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available_software [2016/01/19 10:39] – pillaiavailable_software [2026/03/19 10:46] (current) – pillai
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-Software that are not part of the Linux distribution are installed to ''<color darkred>/opt/perun</color>'' on the compute nodes. ''<color darkred>/opt/perun/bin</color>'' is already included in the ''<color darkred>PATH</color>''. Some software not included in the ''<color darkred>PATH</color>'' like ''<color red>Trinity</color>'' are available for use at ''<color darkred>/opt/perun</color>''.+Bulk of the software is installed via ''<color darkred>Conda</color>''. 
  
  
-**__<color blue>Commercial Software</color>__**  
  
-  +|  **List all env**  ||  ''<color darkred>conda env list</color>''  | 
 +|  **Use an env**  ||  ''<color darkred>source activate <env name></color>''  | 
 +|  **Show versions**  ||  ''<color darkred>conda list -n <env name></color>''  | 
 +|  **Exit an env**  ||  ''<color darkred>source deactivate</color>''  | 
 +|  **To use an old environment from previous setup**  ||  ''<color darkred>source activate /scratch2/software/anaconda/envs/<env name></color>''  |
  
-^  Software List      ^  Installed Version       ^  +**To enable old environments with priority to new environments when present**
-|**[[http://www.nag.com/doc/inun/fs23/l6adfl/un.html|Nag SMP Libraries]]        **  ([[Example Usage]])  |   ''**<color red>Mark 23</color>**''   |  +
-|**[[http://spotfire.tibco.com/|Splus]]**            |   ''**<color  red>8.1.1</color>**''     | +
-|**[[http://www.mathworks.com/products/matlab/|Matlab]]**    |   ''**<color red>2015a</color>**''     | +
-|**[[http://www.maplesoft.com/products/Maple/professional/|Maple]]**         |   ''**<color red>18</color>**''        | +
- +
  
-**__<color blue>Open Source and free for academic use Software  (not part of Linux distribution)</color>__**+**__<color blue>Add the following to your ~/.condarc</color>__**
  
-^  Software List      ^  Installed Version       ^ +<code bash>
-|**[[http://www.bcgsc.ca/platform/bioinfo/software/abyss/releases/1.5.0|Abyss]]**                                         |   ''**<color red>1.5.0</color>**''    | +
-|**[[http://www.broadinstitute.org/software/allpaths-lg/blog/|Allpathslg]]**                                     |   ''**<color red>49807</color>**''     | +
-|**[[http://sourceforge.net/projects/amos/files/amos/3.1.0/|Amos]]**                                            |   ''**<color red>3.1.0</color>**''     | +
-|**[[http://molpopgen.org/software/analysis/|Analysis]]**                                        |    ''**<color red>0.8.3</color>**''    |  +
-|**[[http://www.nematodes.org/bioinformatics/annot8r/|Annot8r]]**                                        |    ''**<color red>1.1.16</color>**''    | +
-|**[[http://mbio-serv2.mbioekol.lu.se/ARAGORN/|Aragorn]]**                                         |   ''**<color red>1.2.36</color>**''    |  +
-|**[[http://www.sanger.ac.uk/resources/software/artemis/|Artemis]]**                                         |   ''**<color red>12.0.0</color>**''    |  +
