Installed Software

Note: Cluster Software Upgrade

One of our goals is to provide our users with a consistent, stable, and current software environment. The compute, login, and interactive nodes within the HPC Center have been running CentOS EL 5 (with updates) for over four years. This is a long time in the open source software world. While our software was consistent and stable, it was no longer current. To remedy that shortcoming we upgraded all our systems to RedHat Enterprise Linux 6.3 (RHEL6). The migration was done without interruptions to user jobs as compute nodes were gradually migrated to RHEL6. The migration also afforded us an opportunity to remove software that was no longer used as we only installed software under RHEL6 on request. Therefore, if the software you need is no longer installed please open a support ticket requesting its installation as usual. If you run software you compiled it likely needs to be rebuilt. This is mandatory for all MPI software as we upgraded both MPI implementations and the Intel Compiler Suite on our systems. We also switched to the "Environment Modules" system for making software available. See the modules documentation for more information on how to use the modules system. If you attempt to run a program and it fails it means you have not loaded the appropriate module.

Installed Software List

Last updated 2012-12-19.

Note: Click on the icons to the right of the column headings to sort the table.

Name	Version	Website	Category
Abyss	1.3.3, 1.3.4, 1.3.4-mpi	[1]	Biology, NGS
ALLPATHS-LG	42316	[2]	Biology, NGS
Amber	11, 12(bugfix: 13(amber12) and 29(AmberTools)	[3]	Simulation, chemistry
Amuse	6.0	[4]	Astrophysics
Affymetrix Power Tools	1.15.0	[5]	Biology, Genomics, Microarray
Augustus	2.6	[6]	Biology, NGS
Bamtools	2.1.1	[7]	Biology, NGS
BamUtil	1.0.2	[8]	Biology, NGS
BayesRate	1.3.43	[9]	Biology, Phylogenetics
Bbcp	12.08.17.00.0	[10]	Network file transfer
BEAST	1.7.2	[11]	Biology, Phylogenetics
BEDTools	2.16.2	[12]	Biology, NGS
BFAST	0.7.0	[13]	Biology, NGS
Bismark	0.7.4, 0.7.7	[14]	Biology, Methylation, NGS
Bioconductor	Latest	[15]	Biology, R, Statistics
BioPerl	1.006901	[16]	Biology, Perl
BioPython	1.59	[17]	Biology, Python
NCBI BLAST	2.2.26 (+ and legacy)	[18]	Biology, Sequence alignment
Blast2go	2.5.0-20120705	[19]	Biology, Annotation
BLAT	20120524	[20]	Biology, Sequence alignment
Boost	1.49.0	[21]	C++, Library
Bwa	0.6.1	[22]	Biology, NGS
Bowtie	0.12.8, 2.0.0b6	[23]	Biology, NGS
CAP3	20120705	[24]	Biology, sequence assembly
CASAVA	1.8.2	[25]	Biology, NGS
CD-HIT	4.6	[26]	Biology, Genomics
Charmm	36a3	[27]	Simulation, Chemistry
CisGenome	2.0	[28]	Biology, Genomics, Peak Calling
ClustalW	2.1	[29]	Biology, Genomics
CMake	2.8.8	[30]	Programming
