-
[comp] ruby/2.5.0 installed on all systems
Ruby 2.5.0 is now installed as module ruby/2.5.0 on all systems.
-
[bio] ANGSD/0.921 installed on all systems
ANGSD (program for analysing next generation sequencing data) 0.921 is now installed as module ANGSD/0.921 on all systems.
-
[bio] bamtools/2.5.1 installed on all systems
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.
-
[bio] fastPHASE/1.4.8 and fastPHASE/1.4.0 available on all systems
fastPHASE (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.
-
[bio] gubbins/2.3.1 installed on all systems
Gubbins (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.
-
[bio] OrthoMCL/2.0.9 now available on all systems
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.
-
[apps] Matlab R2018a installed
Matlab R2018a is installed as matlab/R2018a on all systems.
-
[comp] intel/18.2 installed
ntel Parallel Studio XE Cluster Edition 2018 update 2 has been installed on Rackham, Irma and Milou.
-
[comp] pgi/18.3 installed
pgi/18.3 is installed on Rackham and Milou
-
[comp] advisor, ampilifier, inspector and itac upgraded
advisor, ampilifier, inspector and itac upgraded has been upgraded to versions included in 2018 update 2.
-
[parallel] openmpi/2.1.3 installed
openmpi/2.1.3 installed on Rackham and Irma
-
[bio] MultiQC/1.5 installed on all systems
MultiQC (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.
-
[bio] gvcftools/0.16.2 and gvcftools/0.17.0 available on all systems
gvcftools (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.
-
[bio] Stacks/1.48 and Stacks/2.0Beta9 installed on all systems
Stacks (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.
-
[apps] PostgreSQL/10.3 installed on all systems
PostgreSQL (open-source relational database) 10.3 is now installed as module PostgreSQL/10.3 on all systems.
-
[bio] canu/1.7 installed on all systems
Canu (assembler for long noisy read data) version 1.7 has been installed as module canu/1.7 on all systems.
-
[apps] ImageMagick-6.9.9-35 installed on all systems
ImageMagick (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.
-
[bio] Salmon/0.9.1 installed on all systems
Salmon (RNA-seq transcript quantification) version 0.9.1 is now installed as module Salmon/0.9.1 on all systems.
-
[bio] mergeSVcallers/161006-23533ef installed on all systems
mergeSVcallers (Software for merging different Tabix merged VCF files) is now installed as module mergeSVcallers/161006-23533ef on all systems.
-
[bio] gmap-gsnap/2018-02-12 installed on all systems
Gmap and gsnap (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.
-
[comp] gcc/7.3.0 installed
gcc 7.3.0 is now installed on Bianca, Irma, Milou and Rackham as gcc/7.3.0
-
[apps] RStudio/1.1.423 installed on rackham, irma and bianca
RStudio version 1.1.423 is installed on rackham, irma and bianca. This precompiled version cannot be installed on milou.
-
[bio] canu/1.6 installed on all systems
Canu (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.
-
[bio] BEETL/1.1.0 installed on all systems
BEETL (Burrows-Wheeler Extended Tool Library) version 1.1.0 is now installed as module BEETL/1.1.0 on all systems.
-
[bio] artemis/16.0.0 installed on all systems
Artemis (genome browser from Wellcome Sanger Institute) version 16.0.0 is now installed as module artemis/16.0.0 on all systems.
-
[bio] phylophlan/0.99 installed on all systems
PhyloPhlAn (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.
-
[bio] CheckM/1.0.11 installed on all systems
CheckM (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.
-
[bio] megahit/1.1.2 installed on all systems
MEGAHIT (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.
-
[bio] beast/1.8.4 installed on all systems except for milou
BEAST (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.
-
[bio] beast2/2.4.8 installed on all systems
BEAST2 (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.
-
[bio] LUMPY/0.2.13-213a417 installed on all systems
LUMPY (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.
-
[bio] supernova/2.0.0 installed on all systems
The 10X Chromium assembler Supernova 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.