-|**[[http://bioinf.uni-greifswald.de/augustus/|Augustus]]**                                        |   ''**<color red>3.0.2</color>**''       | +
-|**[[http://www.bch.umontreal.ca/Software/AutoFACT.htm|AutoFACT]]**                                        |   ''**<color red>3.4</color>**''       | +
-|**[[http://faculty.biomath.ucla.edu/msuchard/bali-phy/|Bali-Phy]]**                                        |   ''**<color red>2.3.1</color>**''     | +
-|**[[https://github.com/pezmaster31/bamtools|Bamtools]]**                                        |   ''**<color red>2.3.0</color>**''     | +
-|**[[http://sourceforge.net/projects/bbmap/|BBMap]]**                                  |    ''**<color red>v34.64</color>**''     | +
-|**[[https://code.google.com/p/beagle-lib/|Beagle Library]]**                                  |    ''**<color red>1.0</color>**''     |          +
-|**[[http://beast.bio.ed.ac.uk/Main_Page|BEAST]]**                                             |    ''**<color red>1.8.1</color>**''   | +
-|**[[http://biojava.org/|BioJava]]**                                            |   ''**<color red>3.0.5</color>**''          | +
-|**[[https://wiki.gacrc.uga.edu/wiki/BMGE|BMGE]]**                                                       |    ''**<color red>1.1</color>**''  | +
-|**[[http://bowtie-bio.sourceforge.net/bowtie2/index.shtml|Bowtie2]]**                                        |    ''**<color red>2.2.4</color>**''  | +
-|**[[http://sourceforge.net/projects/rnaseqassembly/|Bridger]]**                                        |    ''**<color red>r2014-12-01</color>**''  | +
-|**[[http://busco.ezlab.org/|Busco]]**                                        |    ''**<color red>1.1</color>**''  | +
-|**[[http://sourceforge.net/projects/bio-bwa/|BWA]]**                                        |    ''**<color red>0.7.10-r960</color>**''  | +
-|**[[https://code.google.com/p/cdhit/|Cd-hit]]**                                               |     ''**<color red>4.6.1</color>**''    | +
-|**[[http://korflab.ucdavis.edu/datasets/cegma/#SCT3|Cegma]]**                                 |      ''**<color red>2.5</color>**''                                                                     | +
-|**[[http://www.girinst.org/downloads/software/censor/|Censor]]**                                   |      ''**<color red>4.2.28</color>**''              | +
-|**[[http://bio.math.berkeley.edu/cgal/|Cgal]]**       |    ''**<color red>0.9.6</color>**''      | +
-|**[[http://www.cbs.dtu.dk/services/ChloroP/|Chlorop]]**       |    ''**<color red>1.1</color>**''      |  +
-|**[[http://megasun.bch.umontreal.ca/People/lartillot/www/index.htm|Coevol]]**  |   ''**<color red>1.3c</color>**''   |    +
-|**[[http://rogerlab.biochemistryandmolecularbiology.dal.ca/Software/Software.htm#Concaterpillar|Concaterpillar]]**            |      ''**<color red>1.4</color>**''    | +
-|**[[http://pacosy.informatik.uni-leipzig.de/49-1-CoRe-PA.html|Core-PA]]**     |    ''**<color red>0.5.1</color>**''   | +
-|**[[http://www.canonware.com/Crux/|Crux]]**     |    ''**<color red>1.2.0</color>**''   | +
-|**[[http://deconseq.sourceforge.net/|DeconSeq]]**     |    ''**<color red>0.4.3</color>**''   | +
