HPCBIOS_2012-94: Bioinformatics & Comp. Biology Productivity EnvironmentΒΆ

Note

Bioinformatics & Computational Biology productivity environment includes a set of HPC tools which are needed for scientific computing and visualization in the respective domain. The following is an attempt to define which ones are relevant for the HPCBIOS communities and set an action plan.

  • BC Policy: HPCBIOS_2012-94
  • Date of Policy: 2013-12-22

The main objective of this policy is to provide the following common productivity environment across any HPCBIOS resources:

Name Prefered version(s) Compliance level Reference URL
Python v2.7.3 MUST http://www.python.org/
Biopython 1.61 MUST http://biopython.org
scipy 0.10.1 MUST http://www.scipy.org
numpy 1.6.1 MUST http://numpy.scipy.org
Cython 0.16 MUST http://pypi.python.org/pypi/Cython/
R language v2.14.2 or v2.15.x MUST http://www.r-project.org
Bioconductor v2.10 SHOULD http://www.bioconductor.org
Perl v5.16.3 MUST http://www.perl.org/
BioPerl 1.6.1 MUST http://www.bioperl.org/
NCBI-Toolkit 9.0.0 MUST http://www.ncbi.nlm.nih.gov/toolkit
BLAST+ v2.2.26 or later MUST http://blast.ncbi.nlm.nih.gov/
mpiBLAST v1.6.0 MUST http://www.mpiblast.org/
HMMER v3 MUST http://hmmer.janelia.org/
MrBayes v3.1.2 MUST http://mrbayes.sourceforge.net
AMOS 3.1.0 MUST http://sourceforge.net/apps/mediawiki/amos
Boost 1.49 or later MUST http://www.boost.org
Bowtie2 2.0.2 MUST http://bowtie-bio.sourceforge.net/bowtie2
BWA 0.6.2 MUST http://bio-bwa.sourceforge.net
ClustalW2 2.1 MUST http://www.ebi.ac.uk/Tools/msa/clustalw2
Cufflinks 2.0.2 MUST http://cufflinks.cbcb.umd.edu
Eigen 3.1.1 MUST http://eigen.tuxfamily.org/index.php?title=Main_Page
FASTX-Toolkit 0.0.13.2 MUST http://hannonlab.cshl.edu/fastx_toolkit
libgtextutils 0.6.1 MUST http://hannonlab.cshl.edu/fastx_toolkit
Infernal 1.1 MUST http://infernal.janelia.org
MUMmer 3.23 MUST http://mummer.sourceforge.net
MetaVelvet 1.2.01 MUST http://metavelvet.dna.bio.keio.ac.jp
RNAz 2.1 MUST http://www.tbi.univie.ac.at/~wash/RNAz
SOAPdenovo 1.05 MUST http://soap.genomics.org.cn/index.html
SAMtools 0.1.18 MUST http://samtools.sourceforge.net
TopHat 2.0.4 MUST http://tophat.cbcb.umd.edu
ViennaRNA 2.0.7 MUST http://www.tbi.univie.ac.at/~ronny/RNA/vrna2.html
Velvet 1.2.07 MUST http://www.ebi.ac.uk/~zerbino/velvet
BFAST 0.7.0a MUST http://bfast.sourceforge.net/
MCL 12.135 MUST http://micans.org/mcl/
MEME 4.8.0 MUST http://meme.nbcr.net/
HH-suite 2.0.16 MUST ftp://toolkit.lmb.uni-muenchen.de/HH-suite/
BLAT 3.5 MUST http://genome.ucsc.edu/FAQ/FAQblat.html
MUSCLE 3.8.31 MUST http://www.drive5.com/muscle/
EMBOSS 6.5.7 MUST http://emboss.sourceforge.net/
GATK 2.6-5 or later MUST http://www.broadinstitute.org/gatk/
PLINK 1.07 MUST http://pngu.mgh.harvard.edu/purcell/plink/
CD-HIT 4.5.5 MUST http://weizhong-lab.ucsd.edu/cd-hit/
RAxML 7.7.5 or later MUST https://github.com/stamatak/standard-RAxML
Oases 0.2.08 MUST http://www.ebi.ac.uk/~zerbino/oases
Glimmer 3.0.2 MUST http://ccb.jhu.edu/software/glimmer
PANDAseq 2.5 MUST https://github.com/neufeld/pandaseq
ABySS 1.3.4 MUST http://www.bcgsc.ca/platform/bioinfo/software/abyss
ALLPATHS-LG 46968 MUST http://www.broadinstitute.org/software/allpaths-lg/blog/
ARB 5.5 MUST http://www.arb-home.de/
bam2fastq 1.1.0 MUST http://www.hudsonalpha.org/gsl/information/software/
BamTools 2.2.3 MUST https://github.com/pezmaster31/bamtools
BEDTools 2.17.0 MUST http://code.google.com/p/bedtools/
BiSearch 20051222 MUST http://bisearch.enzim.hu/
Bowtie 1.1.0 MUST http://bowtie-bio.sourceforge.net/index.shtml
CAP3 20071221 MUST http://seq.cs.iastate.edu/
cutadapt 1.3 MUST http://code.google.com/p/cutadapt/
FASTA 36.3.5e MUST http://fasta.bioch.virginia.edu
fastahack 20110215 MUST https://github.com/ekg/fastahack
FoldX 2.5.2 MUST http://http://foldx.crg.es/
FRC_align 20130521 MUST https://github.com/vezzi/FRC_align
FreeSurfer 2.5 MUST http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferWiki
FSL 4.1.9 MUST http://www.fmrib.ox.ac.uk/fsl/
GLIMMER 3.02b MUST http://www.cbcb.umd.edu/software/glimmer/
Mothur 1.30.2 MUST http://www.mothur.org/
orthomcl 2.0.8 MUST http://orthomcl.org/
PAML 4.7 MUST http://abacus.gene.ucl.ac.uk/software/paml.html
PASHA 1.0.3 MUST http://pasha.sourceforge.net/
Picard 1.100 MUST http://picard.sourceforge.net/
Primer3 2.3.0 MUST http://primer3.sourceforge.net
RNAz 2.1 MUST http://www.tbi.univie.ac.at/~wash/RNAz
SHRiMP 2.2.3 MUST http://compbio.cs.toronto.edu/shrimp/
Stacks 1.03 MUST http://creskolab.uoregon.edu/stacks/
Stride 1.0 MUST http://structure.usc.edu/stride/
SURF 1.0 MUST http://www.ks.uiuc.edu/Research/vmd/vmd-1.7/ug/node65.html
Trinity 2013-02-25 MUST http://trinityrnaseq.sourceforge.net/