-
[bio] bcl2fastq/2.20.0 installed on all systems
The Illumina base caller bcl2fastq version 2.20.0 is now installed as module bcl2fastq/2.20.0 on all systems.
-
[bio] infernal/1.1.2 installed on all systems
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.
-
[bio] prokka/1.12-12547ca installed on all systems
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.
-
[comp] git/2.16.1 now installed on all systems
The most recent version of Git source control system is installed as module git/2.16.1 on all systems.
-
[bio] tbl2asn/25.3 available on all systems, and version 24.9 removed from all systems
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.
-
[bio] aragorn/1.2.38 installed on all systems
ARAGORN (tRNA and tmRNA detection) 1.2.38 is installed as module aragorn/1.2.38 on all systems.
-
[bio] iqtree/1.5.4-omp-mpi installed on all systems
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.
-
[bio] snakemake/4.5.0 installed on all systems
Snakemake (A workflow management tool to create reproducible and scalable data analyses) version 4.5.0 is now installed as module snakemake/4.5.0 on all systems.
-
[bio] samtools/1.6, bcftools/1.6, htslib/1.6 installed on all systems
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.
-
[bio] spades/3.11.1 installed on all systems
SPAdes assembler version 3.11.1 is now installed as module spades/3.11.1 on all systems.
-
[bio] CONSEL/0.2.0 installed on all systems
CONSEL (Program for assessing the confidence of phylogenetic tree selection) is now installed as module CONSEL/0.2.0 on all systems.
-
[bio] plinkseq 0.10 installed on all systems
PLINK/SEQ (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.
-
[bio] ATSAS/2.8.3-1 installed on all systems
ATSAS (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.
-
[bio] BEDTools/2.27.1 installed on all systems
BEDTools (a powerful toolset for genome arithmetic) version 2.27.1 is now installed as module BEDTools/2.27.1 on all systems.
-
[bio] VCFaid/20170616-f0732ae installed on all systems
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.
-
[bio] svprops/20171020-ebf6762 installed on all systems
svprops (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.
-
[bio] Strelka2/2.8.4 installed on all systems
Strelka2 (germline and somatic small variant caller) version 2.8.4 is now installed as module Strelka2/2.8.4 on all systems.
-
[bio] GATK/4.beta.5 installed on all systems
The Beta 5 version of GATK 4 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.
-
[bio] pplacer/1.1.alpha19 installed on all systems
pplacer (place reads on a phylogenetic tree) version 1.1.alpha19 has been installed as module pplacer/1.1.alpha19 on all systems.
-
[bio] freebayes/1.1.0 installed on all systems
Freebayes 1.1.0 (variant calling) has been installed on all systems as module freebayes/1.1.0.
-
[apps] R/3.4.3 and omnibus package module R_packages/3.4.3 installed on all systems
R 3.4.3 together with the omnibus package module R_packages 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.
-
[bio] MEGAN/6.10.5 installed on all systems
MEGAN (interactive microbiome analysis tool) 6.10.5 Academic Edition is installed as module MEGAN/6.10.5 on all systems.
-
[bio] cramtools/3.0 installed on all systems
Cramtools 3.0 is installed as module cramtools/3.0 on all systems.
-
[apps] MariaDB/10.1.29 and /10.2.11 installed on all systems
MariaDB (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.
-
[bio] bowtie2/2.3.3.1 installed on all systems
Bowtie2 2.3.3.1 has been installed as module bowtie2/2.3.3.1 on all systems.
-
[comp] java/sun_jdk1.8.0_151 installed on all systems
The Sun Java Development Kit 8.0 release 151 has been installed as module java/sun_jdk1.8.0_151 on all systems.
-
[apps] vim/8.0-1360 installed on all systems
VIM 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.
-
[bio] SMRT/5.0.1 installed on all systems
SMRT Link 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.
-
[bio] blasr/5.3-20171117-f72428d installed on all systems
Blasr 5.3.f72428d (PacBio long-read aligner) has been installed as module blasr/5.3-20171117-f72428d on all systems.
