RStudio/1.1.463 installed on all systems</h1> <p>Tue, 19 Mar 2019 15:25:00 GMT</p> <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> </article> <article> <h1>[bio] SNPTEST/2.5.5 installed on all systems</h1> <p>Tue, 19 Mar 2019 15:13:00 GMT</p> <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> </article> <article> <h1>[bio] qctool/2.0.1 installed on all systems</h1> <p>Tue, 19 Mar 2019 15:12:00 GMT</p> <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> </article> <article> <h1>[bio] fineSTRUCTURE/4.0.1 installed on all systems</h1> <p>Mon, 18 Mar 2019 15:35:00 GMT</p> <p><a href="https://people.maths.bris.ac.uk/~madjl/finestructure/finestructure.html">FineSTRUCTURE</a> (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. See 'module help fineSTRUCTURE/4.0.1' for more information.</p> </article> <article> <h1>[comp] python/3.7.2 installed on all systems</h1> <p>Mon, 18 Mar 2019 13:43:00 GMT</p> <p><a href="https://www.python.org/">Python</a> version 3.7.2 is now installed as module python/3.7.2 on all systems. 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> </article> <article> <h1>[bio] iqtree/1.6.10-omp-mpi now installed on all systems</h1> <p>Sat, 16 Mar 2019 13:48:00 GMT</p> <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. Several different executables with different multithreading capabilities are available; see 'module help iqtree/1.6.10-omp-mpi' for more information.</p> </article> <article> <h1>[bio] eggNOG-mapper/1.0.3 and EggNOG 4.5.1 databases installed</h1> <p>Sat, 16 Mar 2019 13:34:00 GMT</p> <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. 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> </article> <article> <h1>[bio] SURVIVOR 1.0.3 installed on all systems</h1> <p>Fri, 15 Mar 2019 12:45:00 GMT</p> <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> </article> <article> <h1>[comp] python/3.6.8 installed on all systems</h1> <p>Thu, 14 Mar 2019 15:58:00 GMT</p> <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. 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> </article> <article> <h1>[bio] phyutility/2.7.3 is now installed on all systems</h1> <p>Thu, 14 Mar 2019 15:36:00 GMT</p> <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> </article> <article> <h1>[bio] SLiM/3.2.1 installed on all systems</h1> <p>Wed, 13 Mar 2019 11:37:00 GMT</p> <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> </article> <article> <h1>[bio] blasr/5.3.2 installed on all systems</h1> <p>Mon, 11 Mar 2019 12:52:00 GMT</p> <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> </article> <article> <h1>[bio] cutadapt/2.0 installed on all systems</h1> <p>Mon, 11 Mar 2019 10:44:00 GMT</p> <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> </article> <article> <h1>[bio] RGT version 0.11.6 installed on all systems</h1> <p>Fri, 08 Mar 2019 12:40:00 GMT</p> <p><a href="https://www.regulatory-genomics.org/">RGT</a> (A python library and set of tools for the integrative analysis of high throughput regulatory genomics data) version 0.11.6 installed on all systems as module RGT/0.11.6</p> </article> <article> <h1>[build] meson/0.49.2 installed</h1> <p>Wed, 06 Mar 2019 13:50:00 GMT</p> <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> </article> <article> <h1>[build] ninja/1.9.0 installed on all systems</h1> <p>Wed, 06 Mar 2019 12:02:00 GMT</p> <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> </article> <article> <h1>[bio] LoRDEC/0.9 installed on all systems</h1> <p>Tue, 05 Mar 2019 16:22:00 GMT</p> <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> </article> <article> <h1>[bio] nibabel version 2.3.3 installed on all systems</h1> <p>Tue, 05 Mar 2019 15:24:00 GMT</p> <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> </article> <article> <h1>[bio] new GATK data bundle installed</h1> <p>Tue, 05 Mar 2019 10:28:00 GMT</p> <p>An updated GATK resource bundle from Broad Institute has been installed at /sw/data/uppnex/GATK/.</p> </article> <article> <h1>[bio] biopython/1.73 (python/2.7.15) and biopython/1.73 (python/3.6.0) installed</h1> <p>Tue, 05 Mar 2019 10:06:00 GMT</p> <p><a href="https://biopython.org/">BioPython</a> 1.73 has been installed on all systems. 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> </article> <article> <h1>[bio] CheckM/1.0.12 installed and data directory installed</h1> <p>Tue, 05 Mar 2019 09:17:00 GMT</p> <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. Also installed and configured are the CheckM data files.</p> </article> <article> <h1>[bio] Drosophila melanogaster genomes installed for ngsplot</h1> <p>Fri, 01 Mar 2019 08:44:00 GMT</p> <p>[bio] Drosophila melanogaster genomes (dm3, dm6) installed for ngsplot.</p> </article> <article> <h1>|apps] Mathematica 11.2 installed</h1> <p>Fri, 01 Mar 2019 08:40:00 GMT</p> <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> </article> <article> <h1>[apps] R/3.5.2 and R_packages/3.5.2 installed on all systems</h1> <p>Fri, 08 Feb 2019 16:46:00 GMT</p> <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. R_packages/3.5.2 contains 13355 CRAN packages installed, out of 13683 available, and 2933 BioConductor-specific packages installed, out of 2959 available. </p> </article> <article> <h1>[bio] annovar/2018.04.16 installed on all systems</h1> <p>Tue, 05 Feb 2019 08:34:00 GMT</p> <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> </article> <article> <h1>[bio] PILER-64/1.0 installed on all systems</h1> <p>Mon, 28 Jan 2019 16:48:00 GMT</p> <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. 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> </article> <article> <h1>[bio] trf/4.09 installed on all systems</h1> <p>Mon, 28 Jan 2019 16:46:00 GMT</p> <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. The legacy version trf/4.07b is now also available on all systems.</p> </article> <article> <h1>[bio] RepeatModeler/1.0.11 installed</h1> <p>Fri, 25 Jan 2019 17:38:00 GMT</p> <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. Several auxiliary programs are provided; see 'module help RepeatModeler/1.0.11' for more details.</p> </article> <article> <h1>[bio] RepeatMasker/4.0.8 installed</h1> <p>Thu, 24 Jan 2019 15:17:00 GMT</p> <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. 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> </article> <article> <h1>[bio] ANTs/2.3.1 installed</h1> <p>Mon, 14 Jan 2019 14:28:00 GMT</p> <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> </article> <article> <h1>[build] cmake/3.13.2 installed</h1> <p>Mon, 14 Jan 2019 14:18:00 GMT</p> <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> </article> <article> <h1>[bio] Stacks/2.2 installed</h1> <p>Tue, 08 Jan 2019 15:27:00 GMT</p> <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> </article> <article> <h1>[bio] MultiQC/1.7 installed</h1> <p>Tue, 08 Jan 2019 14:35:00 GMT</p> <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> </article> <article> <h1>[bio] cellranger/3.0.1 installed together with Cell Ranger data 3.0.0</h1> <p>Tue, 08 Jan 2019 13:31:00 GMT</p> <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. See 'module help cellranger/3.0.1' for more information.</p> </article> <article> <h1>[bio] gmap-gsnap/2018-07-04 installed</h1> <p>Mon, 07 Jan 2019 13:34:00 GMT</p> <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. </p> </article> <article> <h1>[bio] rrbgen 0.0.6 and STITCH 1.5.4 installed to R_packages/3.5.0</h1> <p>Mon, 07 Jan 2019 13:25:00 GMT</p> <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> </article> <article> <h1>[bio] bowtie2/2.3.4.3 installed on all systems</h1> <p>Thu, 13 Dec 2018 09:35:00 GMT</p> <p>Bowtie2 (short read aligner) version 2.3.4.3 has been installed as module bowtie2/2.3.4.3 on all systems.</p> </article> <article> <h1>[bio] chipster module fixed</h1> <p>Mon, 10 Dec 2018 13:25:00 GMT</p> <p>The URL used by the chipster/webstart module has been updated to use https. The use of chipster via this module still requires an account at https://chipster.csc.fi/, and it will request account credentials when started.</p> </article> <article> <h1>[bio] HiCExplorer version 2.2-beta installed on all systems</h1> <p>Wed, 28 Nov 2018 14:48:00 GMT</p> <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> </article> <article> <h1>[bio] TIDDIT version 2.3.0 installed on all systems</h1> <p>Wed, 28 Nov 2018 10:15:00 GMT</p> <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> </article> <article> <h1>[bio] Minimac4 version 1.0.0 installed on all systems</h1> <p>Wed, 28 Nov 2018 09:45:00 GMT</p> <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> </article> <article> <h1>[bio] tigment/1.1.2 now installed on all systems</h1> <p>Mon, 26 Nov 2018 14:06:00 GMT</p> <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> </article> <article> <h1>[bio] MUMmer/4.0.0beta2 installed on all systems</h1> <p>Mon, 26 Nov 2018 13:41:00 GMT</p> <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> </article> <article> <h1>[bio] qiime2 version 2018.11.0 installed on all systems</h1> <p>Thu, 22 Nov 2018 18:14:00 GMT</p> <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> </article> <article> <h1>[bio] MaxBin version 2.2.5 installed on all systems</h1> <p>Thu, 22 Nov 2018 11:47:00 GMT</p> <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> </article> <article> <h1>[bio] CONCOCT version 0.5.0 installed on all systems</h1> <p>Tue, 20 Nov 2018 12:56:00 GMT</p> <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> </article> <article> <h1>[bio] albacore build 4aee41d installed on all systems</h1> <p>Mon, 19 Nov 2018 14:10:00 GMT</p> <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> </article> <article> <h1>[bio] LASER/2.04 installed on all systems</h1> <p>Tue, 13 Nov 2018 12:51:00 GMT</p> <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. The earlier versions LASER/2.01 and LASER/2.02 were also provided for all systems.</p> </article> <article> <h1>[bio] RAxML-NG/0.7.0b and RAxML-NG/0.7.0b-mpi now installed on all systems</h1> <p>Thu, 08 Nov 2018 16:25:00 GMT</p> <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> </article> <article> <h1>[bio] MACS/2.1.2 installed on all systems</h1> <p>Thu, 08 Nov 2018 14:07:00 GMT</p> <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> </article> <article> <h1>[bio] hichipper/0.7.3 installed on all systems</h1> <p>Thu, 08 Nov 2018 12:35:00 GMT</p> <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> </article> <article> <h1>[bio] OrthoMCL/2.0.9 now creates goodProteins.fasta database with -parse_seqids option</h1> <p>Thu, 08 Nov 2018 09:23:00 GMT</p> <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> </article> <article> <h1>[bio] pyGenomeTracks/2.1 installed on all systems</h1> <p>Tue, 06 Nov 2018 09:54:00 GMT</p> <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> </article> <article> <h1>[bio] HiC-Pro/2.11.1 installed on all systems</h1> <p>Fri, 26 Oct 2018 13:51:00 GMT</p> <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> </article> <article> <h1>[bio] Kourami/0.9.6 installed on all systems</h1> <p>Wed, 24 Oct 2018 14:37:00 GMT</p> <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> </article> <article> <h1>[bio] MIP/6.0.0 installed on all systems</h1> <p>Wed, 24 Oct 2018 12:37:00 GMT</p> <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> </article> <article> <h1>[bio] Stampy/1.0.32 installed on all systems</h1> <p>Mon, 22 Oct 2018 15:25:00 GMT</p> <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> </article> <article> <h1>[bio] Mothur/1.41.0 installed on all systems</h1> <p>Tue, 09 Oct 2018 09:58:00 GMT</p> <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> </article> <article> <h1>[bio] Kraken2/2.0.7-beta-bc14b13 installed on all systems</h1> <p>Wed, 26 Sep 2018 12:24:00 GMT</p> <p>The <a href="http://ccb.jhu.edu/software/kraken/MANUAL.html">Kraken2</a> sequence classificiation system version 2.0.7-beta as of the commit tagged bc14b13 has been installed as Kraken2/2.0.7-beta-bc14b13 on all systems. The default database, as well as the special greengenes, rdp and silva databases have been built and will be rebuilt monthly. See 'module help Kraken2/2.0.7-beta-bc14b13' for more.</p> </article> <article> <h1>[parallel] gnuparallel/20180822 installed on all systems</h1> <p>Thu, 20 Sep 2018 12:58:00 GMT</p> <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> </article> <article> <h1>[bio] InterProScan/5.30-69.0 installed on all systems</h1> <p>Thu, 06 Sep 2018 15:29:00 GMT</p> <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 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 Phobius/1.01, SignalP/4.1f, and tmhmm/2.0c.</p> </article> <article> <h1>[bio] Phobius/1.01 installed on all systems</h1> <p>Thu, 06 Sep 2018 15:04:00 GMT</p> <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. The 64-bit executable is used for the subsidiary tool decodeanhmm. </p> </article> <article> <h1>[bio] umi_tools/0.5.3 and umi_tools/0.5.4 installed on all systems</h1> <p>Fri, 17 Aug 2018 08:13:00 GMT</p> <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> </article> <article> <h1>[bio] samstat/1.5.1 installed on all systems</h1> <p>Thu, 16 Aug 2018 12:44:00 GMT</p> <p><a href="http://samstat.sourceforge.net/">Samstat</a> (sequence statistics) has been installed as module samstat/1.5.1 on all systems. This module requires samtools, and the samtools/1.8 module will be loaded if another module version of samtools is not already loaded.</p> </article> <article> <h1>[bio] Mothur 1.40.5 installed on all systems</h1> <p>Thu, 16 Aug 2018 08:02:00 GMT</p> <p>Mothur, a bioinformatics package developed by and 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 "module load Mothur/1.40.5".</p> </article> <article> <h1>[bio] GenomeThreader/1.7.0 installed on all systems</h1> <p>Mon, 13 Aug 2018 12:28:00 GMT</p> <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> </article> <article> <h1>[bio] clustalo/1.2.4 installed on all systems</h1> <p>Mon, 06 Aug 2018 12:33:00 GMT</p> <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> </article> <article> <h1>[bio] MAFFT/7.407 installed on all systems</h1> <p>Mon, 06 Aug 2018 12:32:00 GMT</p> <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. This includes MAFFT extensions.</p> </article> <article> <h1>[apps] R_packages/3.5.0 updated</h1> <p>Thu, 26 Jul 2018 16:40:00 GMT</p> <p>The R_packages omnibus module containing R packages has been updated with modules R2jags, rjags, units, and others. R_packages/3.5.0 contains 11746 CRAN packages, out of 12772 available, and 14544 BioConductor packages, out of 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> </article> <article> <h1>[apps] JAGS/4.3.0 installed on all systems</h1> <p>Thu, 26 Jul 2018 14:49:00 GMT</p> <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> </article> <article> <h1>[libs] UDUNITS/2.2.26 installed on all systems</h1> <p>Thu, 26 Jul 2018 13:39:00 GMT</p> <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. This module should be loaded before loading the package 'units' from R_packages/3.5.0.</p> </article> <article> <h1>[bio] Centrifuge/1.0.4-beta installed on all systems</h1> <p>Tue, 24 Jul 2018 11:53:00 GMT</p> <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. The indices p_compressed p_compressed+h+v p+h+v p+v v are prebuilt and available in $CENTRIFUGE_DB, set to the appropriate location when the module is loaded.</p> </article> <article> <h1>[bio] deepTools/3.1.0 installed on all systems</h1> <p>Thu, 19 Jul 2018 12:45:00 GMT</p> <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> </article> <article> <h1>[bio] GATK/3.8-0 now includes gatk wrapper script</h1> <p>Thu, 19 Jul 2018 11:29:00 GMT</p> <p>The GATK/3.8-0 module now includes the <strong>gatk</strong> 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 <strong>gatk ...</strong> or <strong>GenomeAnalysisTK ...</strong> directly.</p> </article> <article> <h1>[bio] sratools/2.9.1-1 installed on all systems</h1> <p>Wed, 18 Jul 2018 09:25:00 GMT</p> <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. This includes the fasterq-dump tool to speed the download of FastQ files from SRA.</p> </article> <article> <h1>[bio] CIRCexplorer/1.1.10 installed on all systems</h1> <p>Wed, 11 Jul 2018 15:32:00 GMT</p> <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> </article> <article> <h1>[bio] rvtests/2.0.6 installed on all systems</h1> <p>Tue, 10 Jul 2018 12:56:00 GMT</p> <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> </article> <article> <h1>[bio] PLINK/2 installed on all systems</h1> <p>Mon, 09 Jul 2018 14:34:00 GMT</p> <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> </article> <article> <h1>[bio] KrakenHLL/0.4.9 installed on all systems</h1> <p>Fri, 06 Jul 2018 15:33:00 GMT</p> <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> </article> <article> <h1>[bio] blobtools/1.0 installed on all systems</h1> <p>Fri, 06 Jul 2018 14:43:00 GMT</p> <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 blobtools/1.0 on all UPPMAX systems.