.. _HPCBIOS_2012-94: HPCBIOS_2012-94: Bioinformatics & Comp. Biology Productivity Environment ================================================================================ .. 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 v3.2.x or later | SHOULD | 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/ | +----------------------------------------+-----------------------------+--------------------+------------------------------------------------------------+ | **IDBA-UD** | 1.1.1 | SHOULD | http://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud | +----------------------------------------+-----------------------------+--------------------+------------------------------------------------------------+ | **Ruby** | v1.9.3-p194 or later | SHOULD | http://www.python.org/ | +----------------------------------------+-----------------------------+--------------------+------------------------------------------------------------+ | **HOMER** | 4.2 | SHOULD | http://homer.salk.edu/homer/ | +----------------------------------------+-----------------------------+--------------------+------------------------------------------------------------+ | **PhyML** | latest | SHOULD | http://www.atgc-montpellier.fr/phyml/ | +----------------------------------------+-----------------------------+--------------------+------------------------------------------------------------+ | **Clustal** | latest | SHOULD | http://www.clustal.org/ | +----------------------------------------+-----------------------------+--------------------+------------------------------------------------------------+ | **PyMOL** | latest | SHOULD | http://pymol.sf.net/ | +----------------------------------------+-----------------------------+--------------------+------------------------------------------------------------+ | **FastQC** | 0.10.0 | SHOULD | http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ | +----------------------------------------+-----------------------------+--------------------+------------------------------------------------------------+ ---- 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 | +----------------------------------------+-----------------------------+--------------------+------------------------------------------------------------+ | BioRuby | latest | SHOULD | http://bioruby.org | +----------------------------------------+-----------------------------+--------------------+------------------------------------------------------------+ | 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 | +----------------------------------------+-----------------------------+--------------------+------------------------------------------------------------+ | 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/ | +----------------------------------------+-----------------------------+--------------------+------------------------------------------------------------+ | PAUP | latest | SHOULD | http://paup.csit.fsu.edu/ | +----------------------------------------+-----------------------------+--------------------+------------------------------------------------------------+ | PHYLIP | latest | SHOULD | http://evolution.genetics.washington.edu/phylip.html | +----------------------------------------+-----------------------------+--------------------+------------------------------------------------------------+ | QuEST | 2.4 | SHOULD | http://mendel.stanford.edu/sidowlab/downloads/quest/ | +----------------------------------------+-----------------------------+--------------------+------------------------------------------------------------+ 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: * http://www.vital-it.ch/software/tools.php * http://wiki.hpc.ufl.edu/doc/Category:Bioinformatics * http://www.csc.fi/english/research/sciences/bioscience/programs/index_html * http://bacpathgenomics.wordpress.com/software/ * http://umbc.rnet.missouri.edu/general/software/alphabetical.html * http://www.broadinstitute.org/software/bsi-sig/ * http://ncgas.org/software, genome assembly, assembly, genomics * http://confluence.rcs.griffith.edu.au:8080/display/GHPC/qiime#qiime-Alignment%2Ctreebuilding%2Ctaxonomyassignment%2COTUpicking%2Candotherdatagenerationsteps%28requiredforalternativepipelines%29 * http://www.bioplexity.org/lectures/ebi-s10.pdf * http://helix.nih.gov/Applications/ * http://openwetware.org/wiki/Image:Tools.png * http://en.wikipedia.org/wiki/List_of_sequence_alignment_software * http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies * http://www.eaglegenomics.com/2012/04/the-elements-of-bioinformatics/ * http://nebc.nerc.ac.uk/tools/bio-linux-5/package-list Kindly notify -if this policy is inadequate for your work- both your local site technical representative & HPCBIOS maintainers.