-
[bio] pysam/0.13-python2.7.1 and pysam/0.13-python3.6.0 installed
PySam 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).
-
[bio] spaln/2.1.4 module now installed on all systems
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.
-
[bio] NCBI taxonomy databases now available
NCBI taxonomy databases are now available as local copies at Uppmax. See our NCBI taxonomy databases page for more information.
-
[bio] UniVec and UniVec_Core databases now available
NCBI UniVec and UniVec_Core databases 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 Blast databases page for more information.
-
[bio] prank/170427 installed on all systems
PRANK (probabilistic multiple alignment) 170427 is now installed as module prank/170427 on all systems.
-
[bio] Minimap2 2.4 installed as minimap2/2.4 on all systems
Minimap2 (versatile sequence alignment program, good for noisy long reads) 2.4 is installed as module minimap2/2.4 on all systems.
-
[bio] bwa/0.7.17 installed on all systems
BWA 0.7.17 is installed as module bwa/0.7.17 on all systems.
-
[bio] TrimGalore/0.4.4 installed on all systems
Trim Galore! 0.4.4 has been installed as module TrimGalore/0.4.4 on all systems.
-
[bio] Nextflow 0.26.0 has been installed on all systems
Nextflow 0.26.0 has been installed as module Nextflow/0.26.0 on all systems.
-
[bio] preseq/2.0 installed on all systems
Preseq 2.0 has been installed as module preseq/2.0 on all systems.
-
[bio] cutadapt/1.14 installed on all systems
Cutadapt 1.14 has been installed as module cutadapt/1.14 on all systems.
-
[bio] Kraken/1.0 installed on all systems
Kraken (system for assigning taxonomic labels to short DNA sequences) 1.0 has been installed as module Kraken/1.0 on all systems.
-
[bio] MultiQC/1.3 installed on all systems
MultiQC 1.3 has been installed on all systems as module MultiQC/1.3.
-
[bio] Blast databases are now being updated
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 resource page for local Blast databases for more information.
-
[bio] vsearch/2.5.2 installed on all systems
Vsearch (open-source alternative to usearch) 2.5.2 has been installed as module vsearch/2.5.2 on all systems.
-
[apps] packages added and updated in R_packages/3.4.0
Several packages have been added and many have been updated in the module R_packages/3.4.0. See http://www.uppmax.uu.se/support/user-guides/r_packages-module-guide/ for a complete list of the available packages.
-
[apps] GAMESS-US installed on Rackham
GAMESS-US, a molecular dynamics package, is now installed on Rackham as module gamess/20170930.
-
[libs] GLPK 4.63 linear programming package installed
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.
-
[bio] sratools/2.8.2-1 installed on all systems
The SRA Toolkit 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 special Blast+ tools that enable searching against the WGS and TSA sequence databases.
-
[bio] plink/1.90b4.9 installed on all systems
PLINK 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).
-
[ apps] VASP 5.4.4 and VASPsol 5.4.4 installed on Rackham
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
-
[bio] NextGenMap/0.5.4 installed on all systems
NextGenMap version 0.5.4 has been installed as module NextGenMap/0.5.4 as part of bioinfo-tools on all systems.
-
[bio] Pilon/1.22 installed on all systems
Pilon (automated genome assembly improvement and variant detection tool) version 1.22 is now installed as module Pilon/1.22 on all systems.
-
[bio] REAPR/1.0.18 installed on all systems
REAPR (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.
-
[bio] SeqTools/4.44.1 installed on all systems
SeqTools (three sequence alignment visualisation tools from the Sanger Institute) 4.44.1 is now installed as module SeqTools/4.44.1 on all systems.
-
[bio] ShoRAH/1.1.0 installed on all systems
ShoRAH (short reads assembly into haplotypes) 1.1.0 is now installed as module ShoRAH/1.1.0 on all systems.
