available_software
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Software that are not part of the Linux distribution are installed to /opt/perun on the compute nodes. /opt/perun/bin is already included in the PATH. Some software not included in the PATH like Trinity are available for use at /opt/perun.
Commercial Software
| Software List | Installed Version |
|---|---|
| Nag SMP Libraries (Example Usage) | Mark 23 |
| Splus | 8.1.1 |
| Matlab | 2015a |
| Maple | 18 |
Open Source and free for academic use Software (not part of Linux distribution)
| Software List | Installed Version |
|---|---|
| Abyss | 1.5.0 |
| Allpathslg | 49807 |
| Amos | 3.1.0 |
| Analysis | 0.8.3 |
| Annot8r | 1.1.16 |
| Aragorn | 1.2.36 |
| Artemis | 12.0.0 |
| Augustus | 3.0.2 |
| AutoFACT | 3.4 |
| Bali-Phy | 2.3.1 |
| Bamtools | 2.3.0 |
| BBMap | v34.64 |
| Beagle Library | 1.0 |
| BEAST | 1.8.1 |
| BioJava | 3.0.5 |
| BMGE | 1.1 |
| Bowtie2 | 2.2.4 |
| Bridger | r2014-12-01 |
| Busco | 1.1 |
| BWA | 0.7.10-r960 |
| Cd-hit | 4.6.1 |
| Cegma | 2.5 |
| Censor | 4.2.28 |
| Cgal | 0.9.6 |
| Chlorop | 1.1 |
| Coevol | 1.3c |
| Concaterpillar | 1.4 |
| Core-PA | 0.5.1 |
| Crux | 1.2.0 |
| DeconSeq | 0.4.3 |
| Dendroscope | 3.2.5 |
| Detonate | 1.8.1 |
| Ea-Utils | 1.1.2-537 |
| EBARDenovo | 2.0.1-20150115 |
| EMIRGE | Jun-2015-git |
| EXpress | 1.5.1 |
| Fasta | 36.3.6f |
| Fastq-tools | 0.7 |
| FastQC | 0.11.2 |
| Fastx_Toolkit | 0.0.14 |
| FFPred2 | 2.0 |
| Gblocks | 0.91b |
| GEM Library | 1.423 |
| Genometools | 1.5.3 |
| GFF-EX | v2.3 |
| Ghostz | 1.0.0 |
| Gmap | 2014-12-17 |
| Hmmer | 3.1b2 |
| IDEA | 2.5.1 |
| Igraph | 0.6.5 |
| Infernal | 1.1.1 |
| Interproscan | 5.7-48.0 |
| IQ-Tree | 1.3.11 |
| JellyFish | 2.1.4 |
| Jemalloc | 3.4.1 |
| Jmodeltest2 | 2.1.5 |
| Kobas2 | 20120208 |
| KmerGenie | 1.6741 |
| Lambda | 0.4.7 |
| Libgtextutils | 0.6.1 |
| LibSequence | 1.7.6 |
| M3l | m3l |
| Mafft | 7.205 |
| MANTiS | 1.1 |
| Mesquite | 2.75 |
| MetaPIGA | 3.1 |
| Migrate | 3.6.8 |
| Mira Assembler | 4.0.2 |
| Mitoprot | 1.101 |
| MultiLoc2 | 26-10-2009 |
| NAMD | 2.10b1 |
| NCBI Blast | 2.3.0+ |
| NCBI Genome Workbench | 2.9.0 |
| NCL | 2.1.18 |
| Newbler | 2.9 |
| Notung | 2.6 |
| Orthofinder | 0.2.8 |
| OrthoMCL | Version 5 |
| PAGIT | 1.64 |
| Paml | 4.8 |
| Parallel | 20130722 |
| Parat | 0.91 |
| PASA2 | 2.0.2 |
| Pasta | Jan 2016 git |
| Phobius | 1.01 |
| PhyloBayes | 1.5a |
| Pear | v0.9.8 |
| Pebble | 1.0 |
| Piler | 1.0 |
| Platanus | 1.2.1 |
| Phylobayes Non MPI | 4.1 |
| Prodigal | 1.20 |
| ProfDist | 0.9.8 |
| Prokka | 1.5.2 |
| ProtoBuf | 2.5.0 |
| PSORTb | 3.0 |
| PyMPI | 2.5.0 |
| Pysam | 0.7.5 |
| Qualimap | 2.1.1 |
| R | 3.2.1 (>6000 contributed packages) |
| RAxML | 8.1.22 |
| Ray | 2.3.1 |
| Reaper | 1.0.17 |
| Recon | 1.08 |
| RepeatMasker | 4.0.5 |
| RepeatModeler | 1.0.8 |
| RepeatScout | 1.0.5 |
| REPET | 2.2 |
| RNAmmer | 1.2 |
| Rsem | 1.2.18 |
| Rstudio | v0.98.1087 |
| Ruffus | 2.2 |
| SEED | Jun 2015 git version |
| Semphy | 2.0-b3 |
| Seq-gen | 1.3.3
|
| Seqtk | 1.0-r72 |
| SGA | 0.10.13 |
| SignalP | 4.0 |
| Soapdenovotrans | 1.0.3 |
| Sparsehash | 2.0.2 |
| Splitstree4 | 4.13.1 |
| Sra Toolkit | 2.3.2 |
| SSpace | 2.0 |
| Staden | 2.0.0b10 |
| Stampy | 1.0.23 |
| Tandem | 2013.02.01.1 |
| TargetP | 1.1 |
| Tbl2asn | 21.9 |
| Tmhmm | 2.0c |
| Topali | 2.5 |
| Tophat | 2.0.13 |
| Tracer | 1.5 |
| Transdecoder | 2.0.1 |
| Transrate | 1.0.0 beta2 |
| Treefinder | March 2011 Version |
| Trimmomatic | 0.32 |
| TrinityRNASeq | 2.0.2 |
| tRNAscan-SE | 1.3.1 |
| Usearch | v8.0.1517 |
| Velvet | 1.2.10 |
| Waffles | 05-07-2014 version |
| WGS assembler | 8.1 |
| Wolfpsort | 0.2 |
Please see /opt/perun/bin and /opt/perun on compute nodes for the full list of available software. Extra python packages are installed to
/opt/perun/python_packages/lib/python2.7/site-packages. It is already included in python path.
available_software.1456332747.txt.gz · Last modified: by pillai