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Software that are not part of the Linux distribution are installed to /opt/perun and '/scratch2/software on the compute nodes. /opt/perun/bin is already included in the PATH.
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.