</p> </article> <article> <h1>[bio] malder/1.0 available for rackham, bianca, irma</h1> <p>Thu, 28 Jun 2018 11:00:00 GMT</p> <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. It was previously available only on milou.</p> </article> <article> <h1>[bio] bbmap/38.08 installed</h1> <p>Thu, 28 Jun 2018 10:37:00 GMT</p> <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> </article> <article> <h1>[apps] siesta/4.1-b3 installed</h1> <p>Wed, 27 Jun 2018 14:20:00 GMT</p> <p>Siesta 4.1-b3</p> </article> <article> <h1>[bio] LDhelmet/1.10 installed</h1> <p>Tue, 26 Jun 2018 13:37:00 GMT</p> <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> </article> <article> <h1>[apps] siesta/4.0.1 installed</h1> <p>Tue, 26 Jun 2018 08:21:00 GMT</p> <p>Siesta 4.0.1</p> </article> <article> <h1>[comp] intel/18.3 installed</h1> <p>Thu, 21 Jun 2018 11:22:00 GMT</p> <p>Intel 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> </article> <article> <h1>[bio] iqtree/1.6.5-omp-mpi installed on all systems</h1> <p>Fri, 01 Jun 2018 10:55:00 GMT</p> <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. Different executables provide single-core, multi-core single-node, MPI, and hybrid MPI solutions. See 'module help iqtree/1.6.5-omp-mpi' for more information.</p> </article> <article> <h1>[bio] cutadapt/1.16 installed on all systems</h1> <p>Mon, 28 May 2018 13:30:00 GMT</p> <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. This version uses a python 3 virtual environment and supports threading.</p> </article> <article> <h1>[bio] vep/92 installed on all systems</h1> <p>Thu, 24 May 2018 14:13:00 GMT</p> <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> </article> <article> <h1>[bio] snpEff/4.3t installed on all systems</h1> <p>Thu, 24 May 2018 13:36:00 GMT</p> <p><a href="http://snpeff.sourceforge.net/">SnpEff</a> (variant annotation) version 4.3t is installed as module snpEff/4.3t on all systems. This installation also includes the databases CanFam3.1.75, CanFam3.1.86, GRCh37.75, GRCh37.p13.RefSeq, GRCh38.86, GRCh38.p7.RefSeq.</p> </article> <article> <h1>[bio] KAT/2.4.2 installed on all systems</h1> <p>Wed, 23 May 2018 11:10:00 GMT</p> <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> </article> <article> <h1>[bio] PBSuite/15.8.24 installed on all systems</h1> <p>Tue, 22 May 2018 22:39:00 GMT</p> <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. It was previously installed only on milou.</p> </article> <article> <h1>[bio] blast/2.7.1+ installed on all systems</h1> <p>Tue, 22 May 2018 22:36:00 GMT</p> <p>Blast+ (sequence search) version 2.7.1+ has been installed as module blast/2.7.1+ on all systems.</p> </article> <article> <h1>[apps] R_packages/3.5.0 installed on all systems</h1> <p>Sun, 20 May 2018 14:51:00 GMT</p> <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. This package includes 11937 <a href="https://ftp.acc.umu.se/mirror/CRAN/">CRAN</a> packages installed, out of 12571 available, and 14735 <a href="http://bioconductor.org/packages/release/BiocViews.html#___Software">BioConductor</a> packages installed, out of 15411 available.</p> </article> <article> <h1>[apps] R/3.5.0 installed on all systems</h1> <p>Sun, 20 May 2018 14:50:00 GMT</p> <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> </article> <article> <h1>[bio] Installed htslib version 1.8 on bianca, irma and rackham</h1> <p>Fri, 18 May 2018 09:45:00 GMT</p> <p>New version of <a href="https://github.com/samtools/htslib">htslib</a> (1.8) installed as module htslib/1.8</p> </article> <article> <h1>[bio] satsuma2/2016-12-07 installed on all systems</h1> <p>Fri, 18 May 2018 08:54:00 GMT</p> <p>Satsuma2 (whole genome alignment) version 2016-12-07 is now available on all Uppmax systems. It was previously available only on milou.</p> </article> <article> <h1>[bio] Kraken/1.1-352e780 has been installed on all systems</h1> <p>Thu, 17 May 2018 10:46:00 GMT</p> <p>Kraken (metagenomic assignment) version 1.1-352e780 has been installed on all systems. This is Kraken 1.1 plus a bugfix for the new paired-reads output mode.</p> </article> <article> <h1>[apps] rspt/2018-03-31_rackham_intel_mkl installed on Rackham</h1> <p>Mon, 14 May 2018 13:58:00 GMT</p> <p>RSPt version released March 31st, 2018 is installed on Rackham.</p> </article> <article> <h1>[parallel] openmpi/3.1.0</h1> <p>Wed, 09 May 2018 10:22:00 GMT</p> <p>openmpi 3.1.0 is now installed on Irma, Milou and Rackham.</p> </article> <article> <h1>[comp] gcc/8.1.0 installed</h1> <p>Wed, 09 May 2018 10:21:00 GMT</p> <p>gcc 8.1.0 is now installed on Bianca, Irma, Milou and Rackham</p> </article> <article> <h1>[apps] amber/ambertools18_intel_python2 installed on Rackham</h1> <p>Tue, 08 May 2018 09:26:00 GMT</p> <p>AmberTools18 (released on April 17, 2018) is installed as a module on Rackham.</p> </article> <article> <h1>[bio] cd-hit/4.6.8-2017-1208 installed on all systems</h1> <p>Thu, 03 May 2018 13:50:00 GMT</p> <p><a href="https://github.com/weizhongli/cdhit">CD-HIT</a> (sequence clustering) version 4.6.8-2017-1208 has been installed as module cd-hit/4.6.8-2017-1208 on all systems.</p> </article> <article> <h1>[bio] FastTree/2.1.10 installed on all systems</h1> <p>Thu, 03 May 2018 13:13:00 GMT</p> <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. Three executables are available, including single- and multi-threaded versions; see 'module help FastTree/2.1.10' for more information.</p> </article> <article> <h1>[bio] eigensoft/7.2.1 installed on all systems</h1> <p>Thu, 26 Apr 2018 13:38:00 GMT</p> <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> </article> <article> <h1>[bio] AdmixTools/5.0-20171024 installed on all systems</h1> <p>Wed, 25 Apr 2018 09:52:00 GMT</p> <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 qpDpart and rolloffp tools, is now installed as module AdmixTools/5.0-20171024 on all systems. Also installed on all systems are AdmixTools/20160803 and AdmixTools/5.0-20170312, previously available only on milou.</p> </article> <article> <h1>[bio] BUSCO/3.0.2b installed on all systems</h1> <p>Mon, 23 Apr 2018 12:18:00 GMT</p> <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> </article> <article> <h1>[comp] ruby/2.5.0 installed on all systems</h1> <p>Wed, 18 Apr 2018 15:23:00 GMT</p> <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> </article> <article> <h1>[bio] ANGSD/0.921 installed on all systems</h1> <p>Wed, 18 Apr 2018 15:21:00 GMT</p> <p><a href="http://www.popgen.dk/angsd/index.php/ANGSD">ANGSD</a> (program for analysing next generation sequencing data) 0.921 is now installed as module ANGSD/0.921 on all systems.</p> </article> <article> <h1>[bio] bamtools/2.5.1 installed on all systems</h1> <p>Tue, 10 Apr 2018 14:37:00 GMT</p> <p>bamtools (BAM file manipulation and API) 2.5.1 is now installed as bamtools/2.5.1 on all systems. Both static and shared libraries are provided.</p> </article> <article> <h1>[bio] fastPHASE/1.4.8 and fastPHASE/1.4.0 available on all systems</h1> <p>Thu, 05 Apr 2018 15:05:00 GMT</p> <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. It was previously available only on milou.</p> </article> <article> <h1>[bio] gubbins/2.3.1 installed on all systems</h1> <p>Thu, 05 Apr 2018 13:48:00 GMT</p> <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> </article> <article> <h1>[bio] OrthoMCL/2.0.9 now available on all systems</h1> <p>Thu, 05 Apr 2018 13:46:00 GMT</p> <p>OrthoMCL (ortholog identification) version 2.0.9 is now installed as module OrthoMCL/2.0.9 on all systems. This was previously available only on milou. See 'module help OrthoMCL/2.0.9' for Uppmax-specific advice.</p> </article> <article> <h1>[apps] Matlab R2018a installed</h1> <p>Thu, 29 Mar 2018 06:57:00 GMT</p> <p>Matlab R2018a is installed as matlab/R2018a on all systems.</p> </article> <article> <h1>[comp] intel/18.2 installed</h1> <p>Thu, 29 Mar 2018 06:55:00 GMT</p> <p>ntel Parallel Studio XE Cluster Edition 2018 update 2 has been installed on Rackham, Irma and Milou.</p> </article> <article> <h1>[comp] pgi/18.3 installed</h1> <p>Thu, 29 Mar 2018 06:53:00 GMT</p> <p>pgi/18.3 is installed on Rackham and Milou</p> </article> <article> <h1>[comp] advisor, ampilifier, inspector and itac upgraded</h1> <p>Thu, 29 Mar 2018 06:51:00 GMT</p> <p>advisor, ampilifier, inspector and itac upgraded has been upgraded to versions included in 2018 update 2.</p> </article> <article> <h1>[parallel] openmpi/2.1.3 installed</h1> <p>Wed, 21 Mar 2018 09:50:00 GMT</p> <p> openmpi/2.1.3 installed on Rackham and Irma</p> </article> <article> <h1>[bio] MultiQC/1.5 installed on all systems</h1> <p>Thu, 15 Mar 2018 23:33:00 GMT</p> <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> </article> <article> <h1>[bio] gvcftools/0.16.2 and gvcftools/0.17.0 available on all systems</h1> <p>Thu, 15 Mar 2018 11:36:00 GMT</p> <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. These were previously available on just milou.</p> </article> <article> <h1>[bio] Stacks/1.48 and Stacks/2.0Beta9 installed on all systems</h1> <p>Tue, 06 Mar 2018 21:17:00 GMT</p> <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> </article> <article> <h1>[apps] PostgreSQL/10.3 installed on all systems</h1> <p>Mon, 05 Mar 2018 22:37:00 GMT</p> <p>PostgreSQL (open-source relational database) 10.3 is now installed as module PostgreSQL/10.3 on all systems.</p> </article> <article> <h1>[bio] canu/1.7 installed on all systems</h1> <p>Mon, 05 Mar 2018 17:19:00 GMT</p> <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> </article> <article> <h1>[apps] ImageMagick-6.9.9-35 installed on all systems</h1> <p>Mon, 05 Mar 2018 17:12:00 GMT</p> <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. In addition to the ImageMagick executables, this module provides libraries and include files for building against ImageMagick (e.g., for the R package 'magick'). The module also includes an installation of libwebp 0.6.1 which includes the cwebp/dwebp executables.</p> </article> <article> <h1>[bio] Salmon/0.9.1 installed on all systems</h1> <p>Thu, 01 Mar 2018 18:57:00 GMT</p> <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> </article> <article> <h1>[bio] mergeSVcallers/161006-23533ef installed on all systems</h1> <p>Thu, 01 Mar 2018 15:08:00 GMT</p> <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> </article> <article> <h1>[bio] gmap-gsnap/2018-02-12 installed on all systems</h1> <p>Thu, 01 Mar 2018 12:32:00 GMT</p> <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. As per the developer's website, versions 2018-mm-dd and later do not yet have support for mapping to genomes >~4Gbp via the programs gmapl and gsnapl. For large genome support, load an earlier module version such as gmap-gsnap/2017-09-11.</p> </article> <article> <h1>[comp] gcc/7.3.0 installed</h1> <p>Tue, 27 Feb 2018 12:17:00 GMT</p> <p>gcc 7.3.0 is now installed on Bianca, Irma, Milou and Rackham as gcc/7.3.0</p> </article> <article> <h1>[apps] RStudio/1.1.423 installed on rackham, irma and bianca</h1> <p>Tue, 20 Feb 2018 16:56:00 GMT</p> <p><a href="https://www.rstudio.com/">RStudio</a> version 1.1.423 is installed on rackham, irma and bianca. This precompiled version cannot be installed on milou.</p> </article> <article> <h1>[bio] canu/1.6 installed on all systems</h1> <p>Tue, 20 Feb 2018 16:21:00 GMT</p> <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. For this version and all canu module versions >= 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. This can be overridden via configuration files or command-line options.</p> </article> <article> <h1>[bio] BEETL/1.1.0 installed on all systems</h1> <p>Tue, 20 Feb 2018 11:24:00 GMT</p> <p>BEETL (Burrows-Wheeler Extended Tool Library) version 1.1.0 is now installed as module BEETL/1.1.0 on all systems.</p> </article> <article> <h1>[bio] artemis/16.0.0 installed on all systems</h1> <p>Mon, 19 Feb 2018 15:58:00 GMT</p> <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> </article> <article> <h1>[bio] phylophlan/0.99 installed on all systems</h1> <p>Mon, 19 Feb 2018 13:53:00 GMT</p> <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> </article> <article> <h1>[bio] CheckM/1.0.11 installed on all systems</h1> <p>Mon, 19 Feb 2018 13:07:00 GMT</p> <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> </article> <article> <h1>[bio] megahit/1.1.2 installed on all systems</h1> <p>Sun, 18 Feb 2018 16:01:00 GMT</p> <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. The installed version is CPU-only, as GPUs are not available at UPPMAX.</p> </article> <article> <h1>[bio] beast/1.8.4 installed on all systems except for milou</h1> <p>Fri, 16 Feb 2018 16:47:00 GMT</p> <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> </article> <article> <h1>[bio] beast2/2.4.8 installed on all systems</h1> <p>Fri, 16 Feb 2018 16:44:00 GMT</p> <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. This module automatically loads the BEAGLE library module beagle/2.1.2.</p> </article> <article> <h1>[bio] LUMPY/0.2.13-213a417 installed on all systems</h1> <p>Fri, 16 Feb 2018 13:41:00 GMT</p> <p><a href="https://github.com/arq5x/lumpy-sv">LUMPY</a> (general probabilistic framework for structural variant discovery) version 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> </article> <article> <h1>[bio] supernova/2.0.0 installed on all systems</h1> <p>Mon, 12 Feb 2018 16:02:00 GMT</p> <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. The previous module versions supernova/{1.0.0,1.1.1,1.1.4} are also now available on all systems.</p> </article> <article> <h1>[bio] bcl2fastq/2.20.0 installed on all systems</h1> <p>Mon, 12 Feb 2018 16:00:00 GMT</p> <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> </article> <article> <h1>[bio] infernal/1.1.2 installed on all systems</h1> <p>Fri, 09 Feb 2018 15:22:00 GMT</p> <p>Infernal (Inference of RNA alignments) 1.1.2 is now installed on all systems as module infernal/1.1.2. The earlier version infernal/1.1.1 is also now available on all systems.</p> </article> <article> <h1>[bio] prokka/1.12-12547ca installed on all systems</h1> <p>Fri, 09 Feb 2018 15:02:00 GMT</p> <p>The most recent Prokka (bacterial genome annotation package) is available as module prokka/1.12-12547ca on all systems. This is version 1.12 updated to the most recent source commit.</p> </article> <article> <h1>[comp] git/2.16.1 now installed on all systems</h1> <p>Fri, 09 Feb 2018 15:01:00 GMT</p> <p>The most recent version of Git source control system is installed as module git/2.16.1 on all systems.</p> </article> <article> <h1>[bio] tbl2asn/25.3 available on all systems, and version 24.9 removed from all systems</h1> <p>Fri, 09 Feb 2018 14:59:00 GMT</p> <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> </article> <article> <h1>[bio] aragorn/1.2.38 installed on all systems</h1> <p>Fri, 09 Feb 2018 14:57:00 GMT</p> <p>ARAGORN (tRNA and tmRNA detection) 1.2.38 is installed as module aragorn/1.2.38 on all systems.</p> </article> <article> <h1>[bio] iqtree/1.5.4-omp-mpi installed on all systems</h1> <p>Tue, 06 Feb 2018 15:37:00 GMT</p> <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. See 'module help iqtree/1.5.4-omp-mpi' for more information.</p> </article> <article> <h1>[bio] snakemake/4.5.0 installed on all systems</h1> <p>Thu, 01 Feb 2018 17:02:00 GMT</p> <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> </article> <article> <h1>[bio] samtools/1.6, bcftools/1.6, htslib/1.6 installed on all systems</h1> <p>Tue, 30 Jan 2018 15:58:00 GMT</p> <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> </article> <article> <h1>[bio] spades/3.11.1 installed on all systems</h1> <p>Tue, 23 Jan 2018 13:14:00 GMT</p> <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> </article> <article> <h1>[bio] CONSEL/0.2.0 installed on all systems</h1> <p>Tue, 09 Jan 2018 15:37:00 GMT</p> <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 CONSEL/0.2.0 on all systems.</p> </article> <article> <h1>[bio] plinkseq 0.10 installed on all systems</h1> <p>Fri, 22 Dec 2017 10:02:00 GMT</p> <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> </article> <article> <h1>[bio] ATSAS/2.8.3-1 installed on all systems</h1> <p>Wed, 20 Dec 2017 22:51:00 GMT</p> <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> </article> <article> <h1>[bio] BEDTools/2.27.1 installed on all systems</h1> <p>Tue, 19 Dec 2017 14:21:00 GMT</p> <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> </article> <article> <h1>[bio] VCFaid/20170616-f0732ae installed on all systems</h1> <p>Mon, 18 Dec 2017 11:12:00 GMT</p> <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> </article> <article> <h1>[bio] svprops/20171020-ebf6762 installed on all systems</h1> <p>Mon, 18 Dec 2017 10:56:00 GMT</p> <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> </article> <article> <h1>[bio] Strelka2/2.8.4 installed on all systems</h1> <p>Mon, 18 Dec 2017 10:27:00 GMT</p> <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> </article> <article> <h1>[bio] GATK/4.beta.5 installed on all systems</h1> <p>Wed, 13 Dec 2017 18:07:00 GMT</p> <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. This is used differently from earlier versions of GATK. See 'module help GATK/4.beta.5' for more information.