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Adhoc software "packaged" for the ancient and deprecated "module system" (http://modules.sf.net/)
branch: master

Merge pull request #22 from ewels/master

Added new package - Trim Galore! (trimmer wrapper based on Cutadapt)
latest commit 3d7e4aa2ea
@Galithil Galithil authored
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AlienTrimmer Added AlienTrimmer adapter trimmer, removed ant (use UPPMAX copy)
CRISP Add support for CRISP - software for analysing pooled samples
GATK set (some) modules to unset path/env changes on module removal
MuTect set (some) modules to unset path/env changes on module removal
OLB Added Illumina Offline Base Caller
RNASeQC Fixed RNASeQC module loader
VarScan Updated VarScan module loader to use generic $version
bamtools set (some) modules to unset path/env changes on module removal
bcbio.variation Added bcbio.variation/0.1.0
bcftools Added bcftools v0.2.0-rc6, upgraded samtools 0.1.19 -> 0.2.0-rc6
bgzip Added bgzip (from tabix)
bismark Added bismark v0.12.2
bowtie2 Updated bowtie to latest version
clc-adapter-trim Change to clc-adapter-trim module file
clojure Adding leiningen scripts
cmake Add modules needed for new pipeline features
cutadapt Adding cutadapt v1.3, trimmomatic v0.30
deactivated/ant Added AlienTrimmer adapter trimmer, removed ant (use UPPMAX copy)
drmaa Add modules needed for new pipeline features
fastqc Updated fastqc module loader to handle PATH correctly
fastqscreen Added fastq_screen 0.4.1, current fastq_screen.conf
fastx_toolkit Updated fastx_toolkit module loader to use generic $version
grabix Added grabix/0.1.2
htseq set (some) modules to unset path/env changes on module removal
igvtools Add igvtools 2.1.7 and snpEff 2.1b
lein Adding leiningen scripts
maven Maven and ant are not available @UPPMAX, but java is installed in the…
mosaik-aligner Adding modulefile for MOSAIK 2.1.33
ngsrich Add ngsrich 0.7.7 and ucsc_tools v 4
picard Updated picard module loaders to use generic $version
samtools Remove samtools v0.2.0-rc6 (buggy)
seqtk Added seqtk
snpEff Add snpEff v3.5d
subread Added subread v1.4.3 (for featureCounts tool)
tabix set (some) modules to unset path/env changes on module removal
tophat set (some) modules to unset path/env changes on module removal
trim_galore Added new package - Trim Galore! (trimmer wrapper based on Cutadapt)
trimmomatic Adding cutadapt v1.3, trimmomatic v0.30
ucsc_tools Add igvtools 2.1.7 and snpEff 2.1b
vcflib Added vcflib module loader (unsure of version -- github clone)
vcftools Added vcftools v0.1.11
README.md Modified README.md for clarity.

README.md

This is just a placeholder for software "packaged" using the ancient and horribly deprecated module system:

http://modules.sf.net

The modules shown here are tailored for our specific environment and no support will be offered.

*** Use it at your own risk ***

You might want to adjust your MODULEPATH environment variable to load those custom/experimental modules, e.g.:

export MODULEPATH=$MODULEPATH:/bubo/home/h5/roman/opt/modules

http://www.pdc.kth.se/resources/software/userenvironment/modules http://www.uppmax.uu.se/faq/software

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