Consed	23.0	[31]	Biology, Genomics
CUDA	4.2	[32]	Programming, Graphics
Cufflinks	1.3.0, 2.0.0, 2.0.2	[33]	Biology, NGS
Cutadapt	1.1	[34]	Biology, NGS
Desmond	3.0.3.1	[35]	Simulation, Biology, Chemistry
DIYABC	many	[36]	Biology, Genomics
Dlpoly	4.03.4	[37]	Simulation, Biology, Chemistry
Dock	6.5	[38]	Chemistry, ligand binding prediction
emboss	6.5.7	[39]	Biology, multi-tool suite
Espresso	5.0.1	[40]	Modeling, Physics
ESPRIT	201211	[41]	Biology, NGS, Metagenomics
ETE2	2.1	[42]	Biology, Phylogenetics
Exonerate	2.2.0	[43]	Biology, Genomics
FAR	2.15	[44]	Biology, Genomics
FASTA	34.26.5	[45]	Biology, Genomics
FastQC	0.9.6, 0.10.1	[46]	Biology, NGS
Fastx_toolkit	0.0.13.2	[47]	Biology, NGS
Ferret	6.82	[48]	Oceanography, Meteorology
FFTW	3.3.2	[49]	Math, Library, C++
FragGeneScan	1.16	[50]	Biology, NGS, Genomics
FreeBayes	0.9.6	[51]	Biology
Garli	2.0	[52]	Biology, Phylogenetics
GATK	1.6.9	[53]	Biology, NGS
Gaussian	E01, G03, G09-A.02, G09-C.01	[54]	Modeling, Computational Chemistry
GeneMark	2012.04	[55]	Biology, Genomics, Metagenomics
Genewise	2.2.0	[56]	Biology, Genomics, Annotation
Gmap	20070928, 20120712	[57]	Biology, Genomics
GnuPlot	4.6.0	[58]	Graphics, Plotting, Programming
Grace	5.1.22	[59]	Graphics, plotting, 2D
GrADS	2.0.1	[60]	Earth Science
Gromacs	4.5.5	[61]	Chemistry, Modeling, Simulation
GSL	1.15	[62]	Library, Math, C++, C
HaMStR	v8b	[63]	Biology, Genomics
HDF5	1.8.9	[64]	Library, Data
HMMER3	3.0	[65]	Biology, Genomics
HTSeq	0.5.3p3	[66]	Biology, NGS
HyPhy	2.1.2.28	[67]	Biology, Phylogenetics
Hypre	2.8.0b	[68]	Library, Math, Physics
IM and IMa	20091217	[69]	Biology, Population
IMa2	20120827	[70]	Biology, Population
Intel Compilers	11.1, 2012	[71]	Programming, Compilers
Iprscan	4.8	[72]	Biology, Genomics
JDK	1.6.0_31, 1.7.0_02	[73]	Java Development Kit
Kent	20120524	[74]	Biology, NGS
Kmer	1934	[75]	Biology, NGS
LAMMPS	28Oct12	[76]	Molecular Dynamics Simulation
Last	193, 247	[77]	Biology, Sequence alignment
Lastz	1.02.00	[78]	Biology, NGS
LIBSVM	3.12	[79]	Machine Learning
MACS	1.4.2	[80]	Biology, ChIP-Seq
mafft	6.903	[81]	Biology, Multiple sequence alignment
Maker	2.10, 2.25b	[82]	Biology, Annotation, Genomics
Maq	0.7.1	[83]	Biology, NGS
Matlab	2012a	[84]	Math, Simulation, Programming
MATS	2.1.0, 3.0.4, 3.0.6	[85]	BIology, NGS
MCNP	5, 6b2	[86]	Physics
MCNPX	2.7.0, 2.7.0-i8	[87]	Physics
Meme	4.8.1	[88]	Biology, Motifs, Sequence analysis
MetaCluster	5.0beta	[89]	Biology
MetaVelvet	1.2.01	[90]	Biology, NGS
MetaGeneMark	2012.04	[91]	Biology, Genomics
Midnight Commander	4.6.1	[92]	Tools, Utilities
Migrate-n	3.3.0	[93]	Biology, Population
MISO	0.4.4	[94]	Biology, NGS
MSMBuilder	2.5.1	[95]	Molecular Dynamics
Molden	5.0	[96]	Molecular, electronic structure
mosaik	2.1.33	[97]	Biology,NGS