</p> </article> <article> <h1>[bio] pplacer/1.1.alpha19 installed on all systems</h1> <p>Fri, 08 Dec 2017 13:33:00 GMT</p> <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> </article> <article> <h1>[bio] freebayes/1.1.0 installed on all systems</h1> <p>Thu, 07 Dec 2017 15:01:00 GMT</p> <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> </article> <article> <h1>[apps] R/3.4.3 and omnibus package module R_packages/3.4.3 installed on all systems</h1> <p>Wed, 06 Dec 2017 14:53:00 GMT</p> <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. See the link for R_packages to see which packages are included.</p> </article> <article> <h1>[bio] MEGAN/6.10.5 installed on all systems</h1> <p>Tue, 05 Dec 2017 16:06:00 GMT</p> <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> </article> <article> <h1>[bio] cramtools/3.0 installed on all systems</h1> <p>Tue, 05 Dec 2017 09:57:00 GMT</p> <p><a href="https://github.com/enasequence/cramtools">Cramtools</a> 3.0 is installed as module cramtools/3.0 on all systems.</p> </article> <article> <h1>[apps] MariaDB/10.1.29 and /10.2.11 installed on all systems</h1> <p>Mon, 04 Dec 2017 15:19:00 GMT</p> <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. Uppmax does not allow persistent database servers beyond the extent of a single job; we recommend using sqlite for serverless SQL databases of convenience. These modules may also be useful for compiling software expecting to use a MySQL client to access remote databases.</p> </article> <article> <h1>[bio] bowtie2/2.3.3.1 installed on all systems</h1> <p>Mon, 04 Dec 2017 15:14:00 GMT</p> <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> </article> <article> <h1>[comp] java/sun_jdk1.8.0_151 installed on all systems</h1> <p>Mon, 04 Dec 2017 12:35:00 GMT</p> <p>The Sun Java Development Kit 8.0 release 151 has been installed as module java/sun_jdk1.8.0_151 on all systems.</p> </article> <article> <h1>[apps] vim/8.0-1360 installed on all systems</h1> <p>Fri, 01 Dec 2017 15:58:00 GMT</p> <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. This installation includes support for python, python3, perl and tcl interpreters. See 'module help vim/8.0-1360 for more information.</p> </article> <article> <h1>[bio] SMRT/5.0.1 installed on all systems</h1> <p>Mon, 20 Nov 2017 15:37:00 GMT</p> <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. This apparently includes all tools previously included in the SMRT Analysis set of tools.</p> </article> <article> <h1>[bio] blasr/5.3-20171117-f72428d installed on all systems</h1> <p>Mon, 20 Nov 2017 13:48:00 GMT</p> <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> </article> <article> <h1>[bio] pysam/0.13-python2.7.1 and pysam/0.13-python3.6.0 installed</h1> <p>Sat, 18 Nov 2017 11:49:00 GMT</p> <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> </article> <article> <h1>[bio] spaln/2.1.4 module now installed on all systems</h1> <p>Tue, 14 Nov 2017 10:58:00 GMT</p> <p>The SPALN spliced alignment tool version 2.1.4 is now installed as module spaln/2.1.4 on all systems. This module includes settings for compiling and linking against SPALN headers/libraries using gcc. The module was compiled with gcc/5.4.0.</p> </article> <article> <h1>[bio] NCBI taxonomy databases now available</h1> <p>Tue, 14 Nov 2017 10:57:00 GMT</p> <p><a href="https://www.ncbi.nlm.nih.gov/guide/taxonomy/">NCBI taxonomy databases</a> are now available as local copies at Uppmax. See our <a href="https://www.uppmax.uu.se/resurser/databases/ncbi-taxonomy-databases">NCBI taxonomy databases</a> page for more information.</p> </article> <article> <h1>[bio] UniVec and UniVec_Core databases now available</h1> <p>Tue, 14 Nov 2017 10:51:00 GMT</p> <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/**. 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**'. See our <a href="https://www.uppmax.uu.se/resurser/databases/blast-databases">Blast databases</a> page for more information.</p> </article> <article> <h1>[bio] prank/170427 installed on all systems</h1> <p>Thu, 09 Nov 2017 15:55:00 GMT</p> <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> </article> <article> <h1>[bio] Minimap2 2.4 installed as minimap2/2.4 on all systems</h1> <p>Thu, 09 Nov 2017 14:51:00 GMT</p> <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> </article> <article> <h1>[bio] bwa/0.7.17 installed on all systems</h1> <p>Thu, 09 Nov 2017 14:33:00 GMT</p> <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> </article> <article> <h1>[bio] TrimGalore/0.4.4 installed on all systems</h1> <p>Thu, 09 Nov 2017 14:01:00 GMT</p> <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> </article> <article> <h1>[bio] Nextflow 0.26.0 has been installed on all systems</h1> <p>Thu, 09 Nov 2017 14:00:00 GMT</p> <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> </article> <article> <h1>[bio] preseq/2.0 installed on all systems</h1> <p>Thu, 09 Nov 2017 13:58:00 GMT</p> <p><a href="http://smithlabresearch.org/software/preseq/">Preseq</a> 2.0 has been installed as module preseq/2.0 on all systems.</p> </article> <article> <h1>[bio] cutadapt/1.14 installed on all systems</h1> <p>Thu, 09 Nov 2017 13:57:00 GMT</p> <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> </article> <article> <h1>[bio] Kraken/1.0 installed on all systems</h1> <p>Sat, 04 Nov 2017 16:48:00 GMT</p> <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> </article> <article> <h1>[bio] MultiQC/1.3 installed on all systems</h1> <p>Fri, 03 Nov 2017 15:20:00 GMT</p> <p>MultiQC 1.3 has been installed on all systems as module MultiQC/1.3.</p> </article> <article> <h1>[bio] Blast databases are now being updated</h1> <p>Tue, 31 Oct 2017 11:43:00 GMT</p> <p>After a long lull, the local copies of Blast databases are now being updated. Some additional databases have been added, and the WGS database (not updated locally since 2014) is no longer available. See the <a href="https://www.uppmax.uu.se/resurser/databases/blast-databases">resource page for local Blast databases</a> for more information.</p> </article> <article> <h1>[bio] vsearch/2.5.2 installed on all systems</h1> <p>Mon, 30 Oct 2017 20:27:00 GMT</p> <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> </article> <article> <h1>[apps] packages added and updated in R_packages/3.4.0</h1> <p>Mon, 30 Oct 2017 14:35:00 GMT</p> <p>Several packages have been added and many have been updated in the module R_packages/3.4.0. See <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> </article> <article> <h1>[apps] GAMESS-US installed on Rackham</h1> <p>Mon, 30 Oct 2017 13:48:00 GMT</p> <p>GAMESS-US, a molecular dynamics package, is now installed on Rackham as module gamess/20170930. </p> </article> <article> <h1>[libs] GLPK 4.63 linear programming package installed</h1> <p>Mon, 30 Oct 2017 13:45:00 GMT</p> <p>GLPK (GNU Linear Programming Kit) package for solving large-scale linear programming (LP), mixed integer programming (MIP), and related problems is now installed on Rackham, Irma, and Bianca as module glpk/4.63.</p> </article> <article> <h1>[bio] sratools/2.8.2-1 installed on all systems</h1> <p>Sun, 29 Oct 2017 12:10:00 GMT</p> <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. 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> </article> <article> <h1>[bio] plink/1.90b4.9 installed on all systems</h1> <p>Wed, 25 Oct 2017 13:20:00 GMT</p> <p><a href="https://www.cog-genomics.org/plink2">PLINK</a> 1.90b4.9 (beta version as of 13 Oct 2017) is now available as module plink/1.90b4.9 on all systems. 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> </article> <article> <h1>[ apps] VASP 5.4.4 and VASPsol 5.4.4 installed on Rackham</h1> <p>Wed, 25 Oct 2017 08:13:00 GMT</p> <h3>VASP version 5.4.4 and VASPsol version 5.4.4 have been installed as modules vasp/5.4.4_intel_mkl and vaspsol/5.4.4_intel_mkl on Rackham</h3> </article> <article> <h1>[bio] NextGenMap/0.5.4 installed on all systems</h1> <p>Tue, 24 Oct 2017 10:23:00 GMT</p> <p><a href="http://cibiv.github.io/NextGenMap/">NextGenMap</a> version 0.5.4 has been installed as module NextGenMap/0.5.4 as part of bioinfo-tools on all systems.</p> </article> <article> <h1>[bio] Pilon/1.22 installed on all systems</h1> <p>Sun, 22 Oct 2017 19:32:00 GMT</p> <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> </article> <article> <h1>[bio] REAPR/1.0.18 installed on all systems</h1> <p>Sun, 22 Oct 2017 17:08:00 GMT</p> <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> </article> <article> <h1>[bio] SeqTools/4.44.1 installed on all systems</h1> <p>Thu, 19 Oct 2017 15:40:00 GMT</p> <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> </article> <article> <h1>[bio] ShoRAH/1.1.0 installed on all systems</h1> <p>Thu, 19 Oct 2017 14:52:00 GMT</p> <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> </article> <article> <h1>[bio] IGV/2.4.2 and IGVtools/2.3.98 installed on all systems</h1> <p>Tue, 17 Oct 2017 12:52:00 GMT</p> <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. 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> </article> <article> <h1>[bio] velvet/1.2.10 and velvet/1.2.10_K128 offer more capabilities</h1> <p>Tue, 17 Oct 2017 10:10:00 GMT</p> <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. See 'module help velvet/1.2.10' and 'module help velvet/1.2.10_K128' for more information.</p> </article> <article> <h1>[misc] POV-Ray installed</h1> <p>Mon, 16 Oct 2017 09:10:00 GMT</p> <p>POV-Ray 3.7 (raytracing engine) has been installed on Rackham, Bianca, and Irma as module povray/3.7.</p> </article> <article> <h1>[bio] LDhelmet/1.9 installed on all systems</h1> <p>Sun, 15 Oct 2017 13:36:00 GMT</p> <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> </article> <article> <h1>[bio] MetaBat/2.12.1 is installed on all systems</h1> <p>Sun, 15 Oct 2017 12:16:00 GMT</p> <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> </article> <article> <h1>[bio] ExpansionHunter/2.5.3 is installed on all systems</h1> <p>Thu, 12 Oct 2017 11:57:00 GMT</p> <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. See 'module help ExpansionHunter/2.5.3' for the location of repeat-specs for several human genome releases.</p> </article> <article> <h1>[bio] maker/3.01.1-beta installed on all systems</h1> <p>Mon, 09 Oct 2017 15:21:00 GMT</p> <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> </article> <article> <h1>[bio] RepeatMasker/4.0.7's RMBlast repaired via patch</h1> <p>Mon, 09 Oct 2017 14:45:00 GMT</p> <p>The RMBlast that is part of the <a href="http://www.repeatmasker.org/">RepeatMasker/4.0.7</a> module has been repaired. If you ever had rmblastn segfault with the message: "Critical: (109.4) CObject::RemoveLastReference: CObject was referenced again" while running RepeatMasker, this should correct that problem.</p> </article> <article> <h1>[bio] GeneMark/4.33-es installed on all systems</h1> <p>Mon, 09 Oct 2017 12:33:00 GMT</p> <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> </article> <article> <h1>[bio] trinotate/3.0.2 now installed on all systems</h1> <p>Tue, 03 Oct 2017 16:37:00 GMT</p> <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> </article> <article> <h1>[bio] SignalP/4.1f is now installed on all systems</h1> <p>Tue, 03 Oct 2017 09:33:00 GMT</p> <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. Use is restricted to academic users only.</p> </article> <article> <h1>[bio] TransDecoder/5.0.1 installed on all systems</h1> <p>Tue, 03 Oct 2017 08:11:00 GMT</p> <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> </article> <article> <h1>[bio] MultiQC/1.2 installed on all systems</h1> <p>Mon, 02 Oct 2017 21:08:00 GMT</p> <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> </article> <article> <h1>[bio] several more modules made available on all systems</h1> <p>Sat, 30 Sep 2017 21:18:00 GMT</p> <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): 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> </article> <article> <h1>[bio] MaSuRCA/3.2.3 installed on all systems</h1> <p>Sat, 30 Sep 2017 20:47:00 GMT</p> <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> </article> <article> <h1>[comp] several more modules added to perl_modules/5.24.1</h1> <p>Thu, 28 Sep 2017 13:08:00 GMT</p> <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> </article> <article> <h1>[bio] VarScan/2.4.2 installed on all systems</h1> <p>Tue, 26 Sep 2017 09:59:00 GMT</p> <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> </article> <article> <h1>[bio] several more modules made available on all systems</h1> <p>Fri, 22 Sep 2017 13:50:00 GMT</p> <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, openblas/0.2.14a, openblas/0.2.19, 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}, 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, pear/{0.9.5,0.9.10}, msmc/0.1.0</p> </article> <article> <h1>[bio] gmap-gsnap/2017-09-11 installed on all systems</h1> <p>Thu, 21 Sep 2017 16:03:00 GMT</p> <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> </article> <article> <h1>[bio] cellranger/2.0.2 installed on all systems</h1> <p>Thu, 21 Sep 2017 15:58:00 GMT</p> <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. 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> </article> <article> <h1>[bio] annovar/2017.07.16 installed on all systems</h1> <p>Wed, 20 Sep 2017 22:45:00 GMT</p> <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. 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> </article> <article> <h1>[bio] bbmap/37.53 installed on all systems</h1> <p>Tue, 19 Sep 2017 14:17:00 GMT</p> <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> </article> <article> <h1>[bio] AdapterRemoval/2.2.2 installed on all systems</h1> <p>Fri, 15 Sep 2017 09:27:00 GMT</p> <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. In addition, the earlier version AdapterRemoval/2.1.7, previously available only on milou, has also been installed on all systems. </p> </article> <article> <h1>[bio] Vmatch/2.3.0 installed on all systems</h1> <p>Thu, 14 Sep 2017 14:12:00 GMT</p> <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> </article> <article> <h1>[bio] BEDOPS/2.4.28 installed on all systems</h1> <p>Thu, 14 Sep 2017 14:11:00 GMT</p> <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> </article> <article> <h1>[bio] several more modules made available on all systems</h1> <p>Thu, 14 Sep 2017 14:03:00 GMT</p> <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): sickle/1.210, samplefq/0.2, sambamba/0.5.9, SBT/0.3, scalpel/0.5.2, selscan/1.1.0, 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, phast/1.4, ncl/2.1.21-dev</p> </article> <article> <h1>[bio] paml/4.9e is installed on all systems</h1> <p>Thu, 14 Sep 2017 13:21:00 GMT</p> <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> </article> <article> <h1>[bio] phylobayes/4.1c installed on all systems</h1> <p>Thu, 14 Sep 2017 12:27:00 GMT</p> <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> </article> <article> <h1>[bio] phylobayesmpi/1.8 installed on all systems</h1> <p>Thu, 14 Sep 2017 12:26:00 GMT</p> <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. </p> </article> <article> <h1>[bio] GATK-Queue/3.8-0 installed on all systems</h1> <p>Wed, 13 Sep 2017 15:42:00 GMT</p> <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> </article> <article> <h1>[apps] RStudio/1.1.233-buggy now available on milou</h1> <p>Wed, 13 Sep 2017 15:15:00 GMT</p> <p>RStudio version 1.1.233 has been built from source and installed as module RStudio/1.1.233-buggy on milou. The most recent prebuilt version available for milou cannot manage figures produced by more recent versions of R. 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. This will not be the default module version for RStudio on milou. Use at your own risk, or better yet use RStudio on another Uppmax system.</p> </article> <article> <h1>[bio] GATK/3.8-0 installed on all systems</h1> <p>Wed, 13 Sep 2017 15:13:00 GMT</p> <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. 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> </article> <article> <h1>[comp] pgi/17.7 installed</h1> <p>Wed, 13 Sep 2017 13:47:00 GMT</p> <p>pgi/17.7 installed on Milou and Rackham</p> </article> <article> <h1>[bio] local data caches for vep/84, vep/86 greatly reduced</h1> <p>Mon, 11 Sep 2017 16:31:00 GMT</p> <p>The local data caches for vep/84 and vep/86 have been reduced to just homo_sapiens. The local data caches for vep/87 and vep/89 remain complete. For more information, see <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> and 'module help vep'.</p> </article> <article> <h1>[bio] BioPerl/1.7.1_Perl5.24.1 installed on all systems</h1> <p>Mon, 11 Sep 2017 14:56:00 GMT</p> <p><a href="http://bioperl.org/">BioPerl</a> 1.7.1 for Perl 5.24.1 has been installed as module BioPerl/1.7.1_Perl5.24.1 on all systems.