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NameCurrent VersionPrevious VersionsHow to LoadLink to Documentation

Notes

2020plus1.2.2-module load 2020plus/1.2.2https://github.com/KarchinLab/2020plus
Anaconda25.0.12.7, 4.0.0, 4.2.0, 4.4.0module load Anaconda2/5.0.1https://www.continuum.io/anaconda-overview
Anaconda35.0.14.0.0, 4.2.0, 4.4.0module load Anaconda3/5.0.1https://www.continuum.io/anaconda-overview
annovar1.0-module load annovar/1.0http://annovar.openbioinformatics.org/en/latest/Databases are located at /tools/app/annovar/humandb
bam-readcount0.8.0-module load bam-readcount/0.8.0https://github.com/genome/bam-readcount
bayesianDeNovoFilter0.1-module load bayesianDeNovoFilter/0.1

bbtools38.25-module load bbtools/38.25https://sourceforge.net/projects/bbmap/Contains all the tools in the bbtools suite.
bcftools1.91.2, 1.3, 1.3.1, 1.5, 1.8module load bcftools/1.9https://github.com/samtools/bcftools/releases/tag/1.9
bedops2.4.26-module load bedops/2.4.26https://bedops.readthedocs.io/en/latest/
bedtools2.26.02.25.0module load bedools/2.26.0https://github.com/arq5x/bedtools2
blast2.7.1-module load blast/2.7.1https://blast.ncbi.nlm.nih.gov/Blast.cgi
blat1.0-module load blat/1.0https://genome.ucsc.edu/cgi-bin/hgBlat
BWA0.7.16a-module load BWA/0.7.16ahttp://bio-bwa.sourceforge.net/
canvas1.34.0.12011.28.0.272, 1.30.0.725module load canvas/1.34.0.1201https://github.com/Illumina/canvas
Clustal-Omega1.2.0-foss-2016b-module load Clustal-Omega/1.2.0-foss-2016bhttp://www.clustal.org/omega/
clusterprod-module load cluster

This module is required to be able to submit jobs via LSF.

CNVkit0.9.4.dev0-module load Anaconda3/5.0.1https://github.com/etal/cnvkitRun cnvkit.py after loading Anaconda3/5.0.1
cromwell31.1-module load cromwell/31.1https://cromwell.readthedocs.io/en/stable/
Delly20.7.9-module load Anaconda2/5.0.1
Run delly after loading Anaconda2
expansionhunter2.5.5-module load ExpansionHunter/2.5.5