-
[bio] IGV/2.4.2 and IGVtools/2.3.98 installed on all systems
The IGV genome viewer 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.
-
[bio] velvet/1.2.10 and velvet/1.2.10_K128 offer more capabilities
The modules for the most recent version of the Velvet 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.
-
[misc] POV-Ray installed
POV-Ray 3.7 (raytracing engine) has been installed on Rackham, Bianca, and Irma as module povray/3.7.
-
[bio] LDhelmet/1.9 installed on all systems
LDhelmet (fine-scale recombination estimates) version 1.9 is now installed as module LDhelmet/1.9 on all systems.
-
[bio] MetaBat/2.12.1 is installed on all systems
MetaBat (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.
-
[bio] ExpansionHunter/2.5.3 is installed on all systems
ExpansionHunter (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.
-
[bio] maker/3.01.1-beta installed on all systems
MAKER (genome annotation pipeline) version 3.01.1-beta has been installed as module maker/3.01.1-beta on all systems.
-
[bio] RepeatMasker/4.0.7's RMBlast repaired via patch
The RMBlast that is part of the RepeatMasker/4.0.7 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.
-
[bio] GeneMark/4.33-es installed on all systems
GeneMark-ES (unsupervised gene-finding in eukaryotic genomes) version 4.33 is now installed as module GeneMark/4.33-es on all systems.
-
[bio] trinotate/3.0.2 now installed on all systems
Trinotate (transcript annotation) version 3.0.2 is now installed as module trinotate/3.0.2 on all systems.
-
[bio] SignalP/4.1f is now installed on all systems
SignalP (signal peptide prediction) version 4.1f is now installed as module SignalP/4.1f on all systems. Use is restricted to academic users only.
-
[bio] TransDecoder/5.0.1 installed on all systems
TransDecoder (identifies candidate coding regions within transcript sequences) 5.0.1 is now installed as module TransDecoder/5.0.1 on all systems.
-
[bio] MultiQC/1.2 installed on all systems
MultiQC 1.2 (comprehensive reporting for bioinformatics analyses) has been installed as module MultiQC/1.2 on all Uppmax systems.
-
[bio] several more modules made available on all systems
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
-
[bio] MaSuRCA/3.2.3 installed on all systems
MaSuRCA 3.2.3 (whole-genome assembler) has been installed as module MaSuRCA/3.2.3 on all systems.
-
[comp] several more modules added to perl_modules/5.24.1
Several more modules have been added to the perl_modules/5.24.1 omnibus module, primarily within Statistics::*.
-
[bio] VarScan/2.4.2 installed on all systems
VarScan (variant detection tool) version 2.4.2 has been installed as module VarScan/2.4.2 on all systems.
-
[bio] several more modules made available on all systems
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
-
[bio] gmap-gsnap/2017-09-11 installed on all systems
GMAP-GSNAP version 2017-09-11 has been installed as module gmap-gsnap/2017-09-11 on all systems.
-
[bio] cellranger/2.0.2 installed on all systems
Chromium Cellranger 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.
-
[bio] annovar/2017.07.16 installed on all systems
ANNOVAR 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.
-
[bio] bbmap/37.53 installed on all systems
BBTools/BBMap (toolkit for read mapping and sequence analysis) has been installed as module bbmap/37.53 on all systems.
-
[bio] AdapterRemoval/2.2.2 installed on all systems
AdapterRemoval (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.
-
[bio] Vmatch/2.3.0 installed on all systems
Vmatch (large-scale sequence analysis software) 2.3.0 has been installed as module Vmatch/2.3.0 on all systems.
-
[bio] BEDOPS/2.4.28 installed on all systems
BEDOPS (BAM file manipulation) version 2.4.28 has been installed as module BEDOPS/2.4.28 on all systems.
-
[bio] several more modules made available on all systems
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
-
[bio] paml/4.9e is installed on all systems
PAML (Phylogenetic Analysis by Maximum Likelihood) 4.9e is installed as module paml/4.9e on all systems.