</p> </article> <article> <h1>[bio] spaln/2.3.1 installed on all systems</h1> <p>Thu, 07 Sep 2017 14:05:00 GMT</p> <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> </article> <article> <h1>[bio] sickle/1.33-20-g4b0dc85-mullins installed on all systems</h1> <p>Tue, 05 Sep 2017 15:41:00 GMT</p> <p><a href="https://github.com/MullinsLab/sickle">Sickle</a> (short read quality-based correction) version 1.33-20-g4b0dc85-mullins, based off a maintained fork of the original source tree, has been installed as module sickle/1.33-20-g4b0dc85-mullins on all systems.</p> </article> <article> <h1>[bio] SHORE/0.9.3 installed on all systems</h1> <p>Tue, 05 Sep 2017 15:40:00 GMT</p> <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> </article> <article> <h1>[bio] sambamba/0.6.6 installed on all systems</h1> <p>Tue, 05 Sep 2017 15:38:00 GMT</p> <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> </article> <article> <h1>[bio] scalpel/0.5.3 installed on all systems</h1> <p>Tue, 05 Sep 2017 15:37:00 GMT</p> <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> </article> <article> <h1>Several more modules now available on all systems</h1> <p>Mon, 04 Sep 2017 11:29:00 GMT</p> <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, multiz/012109 </p> <div></div> </article> <article> <h1>[bio] MAFFT/7.310 installed on all systems</h1> <p>Mon, 04 Sep 2017 11:12:00 GMT</p> <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> </article> <article> <h1>[libs] jemalloc/5.0.1 installed on all systems</h1> <p>Mon, 04 Sep 2017 08:27:00 GMT</p> <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. The earlier installed module version jemalloc/3.6.0 is also now available on all systems.</p> </article> <article> <h1>[bio] trinity/2.4.0 installed on all systems</h1> <p>Sun, 03 Sep 2017 19:56:00 GMT</p> <p>Trinity 2.4.0 (transcriptome assembler) is installed as module trinity/2.4.0 on all systems.</p> </article> <article> <h1>[bio] khmer/2.1.1 installed on all systems</h1> <p>Sun, 03 Sep 2017 12:35:00 GMT</p> <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> </article> <article> <h1>[bio] NGSadmin/32 and fastNGSadmin/20170825-099ab7f are installed on all systems</h1> <p>Sat, 02 Sep 2017 18:44:00 GMT</p> <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> </article> <article> <h1>[bio] lastz/1.04.00 installed on all systems</h1> <p>Fri, 01 Sep 2017 15:25:00 GMT</p> <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> </article> <article> <h1>[bio] rtgcore/3.8.3 installed on all systems</h1> <p>Fri, 01 Sep 2017 12:49:00 GMT</p> <p>The non-commercial version of <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. This includes all functionality of rtgtools/3.8.3 as well as additional commands.</p> </article> <article> <h1>[bio] rtgtools/3.8.3 installed on all systems</h1> <p>Fri, 01 Sep 2017 12:48:00 GMT</p> <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> </article> <article> <h1>[bio] fastq_screen/0.11.1 installed on all systems</h1> <p>Fri, 01 Sep 2017 10:58:00 GMT</p> <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> </article> <article> <h1>[bio] anfo/0.98 now available for all systems</h1> <p>Fri, 01 Sep 2017 09:53:00 GMT</p> <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. 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. This version of the program is quite old (~8 y).</p> </article> <article> <h1>[apps] gnuplot/5.0.7 installed on all systems</h1> <p>Thu, 31 Aug 2017 15:03:00 GMT</p> <p><a href="http://www.gnuplot.info/">Gnuplot</a> 5.0.7 is installed as module gnuplot/5.0.7 on all systems.</p> </article> <article> <h1>[apps] awscli/1.11.140 now available on all systems</h1> <p>Fri, 25 Aug 2017 14:56:00 GMT</p> <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> </article> <article> <h1>Several more modules now available on all systems</h1> <p>Fri, 25 Aug 2017 14:50:00 GMT</p> <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 mbuffer/20151002.</p> </article> <article> <h1>[bio] htseq/0.9.1 installed on all systems</h1> <p>Fri, 25 Aug 2017 11:43:00 GMT</p> <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> </article> <article> <h1>[comp] gcc/6.4.0 installed</h1> <p>Fri, 25 Aug 2017 10:19:00 GMT</p> <p>gcc 6.4.0 is now installed on Bianca, Irma, Milou and Rackham as gcc/6.4.0</p> </article> <article> <h1>[bio] ITSx/1.0.11 and ITSx/1.1-beta installed on all systems</h1> <p>Fri, 25 Aug 2017 09:23:00 GMT</p> <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. Both versions are new installations for all systems; note that 1.1-beta is a beta (preliminary) release.</p> </article> <article> <h1>[bio] rseqc/2.6.4 installed on all systems</h1> <p>Thu, 24 Aug 2017 12:50:00 GMT</p> <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> </article> <article> <h1>[bio] MaSuRCA/3.2.2 installed on all systems</h1> <p>Mon, 21 Aug 2017 13:22:00 GMT</p> <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> </article> <article> <h1>[bio] KAT/2.3.4 installed on all systems</h1> <p>Wed, 16 Aug 2017 14:12:00 GMT</p> <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> </article> <article> <h1>[comp] gcc/7.2.0 installed</h1> <p>Tue, 15 Aug 2017 10:58:00 GMT</p> <p>gcc 7.2.0 is now installed in Bianca, Irma, Milou and Rackham as gcc/7.2.0.</p> </article> <article> <h1>[bio] RealTime Genomics reference databases now available</h1> <p>Sat, 12 Aug 2017 12:28:00 GMT</p> <p><a href="https://www.realtimegenomics.com/news/pre-formatted-reference-datasets">RealTime Genomics' preformatted reference databases</a> are now available on Uppmax systems. See 'module help rtgtools/3.8.1' for more information.</p> </article> <article> <h1>[bio] pblat-cluster/0.3 installed on all systems</h1> <p>Fri, 11 Aug 2017 09:27:00 GMT</p> <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. Note that module pblat/2.0, with single-node multithreading, is also available.</p> </article> <article> <h1>[bio] pblat/2.0 installed on all clusters</h1> <p>Fri, 11 Aug 2017 09:25:00 GMT</p> <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> </article> <article> <h1>[bio] all bioinformatics modules will default to the latest version</h1> <p>Thu, 10 Aug 2017 14:14:00 GMT</p> <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'. All such restrictions on default versions have now been removed. To improve reproducibility of results, a specific module version should <em><strong>always</strong></em> be specified when loading tools via the module system.</p> </article> <article> <h1>[apps] Matlab R2017a installed</h1> <p>Wed, 09 Aug 2017 12:05:00 GMT</p> <p>Matlab R2017a has been installed as module matlab/R2017a on Milou and Rackham.</p> </article> <article> <h1>[bio] EPACTS/3.3.0-a5209db installed on all systems</h1> <p>Tue, 08 Aug 2017 14:52:00 GMT</p> <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> </article> <article> <h1>[bio] MELT/2.0.2 installed on all systems</h1> <p>Tue, 08 Aug 2017 12:46:00 GMT</p> <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> </article> <article> <h1>[bio] AMOS/3.0.0, AMOS/3.1.0, blat/34 and blat/35 now on rackham, irma, bianca</h1> <p>Mon, 07 Aug 2017 15:42:00 GMT</p> <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> </article> <article> <h1>[bio] kallisto/0.43.1 installed on all systems</h1> <p>Mon, 07 Aug 2017 15:40:00 GMT</p> <p><a href="https://pachterlab.github.io/kallisto/">The RNA-seq pseudoalignment tool kallisto</a> version 0.43.1 has been installed on all systems as module kallisto/0.43.1.</p> </article> <article> <h1>[bio] cufflinks/2.2.1-b55bb21 installed on all systems</h1> <p>Mon, 07 Aug 2017 13:38:00 GMT</p> <p>An updated version of cufflinks has been installed as module cufflinks/2.2.1-b55bb21 on all systems. 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> </article> <article> <h1>[apps] several packages added to R_packages/3.4.0</h1> <p>Mon, 31 Jul 2017 14:33:00 GMT</p> <p>The R packages Lahman, RJSONIO, ecodist, gee, hflights, igraph, optparse, proto, and reshape and the BioConductor packages ROC, TCC, baySeq, multtest, and phyloseq, together with their dependencies, have been added to the R_packages/3.4.0 module. For a complete list of packages available, see the <a href="https://www.uppmax.uu.se/support-sv//r_packages-module-guide">R_packages user guide</a>.</p> </article> <article> <h1>[bio] picard/2.10.3 installed on all systems</h1> <p>Thu, 20 Jul 2017 21:48:00 GMT</p> <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> </article> <article> <h1>[bio] samtools/1.5, htslib/1.5, bcftools/1.5 installed on all systems</h1> <p>Thu, 20 Jul 2017 21:45:00 GMT</p> <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 <a href="https://github.com/samtools/bcftools">bcftools/1.5</a> have been installed on all systems. 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> </article> <article> <h1>[bio] augustus/3.2.2 available on irma, bianca, rackham</h1> <p>Tue, 18 Jul 2017 21:27:00 GMT</p> <p>The module augustus/3.2.2, previously available only on milou, is now also available on irma, bianca and rackham.</p> </article> <article> <h1>[bio] Longranger upgraded to 2.1.4 on all systems</h1> <p>Wed, 12 Jul 2017 07:37:00 GMT</p> <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> </article> <article> <h1>[bio] bismark/0.18.2 installed on all systems</h1> <p>Wed, 28 Jun 2017 12:05:00 GMT</p> <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. The earlier bismark module versions 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> </article> <article> <h1>[bio] vsearch/2.4.3 installed on all systems</h1> <p>Tue, 27 Jun 2017 12:36:00 GMT</p> <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> </article> <article> <h1>[bio] VEP 89 upgraded</h1> <p>Tue, 27 Jun 2017 10:44:00 GMT</p> <p>VEP (Variant Effect Predictor) has been upgraded to version 89 on all systems.</p> </article> <article> <h1>STAR-Fusion Installed on all the systems</h1> <p>Thu, 22 Jun 2017 16:22:00 GMT</p> <p>STAR-Fusion/1.0.0 is Installed and is available on all the systems.</p> </article> <article> <h1>Eigensoft upgraded to 7.2.0</h1> <p>Thu, 22 Jun 2017 16:19:00 GMT</p> <p>eigensoft/7.2.0 is now available on all the systems.</p> </article> <article> <h1>STAR upgraded to 2.5.3a</h1> <p>Wed, 21 Jun 2017 17:25:00 GMT</p> <p>star/2.5.3a is now available on all the systems.</p> </article> <article> <h1>HISAT2 upgraded to 2.1.0</h1> <p>Wed, 21 Jun 2017 09:23:00 GMT</p> <p>HISAT2/2.1.0 is now available on all the systems.</p> </article> <article> <h1>[geo] libgeotiff/1.4.1 available on rackham</h1> <p>Fri, 16 Jun 2017 14:34:00 GMT</p> <p>The libgeotiff/1.4.1 module is now available on rackham; it was previously available only on milou.</p> </article> <article> <h1>[geo] GEOS/3.4.0, GDAL/2.1.0, PROJ.4/4.9.2, FYBA/4.1.1 now on all systems</h1> <p>Fri, 16 Jun 2017 13:55:00 GMT</p> <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. These were already available on milou and were previously available on tintin. These are fresh installations of the modules from tintin, so are not necessarily the latest versions of these tools.</p> </article> <article> <h1>delly upgraded to 0.7.7</h1> <p>Wed, 07 Jun 2017 08:13:00 GMT</p> <p>delly/0.7.7 has been installed on all the systems.</p> </article> <article> <h1>[bio] rtgtools/3.8.1 installed on all systems</h1> <p>Mon, 05 Jun 2017 14:00:00 GMT</p> <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> </article> <article> <h1>[bio] MAGeCK/0.5.6 installed on all systems</h1> <p>Mon, 05 Jun 2017 13:39:00 GMT</p> <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> </article> <article> <h1>[bio] cufflinks/2.2.1 installed on all systems</h1> <p>Fri, 02 Jun 2017 22:54:00 GMT</p> <p>Cufflinks 2.2.1 has been installed as module cufflinks/2.2.1 on all systems. The earlier version cufflinks/2.1.1 has also been installed on rackham; it was all ready available on all other systems.</p> </article> <article> <h1>[bio] bowtie2/2.3.2 installed on all systems</h1> <p>Fri, 02 Jun 2017 22:51:00 GMT</p> <p>Bowtie2 2.3.2 has been installed as module bowtie2/2.3.2 on all systems.</p> </article> <article> <h1>[bio] bowtie/1.2.0 installed on all systems</h1> <p>Fri, 02 Jun 2017 22:47:00 GMT</p> <p>Bowtie 1.2.0 has been installed as module bowtie/1.2.0 on all systems.</p> </article> <article> <h1>[bio] tophat/2.1.1 installed on all systems</h1> <p>Fri, 02 Jun 2017 22:41:00 GMT</p> <p>Tophat 2.1.1 has been installed as module tophat/2.1.1 on all systems. The earlier versions tophat/2.0.10 and tophat/2.0.12 have also been made available on rackham, irma and/or bianca.</p> </article> <article> <h1>[bio] MrBayes installed on Rackham</h1> <p>Fri, 02 Jun 2017 08:21:00 GMT</p> <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. </p> </article> <article> <h1>[bio]Beagle-lib installed on Rackham</h1> <p>Fri, 02 Jun 2017 08:18:00 GMT</p> <p><a href="https://github.com/beagle-dev/beagle-lib">Beagle-lib</a> (general purpose library for evaluating the likelihood of sequence evolution on trees) is now installed on Rackham as module beagle/2.1.2. </p> </article> <article> <h1>[bio] MultiQC/1.0 installed on all systems</h1> <p>Tue, 30 May 2017 12:24:00 GMT</p> <p><a href="http://multiqc.info/">MultiQC</a> 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> </article> <article> <h1>[bio] several bioinfo-tools/misc modules now also available on rackham</h1> <p>Wed, 24 May 2017 15:21:00 GMT</p> <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: 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> </article> <article> <h1>[bio] deepTools/2.5.1 installed on all systems</h1> <p>Wed, 24 May 2017 15:16:00 GMT</p> <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> </article> <article> <h1>[bio] deepTools/2.4.3 installed on all systems</h1> <p>Wed, 24 May 2017 15:02:00 GMT</p> <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> </article> <article> <h1>[bio] seqtk/1.2-r101 available on all systems</h1> <p>Wed, 24 May 2017 11:36:00 GMT</p> <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. The earlier version 1.0-r57 has also been installed on all systems as module seqtk/1.0-r57, and the module versions seqtk/1.0-r31 and seqtk/1.0-r68e, previously available only on milou, have been installed on rackham, irma and bianca.</p> </article> <article> <h1>[comp] pgi/17.4 installed</h1> <p>Wed, 24 May 2017 10:01:00 GMT</p> <p>pgi/17.4 installed on Milou and Rackham</p> </article> <article> <h1>[parallel] openmpi/2.1.1</h1> <p>Wed, 24 May 2017 06:36:00 GMT</p> <p>openmpi/2.1.1 has been installed on Irma, Milou and Rackham</p> </article> <article> <h1>[comp] advisor, ampilifier, inspector and itac upgraded</h1> <p>Wed, 24 May 2017 06:35:00 GMT</p> <p>advisor, ampilifier, inspector and itac upgraded</p> </article> <article> <h1>[comp] intel/17.4 installed</h1> <p>Wed, 24 May 2017 06:33:00 GMT</p> <p>intel/17.4 has been installed on all systems.</p> </article> <article> <h1>[bio] TEtools/1.0.0-283c1ca installed on all systems</h1> <p>Fri, 19 May 2017 14:23:00 GMT</p> <p><a href="https://github.com/l-modolo/TEtools">TEtools</a> 1.0.0 up through commit 283c1ca has been installed as module TEtools/1.0.0-283c1ca on all systems. 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> </article> <article> <h1>[comp] perl_modules/5.24.1 installed on all systems</h1> <p>Mon, 15 May 2017 14:16:00 GMT</p> <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. 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. Note that perl/5.24.1 uses 64-bit integers and pointers. See the linked page for a list of the contents of this omnibus module.</p> </article> <article> <h1>[comp] perl6/rakudo-star-2017.04 installed on all systems</h1> <p>Mon, 15 May 2017 10:25:00 GMT</p> <p><a href="https://perl6.org">Perl6</a> <a href="http://rakudo.org/2017/05/01/announce-rakudo-star-release-2017-04/">Rakudo Star 2017.04</a> has been installed as module perl6/rakudo-star-2017.04 on all systems. This module also modifies the environment for development against MoarVM if so desired.</p> </article> <article> <h1>[apps] emacs/25.2 installed on all systems</h1> <p>Sun, 14 May 2017 01:18:00 GMT</p> <p>The editor <a href="https://www.gnu.org/software/emacs/">emacs</a> has been installed as module emacs/25.2 on all systems. Emacs is already installed on all systems but this module provides the most recent version.</p> </article> <article> <h1>[libs] giflib/5.1.4 installed on all systems</h1> <p>Sun, 14 May 2017 01:16:00 GMT</p> <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> </article> <article> <h1>[bio] ATLAS_aDNA/20170510 installed on all systems</h1> <p>Sat, 13 May 2017 17:55:00 GMT</p> <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. Note the module name is <strong>ATLAS_aDNA</strong>, because the name ATLAS has already being given to a module for the widely used numeric library.