fastqc0.11.7-module load fastqc/0.11.7https://www.bioinformatics.babraham.ac.uk/projects/fastqc
fastx-toolkit0.0.13.2-module load fastx_toolkit/0.0.13.2http://hannonlab.cshl.edu/fastx_toolkit/
gatk4.0.4.0-module load gatk/4.0.4.0http://www.broadinstitute.org/gatk/
gvcfgenotyper1.0-module load gvcfgenotyper/1.0https://github.com/Illumina/gvcfgenotyper
gvcftools0.17-module load gvcftools/0.17https://github.com/sequencing/gvcftools
hapcompass0.7.7-module load hapcompass/0.7.7https://www.brown.edu/Research/Istrail_Lab/hapcompass.php
htslib1.91.1, 1.2.1, 1.3, 1.3.1, 1.5, 1.8module load htslib/1.9https://www.htslib.org/
impute22.3.2_x86_64_static2.3.0_x86_64_dynamic, 2.3.0_x86_64_static, v2.3.1, 2.3.2_x86_64_dynamicmodule load impute2/2.3.2_x86_64_statichttp://mathgen.stats.ox.ac.uk/impute/impute_v2.html
javajdk1.8.0_45-module load java/1.8.0_45http://java.com/
Java1.8.0_1441.8.0_65, 1.8.0_131module load Java/1.8.0_144http://java.com/
Jellyfish1.1.11-foss-2016b-module load Jellyfish/1.1.11-foss-2016bhttp://www.cbcb.umd.edu/software/jellyfish/
kallisto0.44.00.43.1module load Anaconda2/5.0.1http://pachterlab.github.io/kallisto/Kallisto 0.44.0 is available as a package under anaconda. This is why it is required to load the Anaconda2 module. There is a module for kallisto, this contains the older 0.43.1 version.
king2.1.41.9, 2.0module load kinghttp://people.virginia.edu/~wc9c/KING
knife0.1-module load knife/0.1https://github.com/lindaszabo/KNIFE/tree/master/circularRNApipeline_Standalone
kraken1.10.10.5-beta-foss-2016b-Perl-5.24.0module load kraken/1.1http://ccb.jhu.edu/software/kraken/
LiftOver1.0-module load LiftOver/1.0https://genome.ucsc.edu/cgi-bin/hgLiftOver
lumpy0.2.13v0.2.11module load lumpy/0.2.13https://github.com/arq5x/lumpy-sv
manta1.2.11.1.1module load manta/1.2.1https://github.com/Illumina/manta
maven3.3.93.2.3, 3.2.5, 3.3.3module load Maven/3.2.9https://maven.apache.org/
meRanTK1.1.1b-module load meRanTK/1.1.1bhttp://www.icbi.at/index.html
MetaGeneAnnotator20080819-x86-64-module load MetaGeneAnnotator/20080819-x86-64http://metagene.nig.ac.jp/
MetaSV0.5.2-module load python/2.7.12http://bioinform.github.io/metasv/To run the main script, load python 2.7.12, then run the run_metasy.py script
minimap22.0rc1-foss-2016b-module load minimap2/2.0rc1-foss-2016bhttps://github.com/lh3/minimap2
multiqc1.5-module load python/3.6.5http://multiqc.info/multiqc is a python package, so it is needed to load python before using it.
MUSCLE3.8.31-i86linux64-module load MUSCLE/3.8.31-i86linux64http://drive5.com/muscle/
NextGenMap0.5.5-foss-2016b-module load NextGenMaphttp://cibiv.github.io/NextGenMap/
OMA2.1.1-module load OMA/2.1.1https://omabrowser.org/standalone/
oncodrivefm1.0.3-module load python/3.6.5
oncodrivefm is a python package, so it is needed to load python before using it.
oncodrivefml2.0.3-module load python/3.6.5
oncodrivefml is a python package, so it is needed to load python before using it.
OpenBLAS0.2.20-GCC-6.4.0

0.2.9-GCC-4.8.3-LAPACK-3.5.0,

0.2.13-GCC-4.8.4-LAPACK-3.5.0,

0.2.13-gompi-1.5.16-LAPACK-3.5.0,

0.2.18-GCC-5.3.0-2.26-LAPACK-3.6.0,

0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1,

0.2.19-GCC-6.3.0-2.27-LAPACK-3.7.0

module load OpenBLAS/0.2.20-GCC-6.4.0http://xianyi.github.com/OpenBLAS/
opencgaresearch1.3.6-module load opencgaresearch/1.3.6https://github.com/opencb/opencga
OpenMPI3.0.0

1.6.5-GCC-4.8.2

1.6.5-GCC-4.8.3

1.7.3-GCC-4.8.2

1.8.1-GCC-4.8.3

1.8.4-GCC-4.8.4

1.10.2-GCC-5.3.0-2.26

1.10.3-GCC-5.4.0-2.26

2.0.2-GCC-6.3.0-2.27

module load OpenMPI/3.0.0http://www.open-mpi.org/
OrfM0.6.1-foss-2016b-module load OrfM/0.6.1-foss-2016bhttps://github.com/wwood/OrfM
perl5.24.1-GCCcore-6.3.0