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[bio] phylobayes/4.1c installed on all systems
PhyloBayes version 4.1c has been installed as phylobayes/4.1c on all systems.
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[bio] phylobayesmpi/1.8 installed on all systems
PhyloBayes MPI version 1.8 is now installed as module phylobayesmpi/1.8 on all systems.
-
[bio] GATK-Queue/3.8-0 installed on all systems
GATK Queue version 3.8-0 has been installed as module GATK-Queue/3.8-0 on all systems.
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[apps] RStudio/1.1.233-buggy now available on milou
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.
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[bio] GATK/3.8-0 installed on all systems
Genome Analysis Toolkit version 3.8-0 is installed on all systems as module GATK/3.8-0. In addition to other improvements, this version corrects core dumps within the PairHMM library that some users have reported.
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[comp] pgi/17.7 installed
pgi/17.7 installed on Milou and Rackham
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[bio] local data caches for vep/84, vep/86 greatly reduced
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 http://www.uppmax.uu.se/resources/databases/other-uppnex-oriented-local-data-resources/ and 'module help vep'.
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[bio] BioPerl/1.7.1_Perl5.24.1 installed on all systems
BioPerl 1.7.1 for Perl 5.24.1 has been installed as module BioPerl/1.7.1_Perl5.24.1 on all systems.
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[bio] spaln/2.3.1 installed on all systems
Spaln (space-efficient spliced alignment) version 2.3.1 is now installed as module spaln/2.3.1 on all systems.
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[bio] sickle/1.33-20-g4b0dc85-mullins installed on all systems
Sickle (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.
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[bio] SHORE/0.9.3 installed on all systems
SHORE (mapping and analysis pipeline for short DNA sequences) 0.9.3 is now installed as module SHORE/0.9.3 on all systems.
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[bio] sambamba/0.6.6 installed on all systems
Sambamba 0.6.6 (SAM/BAM file processing) has been installed as module sambamba/0.6.6 on all systems.
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[bio] scalpel/0.5.3 installed on all systems
Scalpel (indel detection) 0.5.3 has been installed as module scalpel/0.5.3 on all systems.
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Several more modules now available on all systems
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
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[bio] MAFFT/7.310 installed on all systems
MAFFT 7.310 (multiple sequence aligner) is installed as module MAFFT/7.310 on all systems.
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[libs] jemalloc/5.0.1 installed on all systems
Jemalloc 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.
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[bio] trinity/2.4.0 installed on all systems
Trinity 2.4.0 (transcriptome assembler) is installed as module trinity/2.4.0 on all systems.
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[bio] khmer/2.1.1 installed on all systems
Khmer 2.1.1 (k-mer counting library) is installed as module khmer/2.1.1 on all systems.
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[bio] NGSadmin/32 and fastNGSadmin/20170825-099ab7f are installed on all systems
NGSadmix version 32 and fastNGSadmix (versioned based on repository date/commit hash) are available as modules NGSadmix/32 and fastNGSadmix/20170825-099ab7f on all systems.
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[bio] lastz/1.04.00 installed on all systems
LASTZ 1.04.00 (pairwise sequence aligner) has been installed as module lastz/1.04.00 on all systems.
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[bio] rtgcore/3.8.3 installed on all systems
The non-commercial version of RTG Core 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.
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[bio] rtgtools/3.8.3 installed on all systems
RTG Tools version 3.8.3 has been installed as module rtgtools/3.8.3 on all systems.
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[bio] fastq_screen/0.11.1 installed on all systems
FastQ Screen version 0.11.1 has been installed as module fastq_screen/0.11.1 on all systems.
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[bio] anfo/0.98 now available for all systems
Anfo (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).
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[apps] gnuplot/5.0.7 installed on all systems
Gnuplot 5.0.7 is installed as module gnuplot/5.0.7 on all systems.
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[apps] awscli/1.11.140 now available on all systems
Amazon Web Services Command-Line Interface version 1.11.140 is now installed as module awscli/1.11.140 on all systems.