-|**[[http://ab.inf.uni-tuebingen.de/software/dendroscope/|Dendroscope]]**    |   ''**<color red>3.2.5</color>**''    | +
-|**[[http://deweylab.biostat.wisc.edu/detonate/|Detonate]]**    |   ''**<color red>1.8.1</color>**''    | +
-|**[[https://code.google.com/p/ea-utils/|Ea-Utils]]**        |    ''**<color red>1.1.2-537</color>**''  | +
-|**[[http://sourceforge.net/projects/ebardenovo/|EBARDenovo]]**        |    ''**<color red>2.0.1-20150115</color>**''  | +
-|**[[https://github.com/csmiller/EMIRGE|EMIRGE]]**        |    ''**<color red>Jun-2015-git</color>**''  | +
-|**[[http://bio.math.berkeley.edu/eXpress/|EXpress]]**        |    ''**<color red>1.5.1</color>**''  | +
-|**[[http://faculty.virginia.edu/wrpearson/fasta/|Fasta]]**        |    ''**<color red>36.3.6f</color>**''  | +
-|**[[http://homes.cs.washington.edu/~dcjones/fastq-tools/|Fastq-tools]]**  |   ''**<color red>0.7</color>**''  | +
-|**[[http://www.bioinformatics.babraham.ac.uk/projects/fastqc/|FastQC]]**      |   ''**<color red>0.11.2</color>**''     | +
-|**[[http://hannonlab.cshl.edu/fastx_toolkit/|Fastx_Toolkit]]**  |   ''**<color red>0.0.14</color>**''  | +
-|**[[http://bioinfadmin.cs.ucl.ac.uk/downloads/ffpred/|FFPred2]]**  |   ''**<color red>2.0</color>**''  | +
-|**[[http://molevol.cmima.csic.es/castresana/Gblocks.html|Gblocks]]**  |   ''**<color red>0.91b</color>**''  | +
-|**[[http://big.crg.cat/services/gem_genome_multi_tool_library|GEM Library]]**  |   ''**<color red>1.423 </color>**''  | +
-|**[[http://genometools.org/|Genometools]]**  |   ''**<color red>1.5.3</color>**''  | +
-|**[[http://bioinfo.icgeb.res.in/gff/gffdownloads/|GFF-EX]]**  |   ''**<color red>v2.3</color>**''  | +
-|**[[http://www.bi.cs.titech.ac.jp/ghostz/|Ghostz]]**  |   ''**<color red>1.0.0</color>**''  | +
-|**[[http://research-pub.gene.com/gmap/|Gmap]]**       |  ''**<color red>2014-12-17</color>**''     | +
-|**[[http://selab.janelia.org|Hmmer]]**       |  ''**<color red>3.1b2</color>**''     | +
-|**[[http://ideanalyses.sourceforge.net/main.html|IDEA]]**     |  ''**<color red>2.5.1</color>**''    | +
-|**[[http://igraph.sourceforge.net/|Igraph]]**  |   ''**<color red>0.6.5</color>**''   | +
-|**[[http://infernal.janelia.org/|Infernal]]**  |   ''**<color red>1.1.1</color>**''   | +
-|**[[http://www.ebi.ac.uk/Tools/pfa/iprscan/|Interproscan]]**  |   ''**<color red>5.7-48.0</color>**''   | +
-|**[[http://www.cibiv.at/software/iqtree/|IQ-Tree]]**  |   ''**<color red>1.3.11</color>**''   | +
-|**[[http://www.cbcb.umd.edu/software/jellyfish/|JellyFish]]**  |    ''**<color red>2.1.4</color>**''    | +
-|**[[http://www.canonware.com/jemalloc/download.html|Jemalloc]]**  |    ''**<color red>3.4.1</color>**''    | +
-|**[[https://code.google.com/p/jmodeltest2|Jmodeltest2]]**  |    ''**<color red>2.1.5</color>**''    | +
-|**[[http://kobas.cbi.pku.edu.cn/download.do|Kobas2]]**  |    ''**<color red>20120208</color>**''    | +
-|**[[http://kmergenie.bx.psu.edu/|KmerGenie]]**  |    ''**<color red>1.6741</color>**''    | +
-|**[[http://www.seqan.de/projects/lambda/|Lambda]]**  |    ''**<color red>0.4.7</color>**''    | +
-|**[[http://hannonlab.cshl.edu/fastx_toolkit/download.html|Libgtextutils]]**   |   ''**<color red>0.6.1</color>**''      |  +