</p> </article> <article> <h1>[libs] Armadillo/7.900.0 installed on all systems</h1> <p>Sat, 13 May 2017 17:54:00 GMT</p> <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> </article> <article> <h1>[bio] hmmer/3.1b2-intel installed on all systems</h1> <p>Sat, 13 May 2017 09:43:00 GMT</p> <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> </article> <article> <h1>[bio] MethylDackel/0.2.1 installed on all systems</h1> <p>Thu, 11 May 2017 16:52:00 GMT</p> <p><a href="https://github.com/dpryan79/MethylDackel">MethylDackel</a> 0.2.1 (renamed continuation of methylation detection tool PileOMeth) is now installed as module MethylDackel/0.2.1 on all systems.</p> </article> <article> <h1>[comp] perl/5.24.1 installed on all systems</h1> <p>Thu, 11 May 2017 16:47:00 GMT</p> <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. 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. All perl modules with versions 5.24+ are built with 64-bit integers and pointers.</p> </article> <article> <h1>[bio] vcftools/0.1.15 installed on all systems</h1> <p>Thu, 11 May 2017 16:09:00 GMT</p> <p>VCFtools version 0.1.15 is now installed as module vcftools/0.1.15 on all systems. vcftools/0.1.14 has also been provided on rackham; it was previously available on milou, bianca and irma.</p> </article> <article> <h1>[build] m4/1.4.17 and libtool/2.4.6 installed on all systems</h1> <p>Thu, 11 May 2017 14:58:00 GMT</p> <p>The scripting language <a href="https://www.gnu.org/software/m4/m4.html">m4</a> 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 on all systems.</p> </article> <article> <h1>[build] cmake/3.5.1 available on rackham, bianca and irma</h1> <p>Thu, 11 May 2017 14:12:00 GMT</p> <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> </article> <article> <h1>[comp] gcc/7.1.0 installed</h1> <p>Thu, 11 May 2017 11:59:00 GMT</p> <p>gcc/7.1.0 installed on all systems.</p> </article> <article> <h1>[bio] malder/1.0 installed on milou</h1> <p>Tue, 09 May 2017 09:20:00 GMT</p> <p><a href="https://github.com/joepickrell/malder">MALDER</a> has been installed as module malder/1.0 on milou.</p> </article> <article> <h1>[apps] p7zip/16.02 now installed on all systems</h1> <p>Mon, 08 May 2017 11:21:00 GMT</p> <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. The executable file is named <strong>7za</strong>.</p> </article> <article> <h1>[bio] ProtExcluder/1.1 installed on all systems</h1> <p>Sat, 06 May 2017 22:57:00 GMT</p> <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> </article> <article> <h1>[bio] mirdeep2/2.0.0.8 installed on all systems</h1> <p>Sat, 06 May 2017 16:58:00 GMT</p> <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> </article> <article> <h1>[bio] MetaSV/0.5.4 installed on all systems</h1> <p>Sat, 06 May 2017 11:37:00 GMT</p> <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> </article> <article> <h1>[bio] spades/3.10.1 installed on all systems</h1> <p>Sat, 06 May 2017 10:52:00 GMT</p> <p>The latest <a href="http://bioinf.spbau.ru/spades">SPAdes</a> assembler is now installed as spades/3.10.1 on all systems. 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> </article> <article> <h1>[bio] AGE/0.4 installed on all systems</h1> <p>Sat, 06 May 2017 09:58:00 GMT</p> <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. The executable <strong>age_align</strong> is built without parallel support, while the executable <strong>age_align_omp</strong> is built with parallel support. See 'module help AGE/0.4' for more information.</p> </article> <article> <h1>[apps] eLSA/20160907-febe2d7a57c8 installed on all systems</h1> <p>Sat, 06 May 2017 09:21:00 GMT</p> <p><a href="https://bitbucket.org/charade/elsa/wiki/Home">eLSA</a> (extended local similarity analysis) has been installed as module eLSA/20160907-febe2d7a57c8 on all systems.</p> </article> <article> <h1>[bio] GEMINI/0.20.0 installed on all systems</h1> <p>Sat, 06 May 2017 01:58:00 GMT</p> <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. The earlier versions GEMINI/0.18.3 and GEMINI/0.20.0 have also been extended to rackham, irma and bianca. As before, the additional CADD and GERP annotation datasets have been included.</p> </article> <article> <h1>[bio] vep/87 and local caches installed on rackham, irma and bianca</h1> <p>Fri, 05 May 2017 11:25:00 GMT</p> <p>The Variant Effects Predictor module vep/87 and its local caches have been installed on rackham, irma and bianca. The module was previously installed only on milou.</p> </article> <article> <h1>[bio] fermikit/0.14-prerelease-96f7820 installed on all systems</h1> <p>Fri, 05 May 2017 11:13:00 GMT</p> <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 fermikit/0.14-prerelease-96f7820 on all systems. The previously installed fermikit/r178 is now also available on rackham, irma and bianca.</p> </article> <article> <h1>[bio] SpeedSeq/0.1.2-20170504-30f8dc6 installed on all systems</h1> <p>Fri, 05 May 2017 09:52:00 GMT</p> <p>The latest <a href="https://github.com/hall-lab/speedseq/">SpeedSeq</a> (rapid genome analysis and interpretation) is installed as module SpeedSeq/0.1.2-20170504-30f8dc6 on all systems. The module version reflects the most recent release, as well as the date and commit of the repository clone for this installed module. See 'module help SpeedSeq/0.1.2-20170504-30f8dc6' for more information on available data.</p> </article> <article> <h1>[bio] CNVnator/0.3.3 installed on all systems</h1> <p>Thu, 04 May 2017 09:45:00 GMT</p> <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> </article> <article> <h1>[apps] ROOT/6.06.08 installed on all systems</h1> <p>Thu, 04 May 2017 09:44:00 GMT</p> <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> </article> <article> <h1>[libs] cairo/1.14.8 installed on all systems</h1> <p>Thu, 04 May 2017 09:42:00 GMT</p> <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> </article> <article> <h1>[libs] Poppler/0.54.0 installed on all systems</h1> <p>Thu, 04 May 2017 09:41:00 GMT</p> <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> </article> <article> <h1>[bio] Salmon/0.8.2 installed on all systems</h1> <p>Tue, 02 May 2017 09:37:00 GMT</p> <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> </article> <article> <h1>[bio] LEON-BIS 20130322 installed on all systems</h1> <p>Tue, 02 May 2017 07:47:00 GMT</p> <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. See 'module help LEON-BIS/20130322' for more information.</p> </article> <article> <h1>[libs] ATLAS/3.10.3 available on all systems</h1> <p>Thu, 27 Apr 2017 14:14:00 GMT</p> <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> </article> <article> <h1>[bio] pysam/0.9.1.4 and pysam/0.10.0 available on all systems</h1> <p>Thu, 27 Apr 2017 14:07:00 GMT</p> <p>Pysam 0.9.1.4 and 0.10.0 are now available on all systems as pysam/0.9.1.4 and pysam/0.10.0. Both are built to run against python/2.7.6. They were previously available only on milou and/or irma.</p> </article> <article> <h1>[bio] MethPipe/3.4.3 installed on all systems</h1> <p>Wed, 26 Apr 2017 07:45:00 GMT</p> <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> </article> <article> <h1>[bio] raxml/8.2.10-gcc, raxml/8.2.10-gcc-mpi installed on all systems</h1> <p>Tue, 25 Apr 2017 16:41:00 GMT</p> <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. The modules are raxml/8.2.10-gcc and raxml/8.2.10-gcc-mpi.</p> </article> <article> <h1>[bio] RAxML-NG/0.2.0b-mpi installed on all systems</h1> <p>Tue, 25 Apr 2017 14:11:00 GMT</p> <p><a href="https://github.com/amkozlov/raxml-ng">RAxML-NG</a> (reimplementation of RAxML) 0.2.0b is installed on all systems. 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> </article> <article> <h1>[bio] wise2/2.2.0, wise2/2.4.1, geneid/1.4.4 installed on rackham, irma, bianca</h1> <p>Tue, 25 Apr 2017 09:19:00 GMT</p> <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> </article> <article> <h1>[bio] cegma/2.5 installed on all systems</h1> <p>Tue, 25 Apr 2017 09:17:00 GMT</p> <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> </article> <article> <h1>[bio] BUSCO/2.0.1 installed on all systems</h1> <p>Tue, 25 Apr 2017 07:19:00 GMT</p> <p><a href="http://busco.ezlab.org/">BUSCO</a> 2.0.1 has been installed as module BUSCO/2.0.1 on all systems. There is an extensive list of BUSCO lineage sets available, see the module help. BUSCO/1.22 has also been installed on rackham, irma and bianca.</p> </article> <article> <h1>[bio] bowtie and bowtie2 modules available on rackham</h1> <p>Mon, 24 Apr 2017 13:27:00 GMT</p> <p>Several versions of the <a href="http://bowtie-bio.sourceforge.net/index.shtml">bowtie</a> and <a href="http://bowtie-bio.sourceforge.net/bowtie2/index.shtml">bowtie2</a> modules have been made available on rackham, irma and bianca. Available are bowtie/0.12.9, bowtie/1.1.2, bowtie2/2.1.0, bowtie2/2.2.9.</p> </article> <article> <h1>[bio] samtools/1.4 and htslib/1.4 installed on all systems</h1> <p>Mon, 24 Apr 2017 11:21:00 GMT</p> <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> </article> <article> <h1>[bio] samblaster/0.1.22 and /0.1.24 installed on all systems</h1> <p>Mon, 24 Apr 2017 09:17:00 GMT</p> <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. Previously, only samblaster/0.1.22 was available, and only on milou.</p> </article> <article> <h1>[bio] seqmonk/1.37.1 installed on all systems</h1> <p>Fri, 21 Apr 2017 18:14:00 GMT</p> <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> </article> <article> <h1>[bio] maker/2.31.9 installed</h1> <p>Thu, 20 Apr 2017 08:41:00 GMT</p> <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. This module also uses updated versions of several external modules (RepeatMasker/4.0.7, augustus/3.2.3, snap/2013-11-29, blast/2.4.0+, openmpi/2.1.0 [if used]) and adds GeneMark/4.32-es as a <em>de novo</em> gene finder.</p> </article> <article> <h1>[bio] SignalP/4.1c installed on rackham, irma, bianca</h1> <p>Thu, 20 Apr 2017 08:38:00 GMT</p> <p><a href="http://www.cbs.dtu.dk/services/SignalP/">SignalP</a> 4.1c has been installed on rackham, irma and bianca. This version was previously available on milou, and given the version number 4.1. On all systems, this module can be loaded with SignalP/4.1c.</p> </article> <article> <h1>[bio] tRNAscan-SE/1.3.1 installed on rackham, irma and bianca</h1> <p>Wed, 19 Apr 2017 12:40:00 GMT</p> <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> </article> <article> <h1>[comp] binutils/2.28 installed on all systems</h1> <p>Wed, 19 Apr 2017 09:14:00 GMT</p> <p><a href="https://www.gnu.org/software/binutils/">GNU binutils</a> 2.28 is now installed as module binutils/2.28 on all systems.</p> </article> <article> <h1>[bio] augustus/3.2.3 installed on all systems</h1> <p>Tue, 18 Apr 2017 14:03:00 GMT</p> <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. This is an update for milou and a new installation for the other systems.</p> </article> <article> <h1>[bio] bamtools/2.3.0 installed on rackham, irma, bianca</h1> <p>Tue, 18 Apr 2017 14:02:00 GMT</p> <p>bamtools/2.3.0, already available on milou, has now been installed on rackham, irma and bianca.</p> </article> <article> <h1>[bio] snap/2013-11-29 installed on all systems</h1> <p>Thu, 13 Apr 2017 15:58:00 GMT</p> <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> </article> <article> <h1>[bio] usearch/9.2.64 installed on all systems</h1> <p>Thu, 13 Apr 2017 15:18:00 GMT</p> <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. All previously installed versions are also now available on all systems.</p> </article> <article> <h1>[bio] delly/0.7.6 installed on all systems</h1> <p>Thu, 06 Apr 2017 23:21:00 GMT</p> <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. The additional tools delly-suave and delly-maze have not been installed.</p> </article> <article> <h1>[bio] MUMmer 3.23 and 3.9.4alpha installed on rackham, irma, bianca</h1> <p>Thu, 06 Apr 2017 23:04:00 GMT</p> <p>The MUMmer/3.23 and MUMmer/3.9.4alpha modules have been installed on rackham, irma and bianca.</p> </article> <article> <h1>[bio] blast/2.2.26 and blast/2.2.31+ installed on rackham, bianca, irma</h1> <p>Thu, 06 Apr 2017 21:02:00 GMT</p> <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> </article> <article> <h1>[bio] last/847 installed on all systems</h1> <p>Thu, 06 Apr 2017 21:00:00 GMT</p> <p>The <a href="http://last.cbrc.jp/">last</a> pairwise sequence aligner version 847 is now installed as module last/847 on all systems.</p> </article> <article> <h1>[bio] vcflib/2017-04-04 installed on all systems</h1> <p>Thu, 06 Apr 2017 12:18:00 GMT</p> <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> </article> <article> <h1>[apps] gawk/4.1.4 installed</h1> <p>Tue, 04 Apr 2017 12:20:00 GMT</p> <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> </article> <article> <h1>[bio] ExAC 0.3.1 and CDD 3.16 installed</h1> <p>Mon, 03 Apr 2017 00:05:00 GMT</p> <p>Two <a href="http://www.uppmax.uu.se/resources/databases/other-uppnex-oriented-local-data-resources/">UPPMAX-local database copies</a> have been updated: ExAC to version 0.3.1 and CDD to version 3.16. </p> </article> <article> <h1>[bio] Pfam 31.0 and pfam_scan/1.6 installed</h1> <p>Mon, 03 Apr 2017 00:00:00 GMT</p> <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. 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> </article> <article> <h1>[bio] vep/87 and local caches installed</h1> <p>Sun, 02 Apr 2017 11:43:00 GMT</p> <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. Locally-cached databases and plugins are also available. Note that this version still uses the script from the Ensembl package (varient_effects_predictor.pl) rather than the new script from the now-separate, beta version (vep).</p> </article> <article> <h1>[bio] IGV/3.0-beta installed</h1> <p>Sat, 01 Apr 2017 14:04:00 GMT</p> <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> </article> <article> <h1>[bio] IGV/2.3.92 and IGVtools/2.3.91 installed</h1> <p>Sat, 01 Apr 2017 14:02:00 GMT</p> <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> </article> <article> <h1>[apps] R/3.3.2 available on irma and bianca</h1> <p>Tue, 28 Mar 2017 10:05:00 GMT</p> <p>The R/3.3.2 module is now available on irma and bianca.</p> </article> <article> <h1>[bio] jellyfish/2.2.6 installed on all systems</h1> <p>Tue, 28 Mar 2017 10:03:00 GMT</p> <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> </article> <article> <h1>[apps] R_packages/3.3.2 now uses R_LIBS_SITE</h1> <p>Sun, 26 Mar 2017 11:41:00 GMT</p> <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. BioConductor is now able to install additional packages not included in R_packages/3.3.2 into users' personal library directories.</p> </article> <article> <h1>[apps] vim/8.0-16 installed on rackham</h1> <p>Thu, 23 Mar 2017 17:11:00 GMT</p> <p>The vim/8.0-16 module is now installed on rackham.</p> </article> <article> <h1>[apps] haskell-stack/1.4.0 installed</h1> <p>Thu, 23 Mar 2017 16:40:00 GMT</p> <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> </article> <article> <h1>[apps] texlive/2016 installed</h1> <p>Thu, 23 Mar 2017 16:29:00 GMT</p> <p><a href="https://www.tug.org/texlive/">Texlive</a> 2016 is now installed as module texlive/2016 on milou and rackham.</p> </article> <article> <h1>[bio] Subread 1.5.2</h1> <p>Wed, 22 Mar 2017 13:25:00 GMT</p> <p>tool kit for processing next-gen sequencing data</p> </article> <article> <h1>[bio] GCTA 1.26.0</h1> <p>Thu, 16 Mar 2017 12:37:00 GMT</p> <p>Genome-wide Complex Trait Analysis</p> </article> <article> <h1>[bio] deepTools 2.4.3</h1> <p>Tue, 21 Mar 2017 07:54:00 GMT</p> <p>tools for exploring deep sequencing data</p> </article> <article> <h1>[bio] ucsc-utilities/v345 installed</h1> <p>Tue, 21 Mar 2017 13:27:00 GMT</p> <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> </article> <article> <h1>[bio] exonerate/2.2.0 and ucsc-utilities/v287 modules installed on rackham</h1> <p>Tue, 21 Mar 2017 13:25:00 GMT</p> <p>The exonerate/2.2.0 and ucsc-utilities/v287 modules are now available on rackham.</p> </article> <article> <h1>[bio] Redundans/0.13a-20170321 installed</h1> <p>Tue, 21 Mar 2017 10:05:00 GMT</p> <p><a href="https://github.com/Gabaldonlab/redundans">Redundans</a> (pipeline that assists assembly of heterozygous/polymorphic genomes) 0.13a-20170321 (version 9.13a with commits up to today) is now installed on milou and rackham.</p> </article> <article> <h1>[bio] RepeatModeler/1.0.8_RM4.0.7 installed</h1> <p>Mon, 20 Mar 2017 17:24:00 GMT</p> <p><a href="http://www.repeatmasker.org/RepeatModeler.html">RepeatModeler</a> 1.0.8_RM4.0.7 is now installed on milou and rackham. 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> </article> <article> <h1>[bio] hmmer/3.1b2 installed on rackham</h1> <p>Mon, 20 Mar 2017 16:17:00 GMT</p> <p>hmmer 3.1b2 is now also available on rackham.</p> </article> <article> <h1>[bio] RepeatMasker/4.0.7 installed</h1> <p>Mon, 20 Mar 2017 16:15:00 GMT</p> <p><a href="http://www.repeatmasker.org/">RepeatMasker</a> 4.0.7 is now installed on Milou and Rackham. This module version also contains updated rmblastn and trf tools and provides nhmmer and cross_match as additional search tools.