Installed Software on the HPC

Compilers

  • Intel C, Fortran and MPI compilers
  • GNU Compilers
  • Cray Compilers
  • PGI Compilers

R 3.1.2, 3.2.2

  • Rstudio – available via interactive session
  • RPackages can be installed from R CLI into user directory

Perl

  • BioPerl
  • BioPhylo

Big Data

  • Hadoop – in progress – testing
  • Spark 1.3.0 built for Hadoop1x and Hadoop2.4 also a Docker version in progress 

Bioinformatics Packages

  • MrBayes3.2.3
  • GARLI2.0.1
  • RAxML
  • BEAST 1.8.1
  • BEAST 2.1.0
  • Samtools 1.1 & 1.2
  • BCFTools1.2
  • HTSlib1.2.1
  • Gene-torrent
  • Tophat 2.0.13
  • Bowtie2 2.2.4
  • Cufflinks-2.2.1
  • Trinity 2.0.4
  • Gene-Torrent 
  • Subread 1.4.6
  • Assemblers
    • Velvet Assembler – 2.0.4
    • MIRA Assembler – 4.02 and 4.9.3-beta
    • Celera Assembler – 8.3rc1
  • RADSeq software
    • PyRAD 3.0.61
    • Stacks 1.35
  • Mothur 1.34.4, 1.25.0
  • Qiime 1.9.1 with dependencies
  • MUSCLE 3.8.31
  • Infernal 1.0.2, 1.1.1
  • AmpliconNoise 1.29
  • CDBFasta 20100722
  • CD-Hit 4.5.4
  • Cytoscape 3.2.1
  • ClearCut 1.0.9
  • Uclust 1.2.22q
  • Usearch 32bit 5.2.236, 6.1.544-beta, 8.0.1623
  • Vsearch 1.4.0
  • EA-Utils 20140925
  • Jellyfish 2.2.3
  • BWA 0.7.12
  • SeqTK 1.0-r82-dirty
  • MircobiomeUtils 20110519
  • PEAR 0.9.8
  • Roche 454 – Data Analysis 2.9
  • RTAX 0.984
  • SeqPrep 20150522
  • SortMeRNA 2.0 20150831
  • SumaClust 1.0.10
  • SWARM 2.1.5
  • BLAT 35
  • MAFFT 7.22
  • BLAST 2.2.30+ (databases on cluster: nr, nt, reseq_genomic, refseq_rna,reseq_protein, uniprot_sprot, uniprot_trembl) last download 9/17/2015
  • BLAST Legacy 2.2.22, 2.2.26 – no database included with these

Python 2.6.6, 2.7.8, 2.7.10, 3.4.3

  • numpy
  • scipy
  • biopython
  • dendropy-3.12.0  2.6.6 & 2.7.8 only
  • ipython
  • matplotlib
  • sympy 
  • nose
  • virtualenv and virtualenv-wrappers for user encapsulated environments and individual package installs

Chemistry

  • Gromacs 

  • GAMESS

  • Gaussian 09

Visualization

  • Blender 2.74
  • Visit 2.9.0

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