Difference between revisions of "Installed Software"

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! scope="col" class="unsortable" | Version  
 
! scope="col" class="unsortable" | Version  
 
! scope="col" | Project/Vendor Website
 
! scope="col" | Project/Vendor Website
−
! scope="col" | Category  
+
! scope="col" | Category
−
!scope="col" class="unsortable" | Notes
+
! scope="col" class="unsortable" style="text-align: center;" | EL5 <ref name="el5">Operating system: CentOS 5 - currently in production at UF HPC</ref>
 +
! scope="col" class="unsortable" style="text-align: center;" | EL6<ref  name="el6">Operating system: RedHat Enterprise Linux 6 - scheduled for production at UF HPC for the Fall of 2012</ref>
 
|-
 
|-
−
| [[Abaqus]] || 6.6-1, 6.9-2 || [http://www.simulia.com/products/abaqus_standard.html Abaqus] || Simulation ||
+
| [[Abaqus]] || 6.6-1, 6.9-2 || [http://www.simulia.com/products/abaqus_standard.html] || Simulation || X ||
 
|-
 
|-
−
| [[Abyss]] || 1.3.1 || [http://www.bcgsc.ca/platform/bioinfo/software/abyss Abyss] || Biology, NGS ||
+
| [[Abyss]] || 1.3.1 || [http://www.bcgsc.ca/platform/bioinfo/software/abyss] || Biology, NGS || X ||
 
|-
 
|-
−
| [[ADMB]] || 9.1, 10.0, 10.1 || [http://admb-project.org/ ADMB] || Modeling, math ||
+
| [[ADMB]] || 9.1, 10.0, 10.1 || [http://admb-project.org/] || Modeling, math || X ||
 
|-
 
|-
−
| [[ALLPATHS-LG]] || 39099, 40122, 41655 || [http://www.broadinstitute.org/software/allpaths-lg/blog/ ALLPATHS-LG] || Biology, NGS ||
+
| [[ALLPATHS-LG]] || 39099, 40122, 41655 || [http://www.broadinstitute.org/software/allpaths-lg/blog/] || Biology, NGS || X ||
 
|-
 
|-
−
| [[Amber]] || 10,11.old, 11, 12 || [http://amber.scripps.edu/ Amber] || Simulation, chemistry ||
+
| [[Amber]] || 10,11.old, 11, 12 || [http://amber.scripps.edu/] || Simulation, chemistry || X ||
 
|-
 
|-
−
| [[Amos]] || 3.0.0 || [http://sourceforge.net/apps/mediawiki/amos/index.php?title=AMOS AMOS] || Biology, Genomics ||
+
| [[Amos]] || 3.0.0 || [http://sourceforge.net/apps/mediawiki/amos/index.php?title=AMOS] || Biology, Genomics || X ||
 
|-
 
|-
−
| [[ANNOVAR]] || 20120308 || [http://www.openbioinformatics.org/annovar/ ANNOVAR] || Biology, Genomics ||
+
| [[ANNOVAR]] || 20120308 || [http://www.openbioinformatics.org/annovar/] || Biology, Genomics || X ||
 
|-
 
|-
−
| [[Ansys]] || 9.0, 10.0 || [http://www.ansys.com/ Ansys] || Simulation, Engineering ||
+
| [[Ansys]] || 9.0, 10.0 || [http://www.ansys.com/] || Simulation, Engineering || X ||
 
|-
 
|-
−
| [[antlr]] || 2.7.7, 3.1.3 || [http://www.antlr.org/ Antlr] || Linguistics, Parser ||
+
| [[antlr]] || 2.7.7, 3.1.3 || [http://www.antlr.org/] || Linguistics, Parser || X ||
 
|-
 
|-
−
| [[arachne]] || 37618 || [http://www.broadinstitute.org/scientific-community/science/programs/genome-sequencing-and-analysis/computational-rd/computational- Arachne] || Biology, Genomics ||
+
| [[arachne]] || 37618 || [http://www.broadinstitute.org/scientific-community/science/programs/genome-sequencing-and-analysis/computational-rd/computational] || Biology, Genomics || X ||
 