MrBayes	3.2.1	[98]	Biology, Phylogenetics
MUMmer	3.23	[99]	Biology, Genomics
MUSCLE	3.8.31	[100]	Biology, Genomics
NAMD	2.9	[101]	Simulation, Chemistry, Biology
Nbody	6	[102]	Astronomy
NCO	4.2.1	[103]	Data exchange tools
NetCDF	4.2	[104]	Data exchange, Tools
Newbler	2.6, 2.7	[105]	Biology, NGS
Novoalign	2.08.02	[106]	Biology, NGS
Oases	0.2.08	[107]	Biology, NGS
OpenFOAM	2.1.1	[108]	Fluid Dynamics
PartitionFinder	1.0.1	[109]	Biology, Phylogenetics, Evolution
Parflow	v615	[110]	Ecology, Modeling
PASA	1.5, r20120625	[111]	Biology, Genomics
PeakSplitter	1.0	[112]	Biology, Chip-Seq
PDT	3.18	[113]	Programming, Profiler
Perl	5.16.0	[114]	Programming, Language
PerM	0.4.0	[115]	Biology, NGS
Phenix	1.8.1069	[116]	Crystallography
PhyML	3.0, 20121109	[117]	Biology, Phylogenetics
Picard	1.69, 1.72, 1.80	[118]	Biology, NGS
Proteinortho	4.26	[119]	Biology, Genomics
python	2.6.8, 2.7.3	[120]	Programming, scripting, language
QIIME	1.5.0	[121]	Biology, Ecology
R	2.15.0, 2.15.1, 2.15.0-mpi, Rmpi/2.15.1	[122]	Statistics, Programming
R8S	1.71	[123]	Biology, Evolution
RADICAL	0.2	[124]	Biology, Phylogenetics, Genomics
RAxML	7.3.2.0705	[125]	Biology, Phylogenetics
RepeatMasker	3.3.0	[126]	Biology, Genomics
Reptile	1.1	[127]	Biology, NGS, error correction
riboPicker	0.4.3	[128]	Biology, Sequence
samtools	0.1.16, 0.1.18	[129]	Biology, NGS
SAS	9.3	[130]	Statistics, Graphing
Schrodinger	2012	[131]	Simulation, chemistry
SeqPrep	0.5	[132]	Biology, NGS
SEQuel	1.0.1	[133]	Biology, NGS
Sickle	1.200	[134]	Biology, NGS, quality filter
Siesta	2.0.2,3.1	[135]	Simulation, Physics, Ab Initio
SIFT	4.0.3b	[136]	Biology, Genomics
Silo	4.7	[137]	Library, Data
Snap	20100728	[138]	Biology, Genomics
SOAPdenovo	1.05	[139]	Biology, NGS
SOAPdenovo-Trans	1.01	[140]	Biology, NGS
SPARTA+	2.60	[141]	Chemistry
SPIMAP	1.1	[142]	Biology, Phylogenetics
SpliceTrap	0.90.5	[143]	Biology, NGS, RNA-Seq
Sputnik	1.0	[144]	Biology, Genomics
SRA	2.1.10	[145]]	biology, NGS
Stacks	0.9995	[146]	Biology, Genomics, NGS
Structure	2.3.3	[147]	Biology, Population
TAU	2.21.4	[148]	Profiling, Tracing, Programming
tgicl	2.1	[149]	Biology, sequencing, clustering
Tophat	1.4.1, 2.0.1	[150]	Biology, NGS
TRF	4.04	[151]	Biology, Genomics
Trinity	r20120608, r20120905, r20121005	[152]	Biology, RNA-Seq
Twinscan	4.1.2	[153]	Biology, Genomics
usearch	5.2.32	[154]	Biology, Sequence analysis
VASP	4.6.34, 5.2.12, 5.3.2	[155]	Quantum Chemistry, Ab Initio
VCFtools	0.1.9, 0.1.10	[156]	Biology, SNPs
velvet	1.2.06, 1.2.07	[157]	Biology, NGS
vmd	1.9.1	[158]	Biology, Visualization
WebLogo	3.3	[159]	Biology, Genomics
WDSSII	1	[160]	Meteorology
wgs	7.0.1.22	[161]	Biology, NGS
wublast	2.0	[162]	Biology, Sequence Alignment

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