-|**[[http://molpopgen.org/software/libsequence.html|LibSequence]]**  |   ''**<color red>1.7.6</color>**''   | +
-|**[[https://code.google.com/p/m3l/|M3l]]**   |   ''**<color red>m3l</color>**''   | +
-|**[[http://mafft.cbrc.jp/alignment/software/|Mafft]]**   |   ''**<color red>7.205</color>**''    | +
-|**[[http://www.mantisdb.org/|MANTiS]]**  |   ''**<color red>1.1</color>**''   | +
-|**[[http://mesquiteproject.org/mesquite/mesquite.html|Mesquite]]**  |   ''**<color red>2.75</color>**''   | +
-|**[[http://www.metapiga.org/|MetaPIGA]]**  |   ''**<color red>3.1</color>**''   | +
-|**[[http://popgen.sc.fsu.edu/Migrate/Download.html|Migrate]]**  |   ''**<color red>3.6.8</color>**''   | +
-|**[[http://mira-assembler.sourceforge.net/|Mira Assembler]]**  |   ''**<color red>4.0.2</color>**''   | +
-|**[[ftp://ftp.biologie.ens.fr/pub/molbio/|Mitoprot]]**  |   ''**<color red>1.101</color>**''   | +
-|**[[http://abi.inf.uni-tuebingen.de/Services/MultiLoc2/multiloc2_download|MultiLoc2]]**  |   ''**<color red>26-10-2009</color>**''   | +
-|**[[http://www.ks.uiuc.edu/Research/namd/|NAMD]]**  |   ''**<color red>2.10b1</color>**''    | +
-|**[[ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/|NCBI Blast]]**  |   ''**<color red>2.2.31+</color>**''    | +
-|**[[http://www.ncbi.nlm.nih.gov/tools/gbench/|NCBI Genome Workbench]]**  |   ''**<color red>2.9.0</color>**''    | +
-|**[[http://sourceforge.net/projects/ncl/|NCL]]**  |   ''**<color red>2.1.18</color>**''    | +
-|**[[http://wiki.genomequest.com/index.php/Newbler_Assembler|Newbler]]**  |    ''**<color red>2.9</color>**''    | +
-|**[[http://www.cs.cmu.edu/~durand/Notung/|Notung]]**   |    ''**<color red>2.6</color>**''      | +
-|**[[http://www.stevekellylab.com/software/orthofinder|Orthofinder]]**   |    ''**<color red>0.2.8</color>**''      | +
-|**[[http://www.orthomcl.org/cgi-bin/OrthoMclWeb.cgi|OrthoMCL]]**  |  ''**<color red>Version 5</color>**''   |  +
-|**[[http://www.sanger.ac.uk/resources/software/pagit/|PAGIT]]**  |   ''**<color red>1.64</color>**''   | +
-|**[[http://abacus.gene.ucl.ac.uk/software/paml.html|Paml]]**  |   ''**<color red>4.8</color>**''   | +
-|**[[http://www.gnu.org/software/parallel/|Parallel]]**  |   ''**<color red>20130722</color>**''   | +
-|**[[http://www.cibiv.at/software/parat/|Parat]]**  |   ''**<color red>0.91</color>**''   | +
-|**[[http://pasa.sourceforge.net/|PASA2]]**  |   ''**<color red>2.0.2</color>**''   | +
-|**[[https://github.com/smirarab/pasta|Pasta]]**  |   ''**<color red>Jan 2016 git</color>**''   | +
-|**[[http://phobius.sbc.su.se/data.html|Phobius]]**  |   ''**<color red>1.01</color>**''   | +
-|**[[http://megasun.bch.umontreal.ca/People/lartillot/www/downloadmpi.html|PhyloBayes]]**  |   ''**<color red>1.5a</color>**''   | +
-|**[[http://sco.h-its.org/exelixis/web/software/pear/doc.html|Pear]]**   |   ''**<color red>v0.9.8</color>**''    | +
-|**[[http://www.cebl.auckland.ac.nz/software2.php|Pebble]]**   |   ''**<color red>1.0</color>**''    | +
-|**[[http://www.drive5.com/piler/|Piler]]**   |    ''**<color red>1.0</color>**''      | +