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Several more modules now available on all systems
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.
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[bio] htseq/0.9.1 installed on all systems
HTSeq version 0.9.1 has been installed as module htseq/0.9.1 on all systems.
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[comp] gcc/6.4.0 installed
gcc 6.4.0 is now installed on Bianca, Irma, Milou and Rackham as gcc/6.4.0
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[bio] ITSx/1.0.11 and ITSx/1.1-beta installed on all systems
ITSx (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.
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[bio] rseqc/2.6.4 installed on all systems
RSeQC 2.6.4 (RNA-Seq quality control) is now installed as module rseqc/2.6.4 on all systems.
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[bio] MaSuRCA/3.2.2 installed on all systems
The MaSuRCA assembler version 3.2.2 is now installed as module MaSuRCA/3.2.2 on all systems.
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[bio] KAT/2.3.4 installed on all systems
KAT (K-mer Analysis Toolkit) version 2.3.4 has been installed as module KAT/2.3.4 on all systems.
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[comp] gcc/7.2.0 installed
gcc 7.2.0 is now installed in Bianca, Irma, Milou and Rackham as gcc/7.2.0.
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[bio] RealTime Genomics reference databases now available
RealTime Genomics' preformatted reference databases are now available on Uppmax systems. See 'module help rtgtools/3.8.1' for more information.
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[bio] pblat-cluster/0.3 installed on all systems
Pblat-cluster (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.
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[bio] pblat/2.0 installed on all clusters
Pblat (threaded version of blat aligner) version 2.0 has been installed as module pblat/2.0 on all systems.
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[bio] all bioinformatics modules will default to the latest version
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 always be specified when loading tools via the module system.
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[apps] Matlab R2017a installed
Matlab R2017a has been installed as module matlab/R2017a on Milou and Rackham.
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[bio] EPACTS/3.3.0-a5209db installed on all systems
EPACTS 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.
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[bio] MELT/2.0.2 installed on all systems
MELT (Mobile Element Locator Tool) version 2.0.2 has been installed as module MELT/2.0.2 on all systems.
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[bio] AMOS/3.0.0, AMOS/3.1.0, blat/34 and blat/35 now on rackham, irma, bianca
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.
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[bio] kallisto/0.43.1 installed on all systems
The RNA-seq pseudoalignment tool kallisto version 0.43.1 has been installed on all systems as module kallisto/0.43.1.
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[bio] cufflinks/2.2.1-b55bb21 installed on all systems
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 here.
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[apps] several packages added to R_packages/3.4.0
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 R_packages user guide.
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[bio] picard/2.10.3 installed on all systems
The most recent version of Picard tools has been installed as module picard/2.10.3 on all systems.
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[bio] samtools/1.5, htslib/1.5, bcftools/1.5 installed on all systems
The modules samtools/1.5, htslib/1.5, and bcftools/1.5 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.
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[bio] augustus/3.2.2 available on irma, bianca, rackham
The module augustus/3.2.2, previously available only on milou, is now also available on irma, bianca and rackham.
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[bio] Longranger upgraded to 2.1.4 on all systems
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.
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[bio] bismark/0.18.2 installed on all systems
Bismark 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.
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[bio] vsearch/2.4.3 installed on all systems
vsearch 2.4.3 has been installed as module vsearch/2.4.3 on all systems.
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[bio] VEP 89 upgraded
VEP (Variant Effect Predictor) has been upgraded to version 89 on all systems.
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STAR-Fusion Installed on all the systems
STAR-Fusion/1.0.0 is Installed and is available on all the systems.
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Eigensoft upgraded to 7.2.0
eigensoft/7.2.0 is now available on all the systems.
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STAR upgraded to 2.5.3a
star/2.5.3a is now available on all the systems.
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HISAT2 upgraded to 2.1.0
HISAT2/2.1.0 is now available on all the systems.