</p> </article> <article> <h1>[bio] StringTie/1.3.3 installed</h1> <p>Mon, 20 Mar 2017 15:30:00 GMT</p> <p>StringTie 1.3.3 is now installed on milou, rackham, irma and bianca and will be available as the module system refreshes.</p> </article> <article> <h1>[libs] blas/3.6.0 installed on rackham</h1> <p>Mon, 20 Mar 2017 13:42:00 GMT</p> <p>blas/3.6.0, which includes BLAS and CBLAS, is now also installed on rackham.</p> </article> <article> <h1>[bio] STAR 2.5.2b</h1> <p>Thu, 16 Mar 2017 13:11:00 GMT</p> <p>RNA-seq aligner</p> </article> <article> <h1>[bio] barrnap 0.8</h1> <p>Mon, 06 Mar 2017 12:56:00 GMT</p> <p>[bio] barrnap 0.8</p> </article> <article> <h1>[bio] Trimmomatic 0.36</h1> <p>Mon, 20 Mar 2017 10:03:00 GMT</p> <p>trim Illumina NGS data</p> </article> <article> <h1>[libs] hdf5/1.8.18 and hdf5/1.8.18_gcc6.3.0 installed</h1> <p>Thu, 16 Mar 2017 14:07:00 GMT</p> <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. SZIP is supported via the szip/2.1.1 module and GZIP is supported via the gzip/1.2.11 module. On both clusters there are two module versions available. <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> </article> <article> <h1>[libs] freetype/2.7.1 installed</h1> <p>Thu, 16 Mar 2017 11:07:00 GMT</p> <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> </article> <article> <h1>[libs] szip/2.1.1 installed</h1> <p>Thu, 16 Mar 2017 10:35:00 GMT</p> <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> </article> <article> <h1>[libs] zlib/1.2.11 installed</h1> <p>Thu, 16 Mar 2017 09:53:00 GMT</p> <p><a href="http://www.zlib.net/">zlib</a> (general compression library) 1.2.11 is installed on milou and rackham. zlib/1.2.8 remains the default module version on milou.</p> </article> <article> <h1>[bio] Ragout/2.0-20170312 installed</h1> <p>Mon, 13 Mar 2017 01:32:00 GMT</p> <p><a href="https://github.com/fenderglass/Ragout">Ragout</a> (chromosome assembly using multiple references) 2.0-20170312 is now installed as module Ragout/2.0-20170312 on milou and rackham.</p> </article> <article> <h1>[bio] SiBELia/3.0.6 installed</h1> <p>Sun, 12 Mar 2017 19:45:00 GMT</p> <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> </article> <article> <h1>[bio] AdmixTools/5.0-20170312 installed</h1> <p>Sun, 12 Mar 2017 18:24:00 GMT</p> <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> </article> <article> <h1>[bio] iqtree/1.5.3-omp installed</h1> <p>Sun, 12 Mar 2017 13:47:00 GMT</p> <p><a href="http://www.iqtree.org/">IQ-TREE</a> 1.5.3 (phylogenomic software by maximum likelihood) is installed as module iqtree/1.5.3-omp as part of the phylogeny subgroup of bioinfo-tools on milou and rackham. The multicore executable is available as <strong>iqtree-omp</strong> and the single core executable as <strong>iqtree</strong>.</p> </article> <article> <h1>[bio] Meerkat/0.189 installed</h1> <p>Wed, 22 Feb 2017 21:16:00 GMT</p> <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> </article> <article> <h1>[bio] Primer3/2.3.7 installed</h1> <p>Wed, 22 Feb 2017 21:04:00 GMT</p> <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> </article> <article> <h1>[bio] BEDTools 2.26.0</h1> <p>Wed, 08 Feb 2017 18:23:00 GMT</p> <p>utilities for a range of genomics analysis tasks</p> </article> <article> <h1>[bio] khmer 2.0</h1> <p>Wed, 08 Feb 2017 18:17:00 GMT</p> <p>In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more</p> </article> <article> <h1>[bio] bwa 0.7.15</h1> <p>Tue, 21 Feb 2017 18:07:00 GMT</p> <p>Burrow-Wheeler Aligner for pairwise alignment between DNA sequences</p> </article> <article> <h1>[bio] 10X Supernova 1.1.4</h1> <p>Fri, 17 Feb 2017 18:04:00 GMT</p> <p>de novo assembly from Chromium Linked-Reads</p> </article> <article> <h1>[bio] 10X Cellranger 1.3.0</h1> <p>Fri, 17 Feb 2017 17:59:00 GMT</p> <p>set of analysis pipelines to process Chromium single cell 3’ RNA-seq output</p> </article> <article> <h1>[lib] boost 1.63.0</h1> <p>Wed, 15 Feb 2017 16:40:00 GMT</p> <p>widely-used C++ library</p> </article> <article> <h1>[parallel] gnuparallel 20170122</h1> <p>Mon, 13 Feb 2017 16:34:00 GMT</p> <p>scripts for running parallel jobs</p> </article> <article> <h1>OpenFOAM v1612+ now installed on Rackham</h1> <p>Tue, 21 Feb 2017 14:51:00 GMT</p> <p>OpenFOAM v1612+ is now available on Rackham as a module. Please run "module load openfoam/v1612+" to load OpenFOAM v1612+.</p> </article> <article> <h1>[bio] eigensoft/6.1.4 installed</h1> <p>Wed, 08 Feb 2017 12:13:00 GMT</p> <p><a href="https://www.hsph.harvard.edu/alkes-price/software/">Eigensoft</a> 6.1.4 is now installed on milou and tintin. As with 6.0.1, this version has support for longer IDs.</p> </article> <article> <h1>[bio] A5-miseq/20160825 installed</h1> <p>Fri, 27 Jan 2017 18:30:00 GMT</p> <p><a href="https://sourceforge.net/projects/ngopt/">A5-miseq</a> version 20160825 is now installed on milou and tintin.</p> </article> <article> <h1>[apps] sqlite/3.11.1 and sqlite/3.16.2 installed</h1> <p>Fri, 20 Jan 2017 14:08:00 GMT</p> <p><a href="https://sqlite.org/">SQLite</a> versions 3.11.1 and 3.16.2 are now installed on milou and tintin. These provide both an <strong>sqlite3</strong> executable as well as libraries and include files for development.</p> </article> <article> <h1>[bio] OrthoMCL/2.0.9 now installed</h1> <p>Fri, 20 Jan 2017 13:42:00 GMT</p> <p><a href="https://github.com/douglasgscofield/OrthoMCL">OrthoMCL</a> 2.0.9 is now available on milou. This uses SQLite by default, rather than MySQL or Oracle, which should work much better at UPPMAX.</p> </article> <article> <h1>[comp] Apache Ant 1.9.8 and 1.10.0</h1> <p>Fri, 20 Jan 2017 10:01:00 GMT</p> <p>build tool</p> </article> <article> <h1>[bio] RTG Tools (new)</h1> <p>Thu, 19 Jan 2017 09:03:00 GMT</p> <p>utilities to manipulate/compare VCF files and other NGS formats</p> </article> <article> <h1>[bio] manta 1.0.3</h1> <p>Fri, 20 Jan 2017 08:59:00 GMT</p> <p>structural variant and indel caller for mapped sequencing data</p> </article> <article> <h1>[bio] Mothur 1.38.1</h1> <p>Fri, 20 Jan 2017 08:51:00 GMT</p> <p>software collection for gene sequence analysis</p> </article> <article> <h1>[bio] RNAfold/2.3.1 (alias ViennaRNA/2.3.1) installed</h1> <p>Wed, 21 Dec 2016 17:06:00 GMT</p> <p>RNAfold (aka ViennaRNA) 2.3.1 is now installed on milou and tintin. This is an update for both systems.</p> </article> <article> <h1>[bio] InterProScan/5.20-59.0 disabled</h1> <p>Tue, 20 Dec 2016 08:41:00 GMT</p> <p>This version of InterProScan requires glibc 2.14. Milou and Tintin only have 2.12 and cannot be upgraded in any reasonable way. Older versions of InterProScan are still installed and appear to function normall. 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 InterProScan.</p> </article> <article> <h1>[bio] GATK/3.7 installed</h1> <p>Mon, 19 Dec 2016 13:12:00 GMT</p> </article> <article> <h1>[bio] GATK-Queue/3.7 installed</h1> <p>Mon, 19 Dec 2016 13:11:00 GMT</p> </article> <article> <h1>[bio] plink repository for custom compilation on milou</h1> <p>Sat, 17 Dec 2016 10:13:00 GMT</p> <p><a href="https://www.cog-genomics.org/plink2">PLINK version 1.90</a> is available as module plink/1.90 and is installed from the prebuilt binaries. 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> </article> <article> <h1>[libs] ATLAS/3.10.3 installed</h1> <p>Sat, 17 Dec 2016 10:05:00 GMT</p> <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> </article> <article> <h1>[libs] blas/3.6.0 installed</h1> <p>Sat, 17 Dec 2016 10:00:00 GMT</p> <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. The openblas and ATLAS modules provide tuned versions of BLAS/CBLAS.</p> </article> <article> <h1>[bio] Trinity 2.3.2</h1> <p>Fri, 16 Dec 2016 06:50:00 GMT</p> <p>assembles transcript sequences from Illumina RNA-Seq data</p> </article> <article> <h1>[bio] Transrate 1.0.3</h1> <p>Tue, 13 Dec 2016 07:30:00 GMT</p> <p>de-novo transcriptome assembly quality analysis</p> </article> <article> <h1>[bio] default blast</h1> <p>Tue, 13 Dec 2016 07:24:00 GMT</p> <p>Default version of blast changed from latest "legacy blast" to latest version overall, i.e., "blast+".</p> </article> <article> <h1>[bio] GATK-Queue/3.6 installed</h1> <p>Fri, 09 Dec 2016 13:01:00 GMT</p> <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. This is an update for milou and a new module for tintin et al.</p> </article> <article> <h1>[bio] EnsEMBL-API/87 installed</h1> <p>Thu, 08 Dec 2016 14:23:00 GMT</p> <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 EnsEMBL-API/87.</p> </article> <article> <h1>[bio] Satsuma2</h1> <p>Wed, 07 Dec 2016 14:50:00 GMT</p> <p>FFT cross-correlation based synteny aligner</p> </article> <article> <h1>[bio] SeqMonk 1.36.0</h1> <p>Tue, 06 Dec 2016 12:31:00 GMT</p> <p>visualise and analyse high throughput mapped sequence data</p> </article> <article> <h1>[bio] 10X Supernova 1.1.1</h1> <p>Sat, 24 Sep 2016 07:44:00 GMT</p> <p>de novo assembly from Chromium Linked-Reads</p> </article> <article> <h1>[bio] 10X Supernova 1.0.0</h1> <p>Tue, 05 Jul 2016 07:41:00 GMT</p> <p><em>de novo</em> assembly from Chromium Linked-Reads</p> </article> <article> <h1>[bio] 10X Cellranger 1.1.0</h1> <p>Tue, 05 Jul 2016 06:57:00 GMT</p> <p>set of analysis pipelines to process Chromium single cell 3’ RNA-seq output</p> </article> <article> <h1>[bio] 10X Longranger 2.0.1</h1> <p>Tue, 05 Jul 2016 06:46:00 GMT</p> <p>set of analysis pipelines to process Chromium sequencing output</p> </article> <article> <h1>[bio] 10X Longranger 2.1.1</h1> <p>Sat, 24 Sep 2016 06:44:00 GMT</p> <p>set of analysis pipelines to process Chromium sequencing output</p> </article> <article> <h1>[bio] 10X Longranger 2.1.2</h1> <p>Tue, 06 Dec 2016 07:32:00 GMT</p> <p>set of analysis pipelines to process Chromium sequencing output</p> </article> <article> <h1>[bio] Prodigal 2.6.3</h1> <p>Wed, 12 Oct 2016 08:48:00 GMT</p> <p>protein-coding gene prediction for prokaryotic genomes</p> </article> <article> <h1>[bio] InterProScan 5.20-59.0</h1> <p>Tue, 25 Oct 2016 08:41:00 GMT</p> <p>scan the InterPro database of protein function prediction</p> </article> <article> <h1>[bio] FastQ Screen 0.9.2</h1> <p>Thu, 27 Oct 2016 08:32:00 GMT</p> <p>screen sequences against a database</p> <p></p> </article> <article> <h1>[bio] blast/2.5.0+ installed</h1> <p>Sun, 04 Dec 2016 09:57:00 GMT</p> <p><a href="https://blast.ncbi.nlm.nih.gov/Blast.cgi">Blast</a> 2.5.0+ has been installed on all systems.</p> </article> <article> <h1>[bio] PileOMeth 0.1.13</h1> <p>Mon, 21 Nov 2016 18:11:00 GMT</p> <p>methylation extractor for BS-seq experiments</p> </article> <article> <h1>[bio] bwa-meth 0.2.0</h1> <p>Mon, 21 Nov 2016 18:07:00 GMT</p> <p>BS-Seq alignment</p> </article> <article> <h1>[bio] piper 1.5.0 (milou)</h1> <p>Tue, 22 Nov 2016 18:02:00 GMT</p> <p>NGI pipeline</p> </article> <article> <h1>[bio] piper 1.5.0 (fix)</h1> <p>Sat, 24 Sep 2016 16:59:00 GMT</p> <p>NGI pipeline</p> </article> <article> <h1>[bio] piper 1.5.0</h1> <p>Tue, 06 Sep 2016 16:49:00 GMT</p> <p>NGI pipeline</p> </article> <article> <h1>[bio] PLINK/SEQ 0.10</h1> <p>Fri, 02 Dec 2016 17:36:00 GMT</p> <p>C/C++ library for working with human genetic variation data</p> </article> <article> <h1>[bio] SRA Tools 2.8.0</h1> <p>Fri, 02 Dec 2016 17:11:00 GMT</p> <p>Collection of tools and libraries for using data in the INSDC Sequence Read Archives</p> </article> <article> <h1>[comp] python/2.7.11 installed</h1> <p>Fri, 02 Dec 2016 17:40:00 GMT</p> <p>Python 2.7.11 is now installed on milou and tintin.</p> </article> <article> <h1>[bio] vsearch/2.3.2 installed</h1> <p>Thu, 01 Dec 2016 14:09:00 GMT</p> <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. This is a new module for both systems.</p> </article> <article> <h1>[bio] progressiveCactus/2016-11-30 installed</h1> <p>Thu, 01 Dec 2016 14:06:00 GMT</p> <p><a href="https://github.com/glennhickey/progressiveCactus">progressiveCactus</a> as of 2016-11-30 is now installed on milou and tintin. This is an update for both systems. If it can be made to work successfully, an additional module version with SLURM support is forthcoming.</p> </article> <article> <h1>[bio] hal/20161130 installed</h1> <p>Thu, 01 Dec 2016 13:55:00 GMT</p> <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. This is an update for both systems.</p> </article> <article> <h1>[bio] phast/1.4 installed</h1> <p>Wed, 30 Nov 2016 16:26:00 GMT</p> <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. This is an update for milou and a new module for tintin.</p> </article> <article> <h1>[bio] blasr/5.3</h1> <p>Sun, 20 Nov 2016 18:53:00 GMT</p> <p>The <a href="https://github.com/PacificBiosciences/blasr">blasr</a> aligner (alignment of long, error-prone reads) version 5.3 is now installed on milou as blasr/5.3. This is an update, created via the PacBio pitchfork build process. This installation represents blasr 5.3.e901e48.</p> </article> <article> <h1>[bio] FALCON-integrate/20161113 installed</h1> <p>Sun, 20 Nov 2016 18:28:00 GMT</p> <p><a href="https://github.com/PacificBiosciences/FALCON-integrate">FALCON-integrate</a><strong> as of the latest commit on 2016-11-13 is now installed as FALCON/20161113 on milou. This replaces the FALCON/20161112 module.</strong></p> </article> <article> <h1>[bio] HISAT2/2.0.5 installed</h1> <p>Sat, 12 Nov 2016 22:14:00 GMT</p> <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> </article> <article> <h1>[bio] diamond/0.8.26 installed</h1> <p>Sat, 12 Nov 2016 21:09:00 GMT</p> <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. See 'module help diamond' for more on availability of prebuilt databases.</p> </article> <article> <h1>[comp] git/2.10.2 installed</h1> <p>Sat, 12 Nov 2016 21:07:00 GMT</p> <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. This is an update.</p> </article> <article> <h1>[bio] FALCON-integrate/20161112 installed</h1> <p>Sat, 12 Nov 2016 21:00:00 GMT</p> <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> </article> <article> <h1>[bio] Krona/2.7 installed</h1> <p>Fri, 11 Nov 2016 19:30:00 GMT</p> <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> </article> <article> <h1>[bio] SortMeRNA/2.1b</h1> <p>Fri, 11 Nov 2016 17:56:00 GMT</p> <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> </article> <article> <h1>[comp] advisor, ampilifier, inspector and itac upgraded</h1> <p>Thu, 10 Nov 2016 09:12:00 GMT</p> <p>advisor, ampilifier, inspector and itac upgraded </p> </article> <article> <h1>[comp] intel/17.1 installed</h1> <p>Thu, 10 Nov 2016 09:11:00 GMT</p> <p>intel/17.1 installed</p> </article> <article> <h1>[parallel] intelmpi/17.1 installed</h1> <p>Thu, 10 Nov 2016 09:07:00 GMT</p> <p>intelmpi/17.1 has been installed on Milou and Tintin</p> </article> <article> <h1>[apps] JAGS/4.2.0 installed</h1> <p>Thu, 03 Nov 2016 22:07:00 GMT</p> <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, tintin and irma. This is a new module for all systems.</p> </article> <article> <h1>[bio] MACE/1.2 installed</h1> <p>Sun, 30 Oct 2016 10:14:00 GMT</p> <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. This is a new module for all systems.</p> </article> <article> <h1>[bio] GEM/2.7 installed</h1> <p>Sun, 30 Oct 2016 10:12:00 GMT</p> <p><a href="https://groups.csail.mit.edu/cgs/gem">GEM 2.7</a> (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. This is a new module for both systems.</p> </article> <article> <h1>[apps] R/3.3.1 and R_packages/3.3.1 installed</h1> <p>Sun, 23 Oct 2016 21:06:00 GMT</p> <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> </article> <article> <h1>jobstats script updated</h1> <p>Sun, 23 Oct 2016 12:26:00 GMT</p> <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 and to include this information as an additional trace in plots (black dotted line).</p> </article> <article> <h1>[bio] Scipio/1.4 installed</h1> <p>Tue, 11 Oct 2016 08:43:00 GMT</p> <p><a href="http://www.webscipio.org/">Scipio 1.4</a> (eukaryotic gene detection) is now installed on milou.</p> </article> <article> <h1>[bio] Vmatch/2.2.5 installed</h1> <p>Sun, 09 Oct 2016 23:33:00 GMT</p> <p><a href="http://www.vmatch.de/">Vmatch 2.2.5</a> (sequence matching tool) has been installed on milou and tintin.</p> </article> <article> <h1>[bio] clusterflow/0.4 installed</h1> <p>Fri, 07 Oct 2016 13:54:00 GMT</p> <p><a href="http://clusterflow.io/">Clusterflow 0.4 installed</a> on milou, irma and bianca. This is an update.</p> </article> <article> <h1>[bio] nextflow/0.22.2 installed</h1> <p>Thu, 06 Oct 2016 11:07:00 GMT</p> <p><a href="https://www.nextflow.io/">Nextflow</a> 0.22.2 is now installed as module nextflow/0.22.2 on milou. Our local installation has been modified to require that the NXF_TEMP variable be set prior to running nextflow to indicate a directory into which temporary files should be written. A message is produced when loading the module as a reminder.</p> </article> <article> <h1>pgi/16.9 installed</h1> <p>Fri, 30 Sep 2016 07:25:00 GMT</p> <p>The portland compiler has been upgraded to pgi/16.9 on Milou and Tintin.