-
[apps] R/3.5.2 and R_packages/3.5.2 installed on all systems
R (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.
-
[bio] annovar/2018.04.16 installed on all systems
ANNOVAR (variant annotation) version 2018.04.06 has been installed as module annovar/2018.04.16 on all systems.
-
[bio] PILER-64/1.0 installed on all systems
PILER-64 (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.
-
[bio] trf/4.09 installed on all systems
TRF (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.
-
[bio] RepeatModeler/1.0.11 installed
RepeatModeler (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.
-
[bio] RepeatMasker/4.0.8 installed
RepeatMasker 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.
-
[bio] ANTs/2.3.1 installed
ANTs (Advanced Normalization Tools for biomedical images) version 2.3.1 is now installed as module ANTs/2.3.1 on all clusters.
-
[build] cmake/3.13.2 installed
CMake (build configuration and automation tool) version 3.13.2 is now installed as cmake/3.13.2 on Uppmax clusters.
-
[bio] Stacks/2.2 installed
Stacks 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.
-
[bio] MultiQC/1.7 installed
MultiQC version 1.7 (results aggregator for bioinformatic analyses) is now installed as module MultiQC/1.7 on all systems.
-
[bio] cellranger/3.0.1 installed together with Cell Ranger data 3.0.0
10X Chromium Cell Ranger 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.
The latest version of Cell Ranger data (3.0.0) is also installed. See 'module help cellranger/3.0.1' for more information.
-
[bio] gmap-gsnap/2018-07-04 installed
GMAP-GSNAP version 2018-07-04 (alignment of transcripts and short reads) is isntalled as gmap-gsnap/2018-07-04 on all Uppmax systems.
-
[bio] rrbgen 0.0.6 and STITCH 1.5.4 installed to R_packages/3.5.0
The R packages rrbgen version 0.0.6 (read and write BGEN SNP files) and STITCH 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.
-
[bio] bowtie2/2.3.4.3 installed on all systems
Bowtie2 (short read aligner) version 2.3.4.3 has been installed as module bowtie2/2.3.4.3 on all systems.
-
[bio] chipster module fixed
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.
-
[bio] HiCExplorer version 2.2-beta installed on all systems
HiCExplorer (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.
-
[bio] TIDDIT version 2.3.0 installed on all systems
TIDDIT (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
-
[bio] Minimac4 version 1.0.0 installed on all systems
Minimac4 (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
-
[bio] tigment/1.1.2 now installed on all systems
Tigmint (assembly correction via linked reads) version 1.1.2 is now installed as module tigmint/1.1.2 on all Uppmax systems.
-
[bio] MUMmer/4.0.0beta2 installed on all systems
MUMmer4 version 4.0.0beta2 is now installed as MUMmer/4.0.0beta2 on all systems.
-
[bio] qiime2 version 2018.11.0 installed on all systems
Qiime2 (next-generation microbiome bioinformatics platform) version 2018.11.0 installed as module qiime2/2018.11.0 on all systems
-
[bio] MaxBin version 2.2.5 installed on all systems
MaxBin (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.
-
[bio] CONCOCT version 0.5.0 installed on all systems
CONCOCT (program for unsupervised binning of metagenomic contigs) development version 0.5.0 installed as module CONCOCT/0.5.0 on all systems
-
[bio] albacore build 4aee41d installed on all systems
albacore (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.
-
[bio] LASER/2.04 installed on all systems
LASER (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.
-
[bio] RAxML-NG/0.7.0b and RAxML-NG/0.7.0b-mpi now installed on all systems
RAxML-NG (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.
-
[bio] MACS/2.1.2 installed on all systems
MACS (tool for identifying transcript factor binding sites) version 2.1.2 was installed as module MACS/2.1.2 on all systems
-
[bio] hichipper/0.7.3 installed on all systems
hichipper (data processing and quality control pipeline for HiChIP data) version 0.7.3 was installed as module hichipper/0.7.3 on all systems
-
[bio] OrthoMCL/2.0.9 now creates goodProteins.fasta database with -parse_seqids option
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.
-
[bio] pyGenomeTracks/2.1 installed on all systems
pyGenomeTracks (visualisation tools for genome tracks) 2.1 is now installed as module pyGenomeTrakcs/2.1 on all systems.
-
[bio] HiC-Pro/2.11.1 installed on all systems
HiC-Pro (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
-
[bio] Kourami/0.9.6 installed on all systems
Kourami (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.