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[geo] libgeotiff/1.4.1 available on rackham
The libgeotiff/1.4.1 module is now available on rackham; it was previously available only on milou.
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[geo] GEOS/3.4.0, GDAL/2.1.0, PROJ.4/4.9.2, FYBA/4.1.1 now on all systems
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.
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delly upgraded to 0.7.7
delly/0.7.7 has been installed on all the systems.
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[bio] rtgtools/3.8.1 installed on all systems
RTG Tools 3.8.1 (utilities for accurate VCF comparison and manipulation) has been installed as module rtgtools/3.8.1 on all systems.
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[bio] MAGeCK/0.5.6 installed on all systems
MAGeCK 0.5.6 (Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout) is now installed as module MAGeCK/0.5.6 on all systems.
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[bio] cufflinks/2.2.1 installed on all systems
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.
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[bio] bowtie2/2.3.2 installed on all systems
Bowtie2 2.3.2 has been installed as module bowtie2/2.3.2 on all systems.
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[bio] bowtie/1.2.0 installed on all systems
Bowtie 1.2.0 has been installed as module bowtie/1.2.0 on all systems.
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[bio] tophat/2.1.1 installed on all systems
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.
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[bio] MrBayes installed on Rackham
MrBayes (Bayesian inference and model choice) is now installed on Rackham as module mrbayes/3.2.6.
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[bio]Beagle-lib installed on Rackham
Beagle-lib (general purpose library for evaluating the likelihood of sequence evolution on trees) is now installed on Rackham as module beagle/2.1.2.
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[bio] MultiQC/1.0 installed on all systems
MultiQC 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.
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[bio] several bioinfo-tools/misc modules now also available on rackham
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
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[bio] deepTools/2.5.1 installed on all systems
deepTools 2.5.1 is now installed as module deepTools/2.5.1 on all systems.
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[bio] deepTools/2.4.3 installed on all systems
deepTools 2.4.3 has been installed as module deepTools/2.4.3 on all systems.
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[bio] seqtk/1.2-r101 available on all systems
The seqtk 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.
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[comp] pgi/17.4 installed
pgi/17.4 installed on Milou and Rackham
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[parallel] openmpi/2.1.1
openmpi/2.1.1 has been installed on Irma, Milou and Rackham
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[comp] advisor, ampilifier, inspector and itac upgraded
advisor, ampilifier, inspector and itac upgraded
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[comp] intel/17.4 installed
intel/17.4 has been installed on all systems.
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[bio] TEtools/1.0.0-283c1ca installed on all systems
TEtools 1.0.0 up through commit 283c1ca has been installed as module TEtools/1.0.0-283c1ca on all systems. The local UPPMAX version has been modified to move some options provided only in config files to command-line options.
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[comp] perl_modules/5.24.1 installed on all systems
The omnibus module perl_modules/5.24.1 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.
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[comp] perl6/rakudo-star-2017.04 installed on all systems
Perl6 Rakudo Star 2017.04 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.
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[apps] emacs/25.2 installed on all systems
The editor emacs 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.
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[libs] giflib/5.1.4 installed on all systems
GIFLIB (library providing GIF support via libgif) is now installed as module libgif/5.1.4 on all systems.
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[bio] ATLAS_aDNA/20170510 installed on all systems
The ATLAS tool for working with ancient DNA has been installed as module ATLAS_aDNA/20170510 on all systems. Note the module name is ATLAS_aDNA, because the name ATLAS has already being given to a module for the widely used numeric library.
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[libs] Armadillo/7.900.0 installed on all systems
The Armadillo C++ linear algebra library has been installed as module Armadillo/7.900.0 on all systems.
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[bio] hmmer/3.1b2-intel installed on all systems
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.
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[bio] MethylDackel/0.2.1 installed on all systems
MethylDackel 0.2.1 (renamed continuation of methylation detection tool PileOMeth) is now installed as module MethylDackel/0.2.1 on all systems.
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[comp] perl/5.24.1 installed on all systems
Perl 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.