Future potential candidates for this policy:

T-Coffee latest SHOULD http://www.tcoffee.org/
GPU-BLAST latest SHOULD http://eudoxus.cheme.cmu.edu/gpublast/gpublast.html
CUDA-BLASTP latest SHOULD https://sites.google.com/site/liuweiguohome/software
mpiCUDA-BLASTP latest SHOULD https://sites.google.com/site/liuweiguohome/mpicuda-blastp
mr-mpi-blast latest SHOULD https://github.com/andreyto/mr-mpi-blast
Ruby v1.9.3-p194 or later SHOULD http://www.python.org/
BioRuby latest SHOULD http://bioruby.org
IDBA-UD 1.0.9 SHOULD http://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud
PolyPhen-2 2.2.2r405 SHOULD http://genetics.bwh.harvard.edu/pph2/dokuwiki/start
SSAHA 31c SHOULD http://www.sanger.ac.uk/resources/software/ssaha/
RepeatMasker latest SHOULD http://www.repeatmasker.org/
ABC-SysBio latest SHOULD http://sourceforge.net/projects/abc-sysbio/
Annovar latest SHOULD http://www.openbioinformatics.org/annovar/
PEMer latest SHOULD http://sv.gersteinlab.org/pemer/
deFuse latest SHOULD http://defuse.sf.net/
TopHat-Fusion latest SHOULD http://tophat.cbcb.umd.edu/fusion_index.html
BreakDancer latest SHOULD http://breakdancer.sourceforge.net/
PANTHER latest SHOULD http://www.pantherdb.org/tools/
HHPRED latest SHOULD http://toolkit.lmb.uni-muenchen.de/hhpred
pysam latest SHOULD http://code.google.com/p/pysam/
ReadSeq latest SHOULD http://iubio.bio.indiana.edu/soft/molbio/readseq/java/
Phrap latest SHOULD http://www.phrap.org/phredphrapconsed.html
Phred latest SHOULD http://www.phrap.org/phredphrapconsed.html
Consed latest SHOULD http://www.phrap.org/consed/consed.html
nesoni latest SHOULD http://bioinformatics.net.au/software.nesoni.shtml
PhyML latest SHOULD http://www.atgc-montpellier.fr/phyml/
galaxy >ca0c4ad2bb39 SHOULD http://galaxy.psu.edu/
swarm latest SHOULD http://biowulf.nih.gov/apps/swarm.html /download/swarm.tar
WU-BLAST latest SHOULD http://blast.wustl.edu/
Clustal latest SHOULD http://www.clustal.org/
PAUP latest SHOULD http://paup.csit.fsu.edu/
PHYLIP latest SHOULD http://evolution.genetics.washington.edu/phylip.html
PyMOL latest SHOULD http://pymol.sf.net/
FastQC 0.10.0 SHOULD http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
QuEST 2.4 SHOULD http://mendel.stanford.edu/sidowlab/downloads/quest/
HOMER 4.2 SHOULD http://homer.salk.edu/homer/

This productivity environment will be supplemented with other related productivity tools as they become available on allocated systems.

Potential sources of information for further future upgrades of this list include:

Kindly notify -if this policy is inadequate for your work- both your local site technical representative & HPCBIOS user-support.

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