</p> </article> <article> <h1>[bio] vt/0.5772 installed</h1> <p>Thu, 29 Sep 2016 21:33:00 GMT</p> <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. This is a new module for both systems.</p> </article> <article> <h1>[bio] GenomeSTRiP/2.00.1685 installed</h1> <p>Thu, 29 Sep 2016 20:54:00 GMT</p> <p><a href="http://software.broadinstitute.org/software/genomestrip/index.html">GenomeSTRiP 2.00.1685</a> (structural variant pipeline) has been installed as module GenomeSTRiP/2.00.1685 on milou. This is an update.</p> </article> <article> <h1>[apps] vim/8.0-16</h1> <p>Tue, 27 Sep 2016 09:31:00 GMT</p> <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> </article> <article> <h1>[parallel] openmpi/1.10.4 and openmpi/2.0.1</h1> <p>Mon, 26 Sep 2016 07:52:00 GMT</p> <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> </article> <article> <h1>[parallel] intelmpi/17.0 installed</h1> <p>Mon, 26 Sep 2016 07:50:00 GMT</p> <p>intelmpi/17.0 has been installed on Milou and Tintin.</p> </article> <article> <h1>[comp] advisor, ampilifier, inspector and itac upgraded</h1> <p>Mon, 26 Sep 2016 07:44:00 GMT</p> <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> </article> <article> <h1>[bio] gvcftools/0.17.0 installed</h1> <p>Sun, 25 Sep 2016 16:52:00 GMT</p> <p><a href="https://sites.google.com/site/gvcftools/home">gvcftools 0.17.0</a> installed on milou and tintin. This is an upgrade for both systems.</p> </article> <article> <h1>[comp] python/3.4.3 for tintin</h1> <p>Fri, 23 Sep 2016 14:19:00 GMT</p> <p>Python 3.4.3 is now available on tintin.</p> </article> <article> <h1>[bio] biopython/1.68 and biopython/1.68-py3</h1> <p>Fri, 23 Sep 2016 14:13:00 GMT</p> <p><a href="http://biopython.org/">BioPython 1.68</a> 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). This is an update for both systems.</p> </article> <article> <h1>[bio] MetAMOS/1.5rc3 installed</h1> <p>Fri, 23 Sep 2016 06:57:00 GMT</p> <p><a href="http://metamos.readthedocs.io/en/v1.5rc3/index.html">MetAMOS 1.5rc3</a> has been installed with core prerequisites as module MetAMOS/1.5rc3 on milou. This is a new module. Additional functionality may be available by loading other modules available on milou; see 'module help MetAMOS' for more details.</p> </article> <article> <h1>[bio] strelka/1.0.15 installed</h1> <p>Wed, 21 Sep 2016 10:33:00 GMT</p> <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. This is a new module for both systems.</p> </article> <article> <h1>[bio] Metaxa2/2.1.3 installed</h1> <p>Tue, 20 Sep 2016 21:23:00 GMT</p> <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. This is a new module for both systems.</p> </article> <article> <h1>[bio] SHAPEIT/v2.r837 installed</h1> <p>Tue, 20 Sep 2016 20:50:00 GMT</p> <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> </article> <article> <h1>[bio] augustus/3.2.2 installed</h1> <p>Tue, 20 Sep 2016 08:15:00 GMT</p> <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> </article> <article> <h1>R_packages/3.3.0 updated with additional packages</h1> <p>Mon, 19 Sep 2016 13:14:00 GMT</p> <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 Gviz, gplots, <span style="font-size:1em; line-height:1.5em">edgeR, </span><span style="font-size:1em; line-height:1.5em">DEXSeq, </span><span style="font-size:1em; line-height:1.5em">goseq, </span><span style="font-size:1em; line-height:1.5em">GO.db, reactome.db, </span><span style="font-size:1em; line-height:1.5em">org.Mm.eg.db</span></p> </article> <article> <h1>[comp] julia/0.4.6 installed</h1> <p>Fri, 16 Sep 2016 13:34:00 GMT</p> <p>julia/0.4.6</p> </article> <article> <h1>[comp] intel/17.0 installed</h1> <p>Thu, 15 Sep 2016 08:18:00 GMT</p> <p>intel/17.0</p> </article> <article> <h1>[comp] gcc/6.2.0 installed</h1> <p>Thu, 15 Sep 2016 07:22:00 GMT</p> <p>gcc/6.2.0</p> </article> <article> <h1>[bio] Metassembler/1.5 installed on tintin</h1> <p>Fri, 09 Sep 2016 12:28:00 GMT</p> <p><a href="https://sourceforge.net/p/metassembler">Metassembler 1.5</a> is installed on tintin; it was previously available only on milou.</p> </article> <article> <h1>[bio] MUMmer/3.9.4alpha installed</h1> <p>Fri, 09 Sep 2016 09:11:00 GMT</p> <p><a href="https://github.com/gmarcais/mummer">MUMmer 3.9.4alpha</a> (the latest alpha version of 'MUMmer4') is now installed on milou and tintin. The default version remains MUMmer/3.23</p> </article> <article> <h1>[bio] KAT/2.1.1 installed</h1> <p>Fri, 02 Sep 2016 14:12:00 GMT</p> <p><a href="https://github.com/TGAC/KAT">KAT 2.1.1</a> (kmer analysis toolkit) has been installed on milou and tintin. This is an upgrade for both systems.</p> </article> <article> <h1>[bio] concaterpillar/1.4 updated</h1> <p>Thu, 01 Sep 2016 06:58:00 GMT</p> <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> </article> <article> <h1>[bio] subread/1.5.1</h1> <p>Tue, 30 Aug 2016 08:32:00 GMT</p> <p><a href="http://subread.sourceforge.net/">Subread 1.5.1</a> is now installed on milou and tintin</p> </article> <article> <h1>[bio] vcflib/2016-08-29 installed</h1> <p>Mon, 29 Aug 2016 09:38:00 GMT</p> <p><a href="https://github.com/vcflib/vcflib">vcflib 2016-08-29</a> installed on milou and tintin</p> <p></p> </article> <article> <h1>[apps] tinyutils/1.4</h1> <p>Wed, 24 Aug 2016 12:52:00 GMT</p> <p>tinyutils 1.4 (tiny utilities for manipulating data) installed</p> </article> <article> <h1>[bio] IQ-TREE 1.4.3-pomo</h1> <p>Fri, 05 Aug 2016 13:44:00 GMT</p> <p>Efficient phylogenomic software by maximum likelihood (polymorphism-aware version)</p> </article> <article> <h1>[bio] blast 2.4.0+</h1> <p>Thu, 28 Jul 2016 09:39:00 GMT</p> <p>Basic Local Alignment Search Tool</p> </article> <article> <h1>[bio] AdmixTools</h1> <p>Wed, 03 Aug 2016 09:00:00 GMT</p> <p>test whether admixture occurred</p> </article> <article> <h1>[bio] MACS 2.1.0 (irma)</h1> <p>Wed, 03 Aug 2016 08:55:00 GMT</p> <p>Model-based Analysis of ChIP-Seq</p> </article> <article> <h1>[bio] ngsplot 2.61 (irma)</h1> <p>Wed, 03 Aug 2016 08:51:00 GMT</p> <p>mining and visualization of NGS data</p> </article> <article> <h1>[bio] SHRiMP 2.2.3</h1> <p>Fri, 05 Aug 2016 08:43:00 GMT</p> <p>SHort Read Mapping Package</p> </article> <article> <h1>[bio] GATK temp</h1> <p>Wed, 27 Jul 2016 06:58:00 GMT</p> <p>Genome Analysis Toolkit</p> </article> <article> <h1>[bio] spades/3.9.0</h1> <p>Wed, 27 Jul 2016 19:38:00 GMT</p> <p><a href="http://bioinf.spbau.ru/spades">Spades 3.9.0</a></p> <p>a flexible assembler for small genomes</p> </article> <article> <h1>[apps] tinyutils/1.3</h1> <p>Wed, 27 Jul 2016 14:48:00 GMT</p> <p><a href="https://github.com/douglasgscofield/tinyutils">Tinyutils 1.3</a></p> <p>small utilities for working with data</p> </article> <article> <h1>[bio] MEMEsuite/4.11.2_1</h1> <p>Mon, 25 Jul 2016 17:00:00 GMT</p> <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> </article> <article> <h1>[bio] ucsc-utilities/v334</h1> <p>Mon, 25 Jul 2016 14:21:00 GMT</p> <p><a href="http://hgdownload.cse.ucsc.edu/admin/exe/">UCSC utilities version 334</a></p> </article> <article> <h1>[bio] deepTools 2.3.1</h1> <p>Sun, 24 Jul 2016 14:31:00 GMT</p> <p>Tools to process and analyze deep sequencing data</p> </article> <article> <h1>[bio] deepTools 2.2.3 (irma)</h1> <p>Sun, 24 Jul 2016 12:41:00 GMT</p> <p>Tools to process and analyze deep sequencing data</p> </article> <article> <h1>[bio] DICE</h1> <p>Fri, 08 Jul 2016 12:24:00 GMT</p> <p>estimate of demography and contamination for nuclear ancient DNA</p> </article> <article> <h1>[bio] verifyBamID 1.1.2</h1> <p>Wed, 06 Jul 2016 12:05:00 GMT</p> <p>verifies whether the reads match previously known genotypes</p> </article> <article> <h1>[bio] pear 0.9.10</h1> <p>Wed, 20 Jul 2016 11:54:00 GMT</p> <p>Paired-End reAd mergeR</p> </article> <article> <h1>[bio] MultiQC 0.7</h1> <p>Tue, 05 Jul 2016 11:29:00 GMT</p> <p>aggregate bioinformatics results into single report</p> </article> <article> <h1>[bio] MultiQC 0.6 (irma)</h1> <p>Sat, 04 Jun 2016 10:56:00 GMT</p> <p>aggregate bioinformatics results into single report</p> </article> <article> <h1>[bio] MultiQC 0.6</h1> <p>Fri, 29 Apr 2016 10:45:00 GMT</p> <p>aggregate bioinformatics results into single report</p> </article> <article> <h1>[bio] phylobayesmpi 1.7a</h1> <p>Tue, 19 Jul 2016 10:25:00 GMT</p> <p>Bayesian monte carlo markov chain sampler for phylogenetic reconstruction (MPI version)</p> </article> <article> <h1>[bio] Bismark 0.16.2 (bugfix)</h1> <p>Tue, 19 Jul 2016 09:59:00 GMT</p> <p>bisulfite read mapper and methylation caller</p> </article> <article> <h1>[bio] SPP 1.11 (irma)</h1> <p>Wed, 13 Jul 2016 09:48:00 GMT</p> <p>ChIP-seq processing pipeline</p> </article> <article> <h1>[bio] phantompeakqualtools 1.1 (Irma)</h1> <p>Wed, 13 Jul 2016 09:33:00 GMT</p> <p>ChIP-Seq enrichment and quality measures</p> </article> <article> <h1>[bio] pysam 0.9.1.4</h1> <p>Sun, 24 Jul 2016 09:20:00 GMT</p> <p>Python module for reading and manipulating samfiles</p> </article> <article> <h1>[bio] vep/84 installed</h1> <p>Wed, 20 Jul 2016 16:50:00 GMT</p> <p><a href="http://www.ensembl.org/info/docs/tools/vep/index.html">Variant Effect Predictor version 84</a></p> </article> <article> <h1>[bio] GEMINI/0.19.0 installed</h1> <p>Mon, 18 Jul 2016 14:25:00 GMT</p> <p><a href="http://gemini.readthedocs.io/en/latest/index.html">GEMINI/0.19.0 (flexible framework for exploring genome variation) installed.</a></p> </article> <article> <h1>[libs] GEOS/3.5.0 installed</h1> <p>Mon, 18 Jul 2016 11:28:00 GMT</p> <p><a href="https://trac.osgeo.org/geos/">GEOS/3.5.0 open-source genometry engine installed</a></p> </article> <article> <h1>[bio] spades/3.8.1</h1> <p>Fri, 01 Jul 2016 16:18:00 GMT</p> <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. This is an update for both systems. /douglas</p> </article> <article> <h1>[bio] MetaBat 0.26.3</h1> <p>Wed, 29 Jun 2016 09:27:00 GMT</p> <p>An Efficient Tool for Accurately Reconstructing Single Genomes from Complex Microbial Communities</p> </article> <article> <h1>[tool] SCons 2.5.0</h1> <p>Wed, 29 Jun 2016 08:44:00 GMT</p> <p>Software construction tool (like make)</p> </article> <article> <h1>[bio] tbl2asn</h1> <p>Tue, 14 Jun 2016 07:23:00 GMT</p> <p>Automates the creation of sequence records for submission to GenBank</p> </article> <article> <h1>[bio] ngsF-HMM</h1> <p>Tue, 14 Jun 2016 07:14:00 GMT</p> <p>Estimate per-individual inbreeding tracts using a two-state Hidden Markov Model</p> </article> <article> <h1>[lib] boost 1.61.0 (gcc 5.3.0)</h1> <p>Mon, 13 Jun 2016 07:05:00 GMT</p> <p>Widely-used C++ library</p> </article> <article> <h1>[lib] sparsehash 2.0.3</h1> <p>Mon, 20 Jun 2016 06:53:00 GMT</p> <p>Various hash-map implementations</p> </article> <article> <h1>[bio] blobtools 0.9.17</h1> <p>Thu, 16 Jun 2016 06:46:00 GMT</p> <p>Visualisation of draft assemblies using TAGC plots</p> </article> <article> <h1>[bio] MinCED 0.2.0</h1> <p>Wed, 15 Jun 2016 06:40:00 GMT</p> <p>Mining CRISPRs in Environmental Datasets</p> </article> <article> <h1>[bio] Installations for Irma</h1> <p>Tue, 21 Jun 2016 05:56:00 GMT</p> <p>Various bio packages installed for Irma, either by linking to packages on Milou or local compilation.</p> </article> <article> <h1>[bio] LoFreq 2.1.2</h1> <p>Mon, 27 Jun 2016 15:39:00 GMT</p> <p>Fast and sensitive variant calling from next-gen sequencing data</p> </article> <article> <h1>[bio] RNAfold (aka ViennaRNA) 2.2.5 installed</h1> <p>Sun, 19 Jun 2016 16:31:00 GMT</p> <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. This is an update for milou and a new module for tintin. /douglas</p> </article> <article> <h1>[bio] CleaveLand4/4.3 installed</h1> <p>Sun, 19 Jun 2016 10:15:00 GMT</p> <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. This is a new module for both systems. /douglas</p> </article> <article> <h1>[comp] binutils/2.26 installed</h1> <p>Sun, 19 Jun 2016 07:54:00 GMT</p> <p><a href="https://www.gnu.org/software/binutils">Gnu binutils</a></p> <p>have been installed as module binutils/2.26 as part of compilers on milou and tintin. The module has been configured with --enable-plugins so that the contained utilities support plugins. This module updates the installed versions on both systems. /douglas</p> </article> <article> <h1>[apps] doxygen/1.8.11 installed</h1> <p>Sun, 19 Jun 2016 05:02:00 GMT</p> <p><a href="http://www.stack.nl/~dimitri/doxygen/">Doxygen</a> version 1.8.11 (tool for generating documentation from source code) has been installed as module doxygen/1.8.11 on milou and tintin. This is an update for both systems. /douglas</p> </article> <article> <h1>[bio] kallisto/0.43.0 installed</h1> <p>Sat, 18 Jun 2016 13:58:00 GMT</p> <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. /douglas</p> </article> <article> <h1>[apps] vim/7.4-1941 installed</h1> <p>Thu, 16 Jun 2016 14:01:00 GMT</p> <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) has been installed as module vim/7.4-1941 on milou and tintin. 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. Using 'gvim' or 'gview' will open an X-windows version. /douglas</p> </article> <article> <h1>[stats] R_packages/3.3.0 installed</h1> <p>Thu, 16 Jun 2016 09:39:00 GMT</p> <p><a href="https://www.uppmax.uu.se/support-sv//r_packages-module-guide">A module containing a modest collection of useful 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> </article> <article> <h1>[bio] DWGSIM/0.1.11-6e9a361 installed</h1> <p>Thu, 16 Jun 2016 07:16:00 GMT</p> <p><a href="https://github.com/nh13/DWGSIM">The DWGSIM sequence simulator</a> ... version 0.1.11 commit 6e9a361 (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> </article> <article> <h1>[bio] BAM-matcher installed</h1> <p>Sat, 11 Jun 2016 14:43:00 GMT</p> <p>Determine whether two BAM files contain reads sequenced from the same sample or patient</p> </article> <article> <h1>[bio] EEMS installed</h1> <p>Sun, 05 Jun 2016 15:10:00 GMT</p> <p>Estimating Effective Migration Surfaces</p> </article> <article> <h1>Bismark has been upgraded to version 0.16.1</h1> <p>Fri, 03 Jun 2016 12:21:00 GMT</p> <p> (bisulfite read mapper and methylation caller)</p> </article> <article> <h1>rnaQUAST has been installed</h1> <p>Thu, 02 Jun 2016 12:20:00 GMT</p> <p> (Quality Assessment Tool for Transcriptome Assemblies) </p> </article> <article> <h1>Infernal has been installed</h1> <p>Thu, 02 Jun 2016 12:19:00 GMT</p> <p>(INFERence of RNA ALignment: search DNA for RNA structure and sequence similarities)</p> </article> <article> <h1>Barrnap has been upgraded to version 0.6</h1> <p>Thu, 02 Jun 2016 12:18:00 GMT</p> <p>(predicts the location of ribosomal RNA genes in genomes)</p> </article> <article> <h1>Bridger has been installed</h1> <p>Thu, 02 Jun 2016 12:18:00 GMT</p> <p> (de-novo RNA-Seq assembly)</p> </article> <article> <h1>NGSUtils 0.5.9 installed</h1> <p>Tue, 31 May 2016 12:17:00 GMT</p> <p>(suite of software tools for working with next-generation sequencing datasets) </p> </article> <article> <h1>SPAdes 3.8.0 is now installed</h1> <p>Tue, 31 May 2016 12:16:00 GMT</p> <p>(flexible small-genome assembly, now with plasmid assembly option) </p> </article> <article> <h1>mrCaNaVeR 0.51 is now installed</h1> <p>Tue, 31 May 2016 12:15:00 GMT</p> <p>(copy-number caller using whole-genome read mappings) </p> </article> <article> <h1>mrFAST 2.6.1.0 is now installed</h1> <p>Tue, 31 May 2016 12:14:00 GMT</p> <p>(short-read aligner)</p> </article> <article> <h1>Bandage 0.8.0 is now installed</h1> <p>Tue, 31 May 2016 12:14:00 GMT</p> <p> (assembly graph visualisation tool)</p> </article> <article> <h1>Perl 5.24.0 is now installed</h1> <p>Mon, 30 May 2016 12:13:00 GMT</p> </article> <article> <h1>Perl 5.22.2 is now installed</h1> <p>Mon, 30 May 2016 12:13:00 GMT</p> </article> <article> <h1>Our local copy of iGenomes is being updated</h1> <p>Sun, 29 May 2016 12:12:00 GMT</p> </article> <article> <h1>Java JDK 1.8 release 92 is now installed</h1> <p>Sat, 28 May 2016 12:11:00 GMT</p> <p>Java JDK 1.8 release 92 is now installed as module java/sun_jdk1.8.0_92 as part of compilerson milou and tintin. This is an update for both systems. /douglas</p> </article> <article> <h1>KAT has been updated to version 2.0.8</h1> <p>Wed, 25 May 2016 12:10:00 GMT</p> <p>(Kmer Analysis Toolkit)</p> </article> <article> <h1>Roary 3.6.2 (high speed stand alone pan genome pipeline) is now installed</h1> <p>Wed, 25 May 2016 12:09:00 GMT</p> </article> <article> <h1>GNU parallel 20150522 is now installed</h1> <p>Tue, 24 May 2016 12:08:00 GMT</p> </article> <article> <h1>The GNU coreutils 8.25 (core Linux utilities) is now available</h1> <p>Tue, 24 May 2016 12:08:00 GMT</p> </article> <article> <h1>cutadapt 1.9.1 (flexible adapter trimming) is now installed</h1> <p>Tue, 24 May 2016 12:07:00 GMT</p> </article> <article> <h1>Trim Galore! 