-
[bio] MIP/6.0.0 installed on all systems
MIP (Mutation Identification Pipeline) version 6.0.0 was installed as module mip/6.0.0 on all systems
-
[bio] Stampy/1.0.32 installed on all systems
The Stampy short read aligner version 1.0.32 is now installed as module Stampy/1.0.32 on all systems.
-
[bio] Mothur/1.41.0 installed on all systems
Mothur (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.
-
[bio] Kraken2/2.0.7-beta-bc14b13 installed on all systems
The Kraken2 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.
-
[parallel] gnuparallel/20180822 installed on all systems
Gnu Parallel version 20180822 has been installed on all systems as module gnuparallel/20180822.
-
[bio] InterProScan/5.30-69.0 installed on all systems
InterProScan (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.
This installation includes support for Panther database 12.0, and the additional analysis tools Phobius/1.01, SignalP/4.1f, and tmhmm/2.0c.
-
[bio] Phobius/1.01 installed on all systems
Phobius (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.
-
[bio] umi_tools/0.5.3 and umi_tools/0.5.4 installed on all systems
UMI-tools (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.
-
[bio] samstat/1.5.1 installed on all systems
Samstat (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.
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[bio] Mothur 1.40.5 installed on all systems
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".
-
[bio] GenomeThreader/1.7.0 installed on all systems
GenomeThreader (robust de novo gene discovery) version 1.7.0 is now installed as module GenomeThreader/1.7.0 on all systems.
-
[bio] clustalo/1.2.4 installed on all systems
Clustal Omega (large multiple sequence alignments) version 1.2.4 has been installed as module clustalo/1.2.4 on all systems.
-
[bio] MAFFT/7.407 installed on all systems
MAFFT multiple sequence alignment version 7.407 is now installed on all systems as module MAFFT/7.407. This includes MAFFT extensions.
-
[apps] R_packages/3.5.0 updated
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 R_packages module guide for a complete list of available R packages.
-
[apps] JAGS/4.3.0 installed on all systems
JAGS (Just Another Gibbs Sampler) version 4.3.0 is now installed as module JAGS/4.3.0 on all systems.
-
[libs] UDUNITS/2.2.26 installed on all systems
The UDUNITS 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.
-
[bio] Centrifuge/1.0.4-beta installed on all systems
Centrifuge (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.
-
[bio] deepTools/3.1.0 installed on all systems
deepTools (tools for exploring deep sequencing data) version 3.1.0 is now installed as module deepTools/3.1.0 on all systems.
-
[bio] GATK/3.8-0 now includes gatk wrapper script
The GATK/3.8-0 module now includes the gatk wrapper script modified from Bioconda, so that GATK can be run from the command line using gatk ... or GenomeAnalysisTK ... directly.
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[bio] sratools/2.9.1-1 installed on all systems
The SRA Toolkit (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.
-
[bio] CIRCexplorer/1.1.10 installed on all systems
CIRCexplorer (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.
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[bio] rvtests/2.0.6 installed on all systems
rvtests (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.
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[bio] PLINK/2 installed on all systems
PLINK (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
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[bio] KrakenHLL/0.4.9 installed on all systems
KrakenHLL (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.
-
[bio] blobtools/1.0 installed on all systems
Blobtools (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.
-
[bio] malder/1.0 available for rackham, bianca, irma
MALDER (admixture estimation) version 1.0 is now available as module malder/1.0 on all UPPMAX systems. It was previously available only on milou.
-
[bio] bbmap/38.08 installed
BBMap package version 38.08 is now installed as module bbmap/38.08 on all UPPMAX systems.
-
[apps] siesta/4.1-b3 installed
Siesta 4.1-b3
-
[bio] LDhelmet/1.10 installed
LDhelmet (statistical inference for fine-scale variable recombination rate estimation) version 1.10 is now installed as module LDhelmet/1.10 on all UPPMAX clusters.
-
[apps] siesta/4.0.1 installed
Siesta 4.0.1
-
[comp] intel/18.3 installed
Intel Parallel Studio XE Cluster Edition upgrade 3 have been installed.
intel/18.3
intelmpi/18.3
advisor/18.3
intelamplifier/18.3
inspector/18.3.0
itac/18.3
have been installed. -
[bio] iqtree/1.6.5-omp-mpi installed on all systems
IQ-Tree (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.
-
[bio] cutadapt/1.16 installed on all systems
Cutadapt (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.
-
[bio] vep/92 installed on all systems
Ensembl Variant Effect Predictor 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.
-
[bio] snpEff/4.3t installed on all systems
SnpEff (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.