5.22.1-foss-2016b, 5.24, 5.24.0-foss-2016b, 5.24.0-GCC-5.4.0-2.26, 5.24.0-GCCcore-5.4.0

module load perl/5.24.1-GCCcore-6.3.0https://www.perl.org/
phylip3.696-module load phylip/3.696http://evolution.genetics.washington.edu/phylip/install.html
picard2.18.91.124, 2.4.1, 2.9.0, 2.10.0, 2.12.1, 2.12.1-Java-1.8.0_144, 2.15.0module load picard/2.18.9https://broadinstitute.github.io/picard/
pindel0.2.5b9-module load pindel/0.2.5b9http://gmt.genome.wustl.edu/packages/pindel/index.html
Platypus0.8.1-module load Platypus/0.8.1https://github.com/andyrimmer/Platypus
PLINK1.9b_4.6-x86_641.07-x86_64, 1.90module load PLINK/1.9b_4.6-x86_64https://www.cog-genomics.org/plink/1.9/
PRIMUSv1.9.0-module load PRIMUS/v1.9.0https://primus.gs.washington.edu/primusweb/res/documentation.htmlrun PRIMUS with the run_primus.pl script.
python22.7.13-GCCcore-6.3.0-bare2.7.12, 2.7.12-withsqlitemodule load python/2.7.13-GCCcore-6.3.0-barehttps://www.python.org/
python33.6.5-module load python/3.6.5https://www.python.org/
R3.5.03.0.0, 3.3.0, 3.3.2, 3.3.3, 3.4.0module load R/3.5.0https://www.r-project.org/
remixt0.5.5-module load Anaconda2/4.0.0https://github.com/amcpherson/remixt
rtg-tools3.8.4-module load rtg-tools/3.8.4https://www.realtimegenomics.com/products/rtg-tools
ruby2.4.02.3.4module load ruby/2.4.0https://www.ruby-lang.org/en/
rvtests2.0.6-module load rvtests/2.0.6https://github.com/zhanxw/rvtests
salmon0.11.2-module load salmon/0.11.2https://combine-lab.github.io/salmon/
Sambamba0.6.6-module load Sambamba/0.6.6http://lomereiter.github.io/sambamba/
samblaster0.1.24v0.1.22module load samblaster/0.1.24https://github.com/GregoryFaust/samblaster
samtools1.91.1, 1.2, 1.3, 1.3.1, 1.5, 1.8module load samtools/1.9https://github.com/samtools/samtools/releases/tag/1.9
ScaLAPACK2.0.2-gompi-2016b-OpenBLAS-0.2.18-LAPACK-3.6.1-module load ScaLAPACK/2.0.2-gompi-2016b-OpenBLAS-0.2.18-LAPACK-3.6.http://www.netlib.org/scalapack/
STAR2.6.1a-module load STAR/2.6.1ahttps://github.com/alexdobin/STAR/blob/master/README.md
star-fusion1.4.0-module load star-fusion/1.4.0https://github.com/STAR-Fusion/STAR-Fusion/wiki
strelka2.9.9-module load strelka/2.9.9https://github.com/Illumina/strelka
STRScan1.0-module load STRScan/1.0https://omictools.com/strscan-tool
THetA0.7-module load THetA/0.7https://github.com/raphael-group/THetA
VarScan2.4.1-module load VarScanhttp://varscan.sourceforge.net/

Run with the following command:

java -jar $EBROOTVARSCAN/VarScan.v2.4.1.jar

vcftools0.1.15-module load vcftools/0.1.15https://vcftools.github.io/index.html
velvetv1.2.10-module load velvet/v1.2.10https://github.com/dzerbino/velvet
vep9289.4module load vep/92http://www.ensembl.org/info/docs/tools/vep/index.html
verifybamid1.0.1-module load verifybamid/1.0.1https://github.com/Griffan/VerifyBamID/releases
ViennaRNA2.3.4-foss-2016b-module load ViennaRNA/2.3.4-foss-2016bhttp://www.tbi.univie.ac.at/RNA/
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