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University of Hawaii System

Installed Software

Installed Software on the HPC

Software already installed on the HPC includes Compilers, packages for PythonR, and Perl, and software tools specifically for Big DataVisualizationImageryGeosciencesGeospatial work, Chemistry, and Bioinformatics.

COMPILERS

  • Intel C, Fortran and MPI compilers
  • GNU Compilers

PYTHON 2.6.6, 2.7.8, 2.7.10, 2.7.11, 2.7.12, 3.4.3, 3.5.1

  • biopython
  • dendropy
  • erange
  • ipython
  • matplotlib
  • mip4py
  • nose
  • numpy
  • ocrpy
  • pyCUDA
  • scipy
  • sympy
  • virtualenv and virtualenv-wrappers for user encapsulated environments and individual package installs
  • Python 2.7 / Anaconda 4.4.0
  • Python 3.6 / Anaconda 4.4.0

R 3.1.2, 3.2.2, 3.3.2

  • RStudio – available via interactive session
  • R packages can be installed from R CLI into user directory

PERL 5.22.1, 6

  • BioPerl
  • BioPhylo
  • Rakudo Star Perl 6 Compiler and modules

MORE LANGUAGES

  • Julia 0.5.2, 0.6.1
  • Scala 2.12.4

BIG DATA

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

VISUALIZATION

  • Blender 2.74
  • Graphviz 2.38.0
  • ImageMagick 6.9.3-7
  • ParaView 5.3.0
  • Visit 2.9.0
  • Xfig 3.2.7a

IMAGE CREATION AND MANAGEMENT

  • GeoTIFF 1.4.2
  • GIFLIB 5.1.4
  • LibGD 2.1.1
  • libjpeg 9b

LIBRARIES

  • GSL 1.16 – GNU Scientific Library
  • HDF5 1.8.15
  • FFTW 3.3.6
  • LevelDB
  • NetCDF 4.x.x

CHEMISTRY

  • Gromacs 4.6.7
  • GAMESS
  • Gaussian 09

GEOLOGY, GEOPHYSICS, GEOSCIENCES

  • BeoPEST 13.6
  • gsflow 1.2.1
  • modflow 1.11.00
  • sutra 2.2
  • MARE2DEM 20180305 and earlier
  • ModEM
  • OCCAM1DCSEM 3.16
  • seiunix 44R2
  • GrADS 2.1.1.b0

GEOSPATIAL

  • GDAL 2.1.1
  • GEOS 3.6.1
  • GRASS 7.2.0
  • PROJ.4/4.9.2

BIOINFORMATICS PACKAGES

  • AmpliconNoise 1.29
  • augustus 3.2.1
  • bamtools 2.4.0
  • BayeScan 2.1
  • BCFTools 1.2
  • bcl2fastq 2.20.0.422
  • BEAST 1.8.1, 2.1.0, 2.3.1, 2.4.3
  • BLAT 35
  • Bowtie 1.0.0, 1.1.2
  • Bowtie2 2.2.4
  • BWA 0.7.12, 0.7.15
  • CDBFasta 20100722
  • CD-Hit 4.5.4
  • ClearCut 1.0.9
  • Cufflinks 2.2.1
  • Cytoscape 3.2.1
  • EA-Utils 20140925
  • exonerate 2.2.0
  • EMBOSS 6.6.0
  • express 1.5.1
  • FALCON 0.3.0
  • faSplit
  • fastQC 0.11.4
  • fastx-toolkit 0.0.14
  • GARLI2.0.1
  • Gene-Torrent
  • HMMR 3.1b2
  • HTSlib 1.2.1
  • Infernal 1.0.2, 1.1.1, 1.1.2
  • ITSx 1.0.11
  • Jellyfish 2.2.3
  • kallisto 0.42.4
  • MACS 1.4.2
  • MACSE 1.01b
  • MAFFT 7.22, 7.245
  • MAKER 2.31.8, 3.00.0-beta
  • mcl 14-137
  • MetaGeneAnnotator (MGA)
  • Metaxa2 2.1.1
  • MircobiomeUtils 20110519
  • Mothur 1.25.0, 1.34.4, 1.36.1, 1.38.1, 1.39.3
  • MrBayes 3.2.2, 3.2.3, 3.2.5
  • MUSCLE 3.8.31
  • PEAR 0.9.8
  • PLINK 1.9b
  • QIIME 1.9.1 with dependencies
  • RAxML
  • Roche 454 – Data Analysis 2.9
  • RSEM 1.2.25
  • RTAX 0.984
  • repeatmasker 4.0.6
  • Samtools 1.1, 1.2, 1.4.1
  • SeqPrep 20150522
  • SeqTK 1.0-r82-dirty
  • slclust 20100202
  • Snap 2013_11_29 (KorfLab)
  • SortMeRNA 2.0, 20150831
  • SPAdes 3.12.0, 3.5.0, 3.6.2
  • STAR 2.4.2a, 2.5.4b
  • Subread 1.4.6
  • SumaClust 1.0.10
  • SWARM 2.1.12, 2.1.5
  • Tophat 2.0.13
  • trf 407b
  • trimmomatic 0.33.0
  • Trinity 2.1.1, 2.4.0
  • Uclust 1.2.22q
  • Usearch 32bit 5.2.236, 6.1.544-beta, 8.0.1623
  • Vsearch 1.4.0, 1.9.10, 2.4.0, 2.7.1
  • 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, 3.0.66
    • STACKs 1.35, 1.46
  • NCBI
    • BLAST+ 2.2.28, 2.2.30, 2.6.0 (databases on cluster: nr, nt, reseq_genomic, refseq_rna,reseq_protein, uniprot_sprot, uniprot_trembl) check last download
    • BLAST Legacy 2.2.22, 2.2.26 – no database included with these
    • SRA_toolkit 2.8.2-1