-|**[[http://platanus.bio.titech.ac.jp/platanus-assembler/platanus-1-2-1/|Platanus]]**   |    ''**<color red>1.2.1</color>**''      | +
-|**[[http://megasun.bch.umontreal.ca/People/lartillot/www/index.htm|Phylobayes Non MPI]]**  |   ''**<color red>4.1</color>**''   | +
-|**[[http://www.biomedcentral.com/1471-2105/11/119|Prodigal]]**  |   ''**<color red>1.20</color>**''   | +
-|**[[http://profdist.bioapps.biozentrum.uni-wuerzburg.de/cgi-bin/index.php?section=installation|ProfDist]]**   |   ''**<color red>0.9.8</color>**''    | +
-|**[[http://www.vicbioinformatics.com/software.prokka.shtml|Prokka]]**  |   ''**<color red>1.5.2</color>**''     | +
-|**[[https://code.google.com/p/protobuf/|ProtoBuf]]**  |   ''**<color red>2.5.0</color>**''     | +
-|**[[http://www.psort.org/downloads/index.html|PSORTb]]**  |   ''**<color red>3.0</color>**''     | +
-|**[[http://pympi.sourceforge.net/|PyMPI]]**   |   ''**<color red>2.5.0</color>**''    | +
-|**[[https://code.google.com/p/pysam/|Pysam]]**   |   ''**<color red>0.7.5</color>**''    | +
-|**[[http://qualimap.bioinfo.cipf.es/doc_html/intro.html|Qualimap]]**   |   ''**<color red>2.1.1</color>**''    | +
-|**[[http://cran.r-project.org/|R]]**                |   ''**<color red>3.2.1 (>6000 contributed packages)</color>**''     | +
-|**[[https://github.com/stamatak/standard-RAxML|RAxML]]**  |  ''**<color red>8.1.22</color>**''   | +
-|**[[http://denovoassembler.sourceforge.net/download.html|Ray]]**   |   ''**<color red>2.3.1</color>**''    | +
-|**[[http://www.sanger.ac.uk/resources/software/reapr/​|Reaper]]**   |   ''**<color red>1.0.17</color>**''     | +
-|**[[http://selab.janelia.org/recon.html|Recon]]**   |   ''**<color red>1.08</color>**''     | +
-|**[[http://www.repeatmasker.org/|RepeatMasker]]**   |   ''**<color red>4.0.5</color>**''     | +
-|**[[http://www.repeatmasker.org/RepeatModeler.html|RepeatModeler]]**  |   ''**<color red>1.0.8</color>**''    | +
-|**[[http://bix.ucsd.edu/repeatscout/|RepeatScout]]**   |   ''**<color red>1.0.5</color>**''   | +
-|**[[http://urgi.versailles.inra.fr/Tools/REPET|REPET]]**   |   ''**<color red>2.2</color>**''   | +
-|**[[http://www.cbs.dtu.dk/cgi-bin/nph-runsafe?man=rnammer|RNAmmer]]**   |   ''**<color red>1.2</color>**''   | +
-|**[[http://deweylab.biostat.wisc.edu/rsem/|Rsem]]**  |   ''**<color red>1.2.18</color>**''  | +
-|**[[http://www.rstudio.com/|Rstudio]]**  |   ''**<color red>v0.98.1087 </color>**''  | +
-|**[[http://www.ruffus.org.uk/|Ruffus]]**  |   ''**<color red>2.2 </color>**''  | +
-|**[[https://github.com/baoe/SEED|SEED]]**  |   ''**<color red>Jun 2015 git version </color>**''  | +
-|**[[http://compbio.cs.huji.ac.il/semphy/|Semphy]]**  |   ''**<color red>2.0-b3</color>**''   | +
-|**[[http://tree.bio.ed.ac.uk/software/seqgen/|Seq-gen]]**  |   ''**<color red>1.3.3 +
-</color>**''   | +
-|**[[https://github.com/lh3/seqtk|Seqtk]]**  |   ''**<color red>1.0-r72</color>**''   | +
-|**[[https://github.com/jts/sga|SGA]]**  |   ''**<color red>0.10.13</color>**''   | +
-|**[[http://www.cbs.dtu.dk/services/SignalP/|SignalP]]**  |   ''**<color red>4.0</color>**''   | +
-|**[[http://sourceforge.net/projects/soapdenovotrans/|Soapdenovotrans]]**  |   ''**<color red>1.0.3</color>**''   | +
