Center for High Performance Computing (CHPC)

Available Software

Open source software packages will be installed as requested. Commercial packages require a discussion about licensing.

For select software packages (Freesurfer and FSL) we maintain local mailing lists. These can be useful for staying informed of software updates, or to discuss problems running the software on our cluster.

Software Package	Version	Location
AFNI	build 7/27/11	/export/AFNI_20110727
Amber	12	/export/amber12
ANNOVAR	-	/export/annovar
APBS	1.2.1b	/export/apbs-1.2.1b
ATSAS	2.5.1-1	/export/atsas-2.5.1-1
AutoDock Suite	4.2.3	/export/autodocksuite-4.2.3
Bamtools	2.3.0	/export/bamtools-2.3.0
BEDTools	2.17.0	/export/BEDTools-2.17.0
Bismark	0.12.2	/export/bismark_v0.12.2
BLASR	-	/export/blasr-20140811
BLAST	2.2.28	/export/ncbi-blast-2.2.28
Bowtie	1.0.1	/export/bowtie-1.0.1
Bowtie2	2.0.0-beta7	/export/bowtie2-2.0.0-beta7
BreakDancer	1.1	/export/breakdancer-1.1_2011_02_21/
BWA	0.5.9-r16	/export/bwa-0.5.9
Caret	5.62	/export/caret/release/caret
CoNIFER	0.2.2	/export/conifer-0.2.2
Critic2	1.0	/export/critic2-1.0
Cufflinks	2.2.1	/export/cufflinks-2.2.1
Desmond	2013-3	/export/schrodinger2013-3
DMAP	-	/export/DMAP_20141014
EMAN	1.9	/export/EMAN-1.9
EMAN2	2.07	/export/EMAN-2.07
EMBOSS	6.4.0	/export/emboss-6.4.0
Enthought Python Distribution	7.0.2	/export/epd-7.0.2
FreeSurfer	5.3	/export/freesurfer-5.3
FSL	5.0.2	/export/fsl-5.0.2
GATE	6.2	/export/gate-6.2
GATK	2.7-4	/export/GenomeAnalysisTK-2.7-4-g6f46d11
Gaussian	09	/export/g09
GeneTorrent	3.8.5a	/export/GeneTorrent-3.8.5a
Gromacs	4.5.3	/export/gromacs-4.5.3
HTSeq	0.6.1	/export/epd-7.0.2/bin/python
Hydra-sv	0.5.3	/export/Hydra-Version-0.5.3
IMPUTE2	2.3.2	/export/impute_v2.3.2
JAGS	3.3.0	/export/JAGS-3.3.0
Maq	0.7.1	/export/maq-0.7.1
MATLAB	R2013a	/export/matlab/R2013a
MEME	4.9.0	/export/meme-4.9.0
MHC_I	2.9.1	/export/mhc_i-2.9.1
MHC_II	2.5.1	/export/mhc_ii-2.5.1
MNE	2.7.3-3268	/export/MNE-2.7.3-3268
Mono	2.11.1	/export/mono-2.11.1
NAMD	2.9	/export/namd_2.9
NetChop	3.1	/export/netchop-3.1
Novoalign	3.02.05	/export/novocraftV3.02.05
Octave	3.6.3	/export/octave-3.6.3
Oases	0.2.8	/export/oases_0.2.8
OpenBabel	2.3.2	/export/openbabel-2.3.2
OpenEye	various	/export/openeye
OpenMEEG	2.1.0	/export/OpenMEEG-2.1.0
PHENIX	1.8.2	/export/phenix-1.8.2-1309/
Picard	1.67	/export/picard-tools-1.67
Pindel	0.2.4t	/export/pindel024t
pIRS	20120516	/export/pIRS_20120516
PLINK	1.90b3	/export/plink-1.90b3d
R	3.1.1	/export/R-3.1.1
Rosetta	3.5	/export/rosetta3.5_bundles
RSEG	0.4.4	/export/rseg-0.4.4
Samtools	0.1.18	/export/samtools-0.1.18
SeqPrep	2014041	/export/SeqPrep-2014041
SHAPEIT	2-r790	/export/shapeit-v2-r790
SIFT	1.03	/export/jcvi-sift-1.03
SMALT	0.7.6	/export/smalt-0.7.6
SNPTEST	2.5	/export/snptest-2.5
Solar Eclipse	7.4.4	/export/solar-eclipse-7.4.4
SPECFEM3D_GLOBE	5.1.5	/export/SPECFEM3D_GLOBE_V5.1.5
SPM	8	/export/spm8
SRA Toolkit	2.3.3-4	/export/sra_sdk-2.3.3-4
STAR	2.4.0b	/export/STAR_2.4.0b
Tabix	0.2.6	/export/tabix-0.2.6
Tinker	6.1.01	/export/tinker-6.1.01
Tophat	1.4.1.1	/export/tophat-1.4.1.1
Tophat2	2.0.6	/export/tophat-2.0.6
Trim Galore	0.3.7	/export/trim_galore-0.3.7
Trinity	2013-02-25	/export/trinityrnaseq_r2013-02-25
USEARCH	6.0.307	/export/usearch-6.0.307
VCFtools	0.1.10	/export/vcftools_0.1.10
Velvet	1.2.10	/export/velvet_1.2.10