-
[bio] KAT/2.4.2 installed on all systems
KAT (Kmer Analysis Toolkit) 2.4.2 is now installed as module KAT/2.4.2 on all systems.
-
[bio] PBSuite/15.8.24 installed on all systems
PBSuite (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.
-
[bio] blast/2.7.1+ installed on all systems
Blast+ (sequence search) version 2.7.1+ has been installed as module blast/2.7.1+ on all systems.
-
[apps] R_packages/3.5.0 installed on all systems
The R_packages omnibus package 3.5.0 is now installed on all systems as packages R_packages/3.5.0. This package includes 11937 CRAN packages installed, out of 12571 available, and 14735 BioConductor packages installed, out of 15411 available.
-
[apps] R/3.5.0 installed on all systems
R (statistical system) version 3.5.0 is now installed as module R/3.5.0 on all systems.
-
[bio] Installed htslib version 1.8 on bianca, irma and rackham
New version of htslib (1.8) installed as module htslib/1.8
-
[bio] satsuma2/2016-12-07 installed on all systems
Satsuma2 (whole genome alignment) version 2016-12-07 is now available on all Uppmax systems. It was previously available only on milou.
-
[bio] Kraken/1.1-352e780 has been installed on all systems
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.
-
[apps] rspt/2018-03-31_rackham_intel_mkl installed on Rackham
RSPt version released March 31st, 2018 is installed on Rackham.
-
[parallel] openmpi/3.1.0
openmpi 3.1.0 is now installed on Irma, Milou and Rackham.
-
[comp] gcc/8.1.0 installed
gcc 8.1.0 is now installed on Bianca, Irma, Milou and Rackham
-
[apps] amber/ambertools18_intel_python2 installed on Rackham
AmberTools18 (released on April 17, 2018) is installed as a module on Rackham.
-
[bio] cd-hit/4.6.8-2017-1208 installed on all systems
CD-HIT (sequence clustering) version 4.6.8-2017-1208 has been installed as module cd-hit/4.6.8-2017-1208 on all systems.
-
[bio] FastTree/2.1.10 installed on all systems
FastTree (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.
-
[bio] eigensoft/7.2.1 installed on all systems
Eigensoft 7.2.1 (with the fix restoring the ploteig tool) is now installed as module eigensoft/7.2.1 on all systems.
-
[bio] AdmixTools/5.0-20171024 installed on all systems
AdmixTools 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.
-
[bio] BUSCO/3.0.2b installed on all systems
BUSCO (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.
-
[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.
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[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.
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[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.
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[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.
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[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.
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[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.
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[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.
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[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.
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[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.
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[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.
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[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.
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[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.
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[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.
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[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.
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[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.
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[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.
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[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.
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[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.
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[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.
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[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.
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[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.
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[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.
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[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.
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[bio] cramtools/3.0 installed on all systems
Cramtools 3.0 is installed as module cramtools/3.0 on all systems.
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[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.
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[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.
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[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.
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[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.
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[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.
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[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.
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[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).
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[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.
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[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.
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[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.
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[bio] prank/170427 installed on all systems
PRANK (probabilistic multiple alignment) 170427 is now installed as module prank/170427 on all systems.
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[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.
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[bio] bwa/0.7.17 installed on all systems
BWA 0.7.17 is installed as module bwa/0.7.17 on all systems.
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[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.
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[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.
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[bio] preseq/2.0 installed on all systems
Preseq 2.0 has been installed as module preseq/2.0 on all systems.
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[bio] cutadapt/1.14 installed on all systems
Cutadapt 1.14 has been installed as module cutadapt/1.14 on all systems.
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[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.
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[bio] MultiQC/1.3 installed on all systems
MultiQC 1.3 has been installed on all systems as module MultiQC/1.3.
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[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.
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[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.
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[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.
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[apps] GAMESS-US installed on Rackham
GAMESS-US, a molecular dynamics package, is now installed on Rackham as module gamess/20170930.
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[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.
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[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.
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[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).
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[ 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
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[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.
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[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.
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[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.
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[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.
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[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.
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[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.
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[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.
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[misc] POV-Ray installed
POV-Ray 3.7 (raytracing engine) has been installed on Rackham, Bianca, and Irma as module povray/3.7.
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[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.
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[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.
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[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.
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[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.
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[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.
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[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.
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[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.
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[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.
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[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.
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[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.
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[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
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[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.
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[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::*.
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[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.
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[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
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[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.
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[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.
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[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.
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[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.
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[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.
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[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.
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[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.
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[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
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[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.
Uppsala Multidisciplinary Center for Advanced Computational Science