0.4.1 (QC wrapper script for FastQC and cutadapt) is now installed</h1> <p>Tue, 24 May 2016 12:06:00 GMT</p> </article> <article> <h1>FastQC 0.4.11 (quality control for FastQ sequences) is now installed</h1> <p>Tue, 24 May 2016 12:06:00 GMT</p> </article> <article> <h1>SPAdes 3.7.1 (flexible small-genome assembly) is now installed</h1> <p>Tue, 24 May 2016 12:05:00 GMT</p> </article> <article> <h1>libgeotiff 1.4.1 (TIFF-based interchange format for georeferenced raster imagery) is now installed</h1> <p>Sat, 21 May 2016 12:04:00 GMT</p> </article> <article> <h1>Poppler 0.43.0 (PDF rendering library) is now installed</h1> <p>Sat, 21 May 2016 12:04:00 GMT</p> </article> <article> <h1>NetCDF 4.4.0 (software libraries and data formats that support array-oriented scientific data) is now available</h1> <p>Sat, 21 May 2016 12:02:00 GMT</p> </article> <article> <h1>FreeType 2.6 (library to render fonts) is now available</h1> <p>Fri, 20 May 2016 12:02:00 GMT</p> </article> <article> <h1>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</h1> <p>Fri, 20 May 2016 12:01:00 GMT</p> </article> <article> <h1>PROJ.4 4.9.2 (Cartographic Projections Library) is now installed</h1> <p>Fri, 20 May 2016 12:00:00 GMT</p> </article> <article> <h1>GDAL 2.1.0 (Geospatial Data Abstraction library) is now installed</h1> <p>Fri, 20 May 2016 12:00:00 GMT</p> </article> <article> <h1>R 3.3.0 (flexible statistical language) is now installed</h1> <p>Thu, 19 May 2016 11:59:00 GMT</p> </article> <article> <h1>PCRE 8.38 (library providing Perl-compatible regular expressions) is now available</h1> <p>Thu, 19 May 2016 11:59:00 GMT</p> </article> <article> <h1>zlib 1.2.8 (widely used general purpose compression library) has been available</h1> <p>Thu, 19 May 2016 11:58:00 GMT</p> </article> <article> <h1>XZ Utils 5.2.2 (high-performance general-purpose compression) is now installed</h1> <p>Thu, 19 May 2016 11:57:00 GMT</p> </article> <article> <h1>Bzip2 1.0.6 (general-purpose compression) is now installed</h1> <p>Thu, 19 May 2016 11:55:00 GMT</p> </article> <article> <h1>Openmpi 1.10.2 was installed for gcc/6.1.0</h1> <p>Fri, 29 Apr 2016 11:53:00 GMT</p> <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> </article> <article> <h1>gcc 6.1.0 was installed</h1> <p>Fri, 29 Apr 2016 11:53:00 GMT</p> <p>gcc 6.1.0 was installed as module gcc/6.1.0 on milou, tintin and irma. /agback</p> </article> <article> <h1>pgi 16.4 was installed</h1> <p>Thu, 28 Apr 2016 11:52:00 GMT</p> <p>pgi 16.4 was installed as module pgi/16.4 on milou and tintin. /agback</p> </article> <article> <h1>Piper (NGI pipeline) has been installed for Irma</h1> <p>Wed, 27 Apr 2016 11:51:00 GMT</p> </article> <article> <h1>GSL (Gnu Scientific Library) has been upgraded to version 2.1</h1> <p>Wed, 27 Apr 2016 11:50:00 GMT</p> </article> <article> <h1>VarDictJava 1.4.5 is now installed</h1> <p>Mon, 25 Apr 2016 11:50:00 GMT</p> </article> <article> <h1>Schmutzi (maximum a posteriori estimate of contamination for ancient samples) has been installed</h1> <p>Sun, 24 Apr 2016 11:49:00 GMT</p> </article> <article> <h1>Platypus (haplotype-based variant caller) has been installed</h1> <p>Fri, 22 Apr 2016 11:47:00 GMT</p> </article> <article> <h1>Haskell Tool Stack (cross-platform program for developing Haskell programming projects) has been installed.</h1> <p>Thu, 21 Apr 2016 11:46:00 GMT</p> </article> <article> <h1>MEGAN (MEtaGenome ANalyzer) has been upgraded to version 5</h1> <p>Thu, 21 Apr 2016 11:46:00 GMT</p> </article> <article> <h1>Several prebuilt databases have been added for use with the DIAMOND tool.</h1> <p>Wed, 20 Apr 2016 11:44:00 GMT</p> </article> <article> <h1>DIAMOND (protein database alignment much faster than BLAST) updated to version 0.7.12</h1> <p>Wed, 20 Apr 2016 11:43:00 GMT</p> </article> <article> <h1>RNA-SeQC (computes quality control metrics for RNA-seq) has been installed</h1> <p>Tue, 19 Apr 2016 11:42:00 GMT</p> </article> <article> <h1>The deepTools package (user-friendly tools for the normalization and visualization of deep-sequencing data) updated to version 2.2.3</h1> <p>Mon, 18 Apr 2016 11:40:00 GMT</p> </article> <article> <h1>BEAST2 (bayesian phylogenetic analysis of molecular sequences) has been upgraded to version 2.4.0</h1> <p>Fri, 15 Apr 2016 11:40:00 GMT</p> </article> <article> <h1>MultiQC (aggregate bioinformatics results into single report) has been updated to version 0.5</h1> <p>Thu, 07 Apr 2016 11:37:00 GMT</p> </article> <article> <h1>BCFtools (VCF and BCF manipulation) has been upgraded to version 1.3</h1> <p>Thu, 07 Apr 2016 11:37:00 GMT</p> </article> <article> <h1>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</h1> <p>Tue, 05 Apr 2016 11:35:00 GMT</p> </article> <article> <h1>HTSlib (C library for high-throughput sequencing data formats) has been installed</h1> <p>Mon, 04 Apr 2016 11:34:00 GMT</p> </article> <article> <h1>Latent Strain Analysis (pre-assembly tool for partitioning metagenomic reads) is now installed</h1> <p>Mon, 04 Apr 2016 11:33:00 GMT</p> </article> <article> <h1>CMake (comprehensive configuration and build tool) upgraded to 3.5.1</h1> <p>Mon, 04 Apr 2016 11:32:00 GMT</p> </article> <article> <h1>SHORE 0.9.3 (Next Generation Sequencing data analysis suite) is now installed</h1> <p>Tue, 29 Mar 2016 11:18:00 GMT</p> </article> <article> <h1>The tinyutils 1.2 collection of small utilities for working on columns of numbers is now installed</h1> <p>Tue, 29 Mar 2016 11:17:00 GMT</p> </article> <article> <h1>Quast (Quality Assessment Tool for Genome Assemblies) was updated to version 3.2</h1> <p>Fri, 25 Mar 2016 12:16:00 GMT</p> </article> <article> <h1>RSEM (RNA-seq by expectation maximization) has been updated to version 1.2.29</h1> <p>Thu, 24 Mar 2016 12:16:00 GMT</p> </article> <article> <h1>Openmpi 1.10.2 was installed</h1> <p>Wed, 23 Mar 2016 12:15:00 GMT</p> <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> </article> <article> <h1>Intel Parallel Studio XE 2016 Cluster Edition update 2 installed</h1> <p>Wed, 23 Mar 2016 12:14:00 GMT</p> <p>Intel Parallel Studio XE 2016 Cluster Edition update 2 is now installed as intel/16.2 on tintin and milou. /agback</p> </article> <article> <h1>intelmpi 5.1.3 is installed</h1> <p>Wed, 23 Mar 2016 12:14:00 GMT</p> <p>intelmpi 5.1.3 is installed as module intelmpi/5.1.3 on tintin and milou. /agback</p> </article> <article> <h1>Intel Advisor XE 2016 updated to update2</h1> <p>Wed, 23 Mar 2016 12:12:00 GMT</p> </article> <article> <h1>canu assembler (a fork of Cabog/Celera Assembler specialised for noisy long reads such as PacBio) updated version 1.1</h1> <p>Tue, 22 Mar 2016 12:11:00 GMT</p> </article> <article> <h1>GEMINI updated to version 0.18.3</h1> <p>Tue, 22 Mar 2016 12:09:00 GMT</p> </article> <article> <h1>MrBayes has been updated to 3.2.6</h1> <p>Wed, 16 Mar 2016 12:09:00 GMT</p> </article> <article> <h1>QualiMap (sequence alignment evaluator) has been updated to version 2.2</h1> <p>Tue, 08 Mar 2016 12:07:00 GMT</p> </article> <article> <h1>iGenomes has been reindexed with the latest version of STAR (2.5.1b)</h1> <p>Mon, 07 Mar 2016 12:06:00 GMT</p> </article> <article> <h1>SPAdes 3.7.0 (flexible small-genome assembly) is now installed</h1> <p>Tue, 01 Mar 2016 12:06:00 GMT</p> </article> <article> <h1>Matlab R2015b has been installed</h1> <p>Tue, 01 Mar 2016 12:05:00 GMT</p> <p>Matlab R2015b has been installed as module matlab/R2015b on milou and tintin. /agback</p> </article> <article> <h1>The ExAC Exome Aggregation Consortium databases releases 0.1, 0.2 and 0.3 downloaded</h1> <p>Fri, 26 Feb 2016 12:02:00 GMT</p> </article> <article> <h1>The h5utils 1.12.1 (utilities for working with hdf4/hdf5-format files) are now installed</h1> <p>Thu, 25 Feb 2016 10:48:00 GMT</p> </article> <article> <h1>SZIP 2.1 library (high-performance file compression) is now installed</h1> <p>Wed, 24 Feb 2016 10:42:00 GMT</p> </article> <article> <h1>HDF4 4.2.11 (libraries and tools supporting a high-performance file format for scientific data) has now been installed</h1> <p>Wed, 24 Feb 2016 10:40:00 GMT</p> </article> <article> <h1>BWA 0.7.13 (NGS read alignment) is now installed</h1> <p>Tue, 23 Feb 2016 10:39:00 GMT</p> </article> <article> <h1>The Guile programming language version 1.8.8 is now installed</h1> <p>Tue, 23 Feb 2016 10:39:00 GMT</p> </article> <article> <h1>snpEff (genetic variant annotation and effect prediction toolbox) has been updated to version 4.2</h1> <p>Tue, 23 Feb 2016 10:38:00 GMT</p> </article> <article> <h1>Delly (structural variant discovery) has been updated to version 0.7.2</h1> <p>Mon, 22 Feb 2016 10:37:00 GMT</p> </article> <article> <h1>MultiQC (aggregate bioinformatics results into single report) has been updated to 0.4</h1> <p>Mon, 22 Feb 2016 10:36:00 GMT</p> </article> <article> <h1>MAKER 2.31.8 (genome annotation pipeline) has been installed</h1> <p>Wed, 17 Feb 2016 10:35:00 GMT</p> </article> <article> <h1>GenomeTools 1.5.8 (versatile open source genome analysis software) is now installed</h1> <p>Tue, 16 Feb 2016 10:35:00 GMT</p> </article> <article> <h1>seqMINER/1.3.3e (genome mapping data interpretation platform) has been installed</h1> <p>Mon, 15 Feb 2016 10:34:00 GMT</p> </article> <article> <h1>ngsplot/2.61 (mining and visualization of NGS data) has been installed</h1> <p>Mon, 15 Feb 2016 10:34:00 GMT</p> </article> <article> <h1>freebayes/1.0.2 (bayesian haplotype-based polymorphism discovery and genotyping) has been updated</h1> <p>Mon, 15 Feb 2016 10:33:00 GMT</p> </article> <article> <h1>RepeatModeler/1.0.8 (de-novo repeat family identification and modeler) has been installed</h1> <p>Mon, 15 Feb 2016 10:32:00 GMT</p> </article> <article> <h1>RepeatMasker/4.0.6 (screens sequences for repeats and low complexity) has been installed</h1> <p>Mon, 15 Feb 2016 10:31:00 GMT</p> </article> <article> <h1>ADMIXTURE 1.3.0 (maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets) is now available</h1> <p>Sat, 13 Feb 2016 10:31:00 GMT</p> </article> <article> <h1>SOAPdenovo-Trans 1.03 and 1.04 (de novo transcriptome assembly) are now available</h1> <p>Fri, 12 Feb 2016 10:30:00 GMT</p> </article> <article> <h1>SGA 0.10.14 (String Graph Assembler) is now available</h1> <p>Fri, 12 Feb 2016 10:29:00 GMT</p> </article> <article> <h1>The tinyutils 1.1 collection of small utilities for working on columns of numbers is now installed</h1> <p>Thu, 11 Feb 2016 10:29:00 GMT</p> </article> <article> <h1>GERP++/20110522 (Genomic Evolutionary Rate Profiling) has been installed</h1> <p>Wed, 10 Feb 2016 10:27:00 GMT</p> </article> <article> <h1>CNV-seq 20140812 (detect CNVs using next-generation sequencing data) is now installed</h1> <p>Tue, 09 Feb 2016 10:26:00 GMT</p> </article> <article> <h1>MEME Suite 4.11.1 (motif-based sequence analysis tools) has been installed</h1> <p>Fri, 05 Feb 2016 10:24:00 GMT</p> </article> <article> <h1>IMPUTE2 2.3.2 (genotype imputation and haplotype phasing program based on ideas from Howie et al. 2009) is now installed</h1> <p>Tue, 02 Feb 2016 10:24:00 GMT</p> </article> <article> <h1>GTOOL 0.7.5 (program for transforming sets of genotype data for use with the programs SNPTEST and IMPUTE) is now installed</h1> <p>Tue, 02 Feb 2016 10:23:00 GMT</p> </article> <article> <h1>qctool 1.4 (program for the analysis of single SNP association in genome-wide studies) is now installed</h1> <p>Tue, 02 Feb 2016 10:22:00 GMT</p> </article> <article> <h1>SNPTEST 2.5.2 (program for the analysis of single SNP association in genome-wide studies) is now installed</h1> <p>Tue, 02 Feb 2016 10:22:00 GMT</p> </article> <article> <h1>MEGAHIT (assembler for large/complex metagenomics) has been installed</h1> <p>Mon, 01 Feb 2016 10:21:00 GMT</p> </article> <article> <h1>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</h1> <p>Sat, 30 Jan 2016 10:21:00 GMT</p> </article> <article> <h1>The canu assembler version 1.0 (a fork of Cabog/Celera Assembler specialised for noisy long reads such as PacBio) is now installed</h1> <p>Fri, 29 Jan 2016 10:20:00 GMT</p> </article> <article> <h1>OPTIMA (alignment of error-prone maps) has been installed</h1> <p>Fri, 29 Jan 2016 10:19:00 GMT</p> </article> <article> <h1>OMBlast (alignment of optical mapping data) has been installed</h1> <p>Fri, 29 Jan 2016 10:19:00 GMT</p> </article> <article> <h1>Alinea DDT 6.0 is installed</h1> <p>Wed, 27 Jan 2016 10:18:00 GMT</p> <p>Alinea DDT 6.0 is installed as module ddt/6.0 on tintin and milou. /agback</p> </article> <article> <h1>FusionCatcher has been upgraded to version 0.99.5a</h1> <p>Wed, 27 Jan 2016 10:17:00 GMT</p> </article> <article> <h1>Subversion version 1.9.3 (source control system) has been installed</h1> <p>Tue, 26 Jan 2016 10:17:00 GMT</p> </article> <article> <h1>The Tablet genome viewer version 1.15.09.01 is now installed</h1> <p>Tue, 26 Jan 2016 10:17:00 GMT</p> </article> <article> <h1>STAR has been upgraded to version 2.5.1b</h1> <p>Tue, 26 Jan 2016 10:16:00 GMT</p> </article> <article> <h1>sratools (SRA Toolkit) has been upgraded to version 2.5.7</h1> <p>Tue, 26 Jan 2016 10:15:00 GMT</p> </article> <article> <h1>The deepTools package version 2.0.1 (user-friendly tools for the normalization and visualization of deep-sequencing data) is now installed</h1> <p>Tue, 26 Jan 2016 10:14:00 GMT</p> </article> <article> <h1>Texinfo 6.0 is available</h1> <p>Thu, 21 Jan 2016 10:14:00 GMT</p> </article> <article> <h1>Additional modules for Intel Parallel Studio XE 2016 CE</h1> <p>Tue, 19 Jan 2016 10:11:00 GMT</p> </article> <article> <h1>Corset 1.04 (transcript quantification) is now available</h1> <p>Tue, 19 Jan 2016 10:11:00 GMT</p> </article> <article> <h1>The pblat-cluster aligner (MPI-enabled blat aligner) version 0.1 is now installed</h1> <p>Fri, 15 Jan 2016 10:10:00 GMT</p> </article> <article> <h1>The pblat aligner (pthread-enabled blat aligner) version 1.6 is now installed</h1> <p>Fri, 15 Jan 2016 10:09:00 GMT</p> </article> <article> <h1>intelmpi 5.1.2 is installed</h1> <p>Fri, 15 Jan 2016 10:08:00 GMT</p> <p>intelmpi 5.1.2 is installed as module intelmpi/5.1.2 on tintin and milou. /agback</p> </article> <article> <h1>Intel Parallel Studio XE 2016 Cluster Edition is now installed</h1> <p>Fri, 15 Jan 2016 10:08:00 GMT</p> <p>Intel Parallel Studio XE 2016 Cluster Edition is now installed as intel/16.1 on tintin and milou. /agback</p> </article> <article> <h1>Openmpi 1.10.1 was installed</h1> <p>Mon, 11 Jan 2016 10:07:00 GMT</p> <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> </article> <article> <h1>pgi 15.10 was installed</h1> <p>Mon, 11 Jan 2016 10:07:00 GMT</p> <p>pgi 15.10 was installed as module pgi/15.10 on milou and tintin. /agback</p> </article> <article> <h1>gcc 5.3.0 was installed</h1> <p>Mon, 11 Jan 2016 10:06:00 GMT</p> <p>gcc 5.3.0 was installed as module gcc/5.3.0 on milou and tintin. /agback</p> </article> <article> <h1>HISAT2 2.0.1-beta (graph-based alignment of next generation sequencing reads to a population of genomes) is now installed</h1> <p>Tue, 05 Jan 2016 10:03:00 GMT</p> </article> <article> <h1>StringTie 1.2.0 (Transcript assembly and quantification for RNA-Seq) is now available</h1> <p>Tue, 05 Jan 2016 10:02:00 GMT</p> </article> <article> <h1>Salmon 0.6.0 (fast transcript quantification from RNA-Seq data) is now available</h1> <p>Fri, 01 Jan 2016 10:01:00 GMT</p> </article> <article> <h1>Jellyfish 2.2.4 (k-mer counting) is now available</h1> <p>Fri, 01 Jan 2016 09:59:00 GMT</p> </article> <article> <h1>[comp] gcc/5.4.0 installed</h1> <p>Fri, 10 Jun 2016 07:18:00 GMT</p> <p>gcc-5.4.0 has been installed on Irma, Milou and Tintin as gcc/5.4.0. /agback</p> </article> <article> <h1>[bio] canu/1.3 assembler installed</h1> <p>Thu, 09 Jun 2016 17:55:00 GMT</p> <p><a href="http://canu.readthedocs.io/en/stable/">The canu assembler</a> assembler (a fork of Celera Assembler specialised for PacBio reads) version 1.3 is now installed as module canu/1.3 as part of the assembly subgroup of bioinfo-tools on milou and tintin. This is an update for both systems. /douglas</p> </article> <article> <h1>[bio] GATK updated</h1> <p>Tue, 07 Jun 2016 12:50:00 GMT</p> <p>Genome Analysis Toolkit</p> </article> <article> <h1>Pilon 1.17 installed</h1> <p>Mon, 16 May 2016 11:58:00 GMT</p> </article> <article> <h1>Micca 1.4.0 installed</h1> <p>Mon, 16 May 2016 11:57:00 GMT</p> </article> <article> <h1>Matlab r2016a installed</h1> <p>Mon, 16 May 2016 11:56:00 GMT</p> </article> <article> <h1>Stacks 1.40 installed</h1> <p>Mon, 16 May 2016 11:55:00 GMT</p> </article> <article> <h1>GMAP/GSNAP modules installed on Milou and Tintin</h1> <p>Mon, 16 May 2016 11:54:00 GMT</p> </article> <article> <h1>Blast databases were updated</h1> <p>Mon, 16 May 2016 11:52:00 GMT</p> </article> <article> <h1>AdapterRemoval installed</h1> <p>Mon, 16 May 2016 11:51:00 GMT</p> </article> <article> <h1>Blast has been upgraded to version 2.2.31+ on Milou and Tintin.</h1> <p>Mon, 07 Dec 2015 09:34:00 GMT</p> </article> <article> <h1>GATK has been upgraded to version 3.5.0 on Milou and Tintin.</h1> <p>Mon, 07 Dec 2015 09:33:00 GMT</p> </article> <article> <h1>We have installed many Perl modules/packages</h1> <p>Tue, 08 Dec 2015 09:31:00 GMT</p> </article> </main></body></html>