-|**[[https://code.google.com/p/sparsehash/|Sparsehash]]**  |   ''**<color red>2.0.2</color>**''    | +
-|**[[http://www.splitstree.org/|Splitstree4]]**  |   ''**<color red>4.13.1</color>**''    | +
-|**[[https://github.com/NCBITools/sratoolkit|Sra Toolkit]]**   |   ''**<color red>2.3.2</color>**''   | +
-|**[[http://www.baseclear.com/landingpages/basetools-a-wide-range-of-bioinformatics-solutions/sspacev12/|SSpace]]**  |   ''**<color red>2.0</color>**''    | +
-|**[[http://staden.sourceforge.net/|Staden]]**  |   ''**<color red>2.0.0b10</color>**''    | +
-|**[[http://www.well.ox.ac.uk/project-stampy|Stampy]]**  |   ''**<color red>1.0.23</color>**''    | +
-|**[[http://www.thegpm.org/TANDEM|Tandem]]**  |   ''**<color red>2013.02.01.1</color>**''    | +
-|**[[http://www.cbs.dtu.dk/services/TargetP/|TargetP]]**  |   ''**<color red>1.1</color>**''    | +
-|**[[http://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/|Tbl2asn]]**  |   ''**<color red>21.9</color>**''   | +
-|**[[http://www.cbs.dtu.dk/services/TMHMM/|Tmhmm]]**  |   ''**<color red>2.0c</color>**''   | +
-|**[[http://www.topali.org/|Topali]]**   |   ''**<color red>2.5</color>**''   | +
-|**[[http://tophat.cbcb.umd.edu/|Tophat]]**   |   ''**<color red>2.0.13</color>**''   | +
-|**[[http://tree.bio.ed.ac.uk/software/tracer/|Tracer]]**   |  ''**<color red>1.5</color>**''   | +
-|**[[http://transdecoder.sourceforge.net/|Transdecoder]]**   |  ''**<color red>2.0.1</color>**''   | +
-|**[[http://hibberdlab.com/transrate/|Transrate]]**  |   ''**<color red>1.0.0 beta2</color>**''   | +
-|**[[http://www.treefinder.de/|Treefinder]]**  |   ''**<color red>March 2011 Version</color>**''   | +
-|**[[http://www.usadellab.org/cms/index.php?page=trimmomatic|Trimmomatic]]**  |   ''**<color red>0.32</color>**''   | +
-|**[[http://trinityrnaseq.sourceforge.net/|TrinityRNASeq]]**  |   ''**<color red>2.0.2</color>**''   | +
-|**[[http://lowelab.ucsc.edu/tRNAscan-SE/|tRNAscan-SE]]**  |   ''**<color red>1.3.1</color>**''   | +
-|**[[http://www.drive5.com/usearch/download.html|Usearch]]**  |   ''**<color red>v8.0.1517</color>**''    | +
-|**[[http://www.ebi.ac.uk/~zerbino/velvet/|Velvet]]**  |   ''**<color red>1.2.10</color>**''    | +
-|**[[http://waffles.sourceforge.net/|Waffles]]**  |  ''**<color red>05-07-2014 version</color>**''   | +
-|**[[http://sourceforge.net/projects/wgs-assembler/files/wgs-assembler/wgs-8.1/|WGS assembler]]**  |  ''**<color red>8.1</color>**''   | +
-|**[[http://wolfpsort.org/WoLFPSORT_package/version0.2/|Wolfpsort]]**  |  ''**<color red>0.2</color>**''   |+
  
 +envs_dirs:
 +  - <personal conda env paths if they exist like ~/.conda/envs>
 +  - /scratch5/software/miniconda3/envs
 +  - /scratch2/software/anaconda/envs
  
  
-Please see ''<color darkred>/opt/perun/bin</color>'' and ''<color darkred>/opt/perun</color>'' on compute nodes  for the full list of available software. Extra python packages are installed to +</code> 
- ''<color darkred>/opt/perun/python_packages/lib/python2.7/site-packages</color>''. It is already included in python path. + 
- +[[conda-env|Existing environments]] 
available_software.1453214340.txt.gz · Last modified: by pillai