|-
 
|-
−
| [[Bamtools]] || 2.1.0 || [https://github.com/pezmaster31/bamtools/wiki Bamtools] || Biology, NGS ||
+
| [[Bamtools]] || 2.1.0 || [https://github.com/pezmaster31/bamtools/wiki] || Biology, NGS || X ||
 
|-
 
|-
−
| [[BamUtil]] || 1.0.2 || [http://genome.sph.umich.edu/wiki/BamUtil BamUtil] || Biology, NGS ||
+
| [[BamUtil]] || 1.0.2 || [http://genome.sph.umich.edu/wiki/BamUtil] || Biology, NGS || X ||
 
|-
 
|-
−
| [[BayesPhylogenies]] || 2.0 || [http://www.evolution.reading.ac.uk/BayesPhy.html BayesPhylogenies] || Biology, Phylogenetics ||
+
| [[BayesPhylogenies]] || 2.0 || [http://www.evolution.reading.ac.uk/BayesPhy.html] || Biology, Phylogenetics || X ||
 
|-
 
|-
−
| [[beast]] || 1.6.2, 1.7.0, 1.7.1 || [http://beast.bio.ed.ac.uk/Main_Page BEAST] || Biology, Phylogenetics ||
+
| [[beast]] || 1.6.2, 1.7.0, 1.7.1 || [http://beast.bio.ed.ac.uk/Main_Page] || Biology, Phylogenetics || X ||
 
|-
 
|-
 
| [[Bedtools|BEDTools]] || 2.16.2 || [http://code.google.com/p/bedtools/ BEDTools] || Biology, NGS ||
 
| [[Bedtools|BEDTools]] || 2.16.2 || [http://code.google.com/p/bedtools/ BEDTools] || Biology, NGS ||
Line 232: Line 233:
 
| [[NCO]] || 4.0.9 || [http://nco.sourceforge.net/ NCO] || Data exchange tools ||  
 
| [[NCO]] || 4.0.9 || [http://nco.sourceforge.net/ NCO] || Data exchange tools ||  
 
|-
 
|-
−
| [[netcdf]] || 3.6.3, 4.1.2, 4.1.3 || [http://www.unidata.ucar.edu/software/netcdf/ NetCDF]|| Data exchange, Tools || HDF5 support in 4.1.3 only
+
| [[netcdf]] || 3.6.3, 4.1.2, 4.1.3 || [http://www.unidata.ucar.edu/software/netcdf/ NetCDF]|| Data exchange, Tools ||
 
|-
 
|-
 
| [[NetLogo]] || 4.1.3 || [http://ccl.northwestern.edu/netlogo/ NetLogo] || Modeling ||
 
| [[NetLogo]] || 4.1.3 || [http://ccl.northwestern.edu/netlogo/ NetLogo] || Modeling ||
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| [[SOAPdenovo]] || 1.05 || [http://soap.genomics.org.cn/soapdenovo.html SOAPdenovo] ||Biology, NGS||
 
| [[SOAPdenovo]] || 1.05 || [http://soap.genomics.org.cn/soapdenovo.html SOAPdenovo] ||Biology, NGS||
 
|-
 
|-
−
| [[SPARTA+]] || 2.60 || [URL: http://spin.niddk.nih.gov/bax/software/SPARTA+/] ||Chemistry||
+
| [[SPARTA+]] || 2.60 || [http://spin.niddk.nih.gov/bax/software/SPARTA+/] ||Chemistry||
 
|-
 
|-
 
| [[SRA]] || 2.1.7 || [http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=software&m=software&s=software SRA]]||biology, NGS||
 
| [[SRA]] || 2.1.7 || [http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=software&m=software&s=software SRA]]||biology, NGS||
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|}
 
|}
  
−
* Many versions available.  <code>/scratch/hpc/osg/app/etc/grid3-locations.txt</code> may have an up-to-date list.  Or look underneath <code>/scratch/hpc/osg/app/cmssoft</code>.
+
<references />
  
 
To add a documentation page for a new piece of software installed into /apps please go to [[Add New App Page]].
 
To add a documentation page for a new piece of software installed into /apps please go to [[Add New App Page]].

Revision as of 03:46, 29 June 2012

The following is a list of the installed software at the UF HPC Center.

Last updated 2012-06-29.

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

Software

Name Version Project/Vendor Website Category EL5 [1] EL6[2]
Abaqus 6.6-1, 6.9-2 [1] Simulation X
Abyss 1.3.1 [2] Biology, NGS X
ADMB 9.1, 10.0, 10.1 [3] Modeling, math X
ALLPATHS-LG 39099, 40122, 41655 [4] Biology, NGS X
Amber 10,11.old, 11, 12 [5] Simulation, chemistry X
Amos 3.0.0 [6] Biology, Genomics X
ANNOVAR 20120308 [7] Biology, Genomics X
Ansys 9.0, 10.0 [8] Simulation, Engineering X
antlr 2.7.7, 3.1.3 [9] Linguistics, Parser X
arachne 37618 [10] Biology, Genomics X
Bamtools 2.1.0 [11] Biology, NGS X
BamUtil 1.0.2 [12] Biology, NGS X
BayesPhylogenies 2.0 [13] Biology, Phylogenetics X
beast 1.6.2, 1.7.0, 1.7.1 [14] Biology, Phylogenetics X
BEDTools 2.16.2 BEDTools Biology, NGS
BFAST 0.7.0 BFAST Biology, NGS
Bioconductor 2011-11-16 Bioconductor Biology, R, Statistics
BioPerl 1.006901 BioPerl Biology, Perl
Biopython 1.59 BioPython Biology, Python
bioscope 1.0.1, 1.2.1 ABI BioScope Biology, NGS
Blast 2.2.24, 2.2.25, 2.2.26 NCBI Biology, Sequence alignment
Blast2go 2.5.0 Blast2go Biology, Annotation
BLAT 34 BLAT Biology, Sequence alignment
Boost 1.38.0, 1.46.1, 1.48.0, 1.49.0 Boost C++, Library
bwa 0.5.9, 0.5.10, 0.6.0 (default) BWA Biology, NGS
Bowtie 0.12.7, 0.12.8 (default), 2.0.0-beta3, 2.0.0-beta5 Bowtie Biology, NGS
BreakDancer 1.1 BreakDancer Biology, NGS, Genomics
CAP3 20071015 CAP3 Biology, sequence assembly
CASAVA 1.8.2 CASAVA Biology, NGS
CD-HIT 4.5.7 CD-HIT Biology, Genomics
CEGMA 2.3 CEGMA Biology, Genomics, Annotation
CGATools 1.5.0.31 CGA Tools Biology, Genomics
Charmm 35b2 Charmm Simulation, Chemistry
Circuit 3.5.1, 3.5.7 Circuitscape GIS
CisGenome 2.0 CisGenome Biology, Genomics, Peak Calling
CMake 2.8.5 Cmake Programming
CNV-seq 07.15.11 CNV-seq Biology, NGS
CNVnator 0.2.5 CNVnator Biology, NGS
CPMD 3.11.1 CPMD Simulation, Chemistry
Cufflinks 1.0.3, 1.1.0, 1.3.0 Cufflinks Biology, NGS
Cutadapt 1.1 Cutadapt Biology, NGS
dar 2.3.9 Dar Backup
deFuse 0.4.3 deFuse Biology, RNA-seq
Desmond 2.4.2.1 Desmond Simulation, Biology, Chemistry
Dindel 1.01 Dindel Biology, NGS, Genomics
dlpoly 3.0.9 DL_POLY Simulation, Biology, Chemistry
dock 6.3, 6.4, 6.5 Dock Chemistry, ligand binding prediction
emacs 21.4.1, 23.4.1 Gnu Website The Emacs editor
EMAN2 2.04 EMAN2 Biology, image processing
emboss 6.4.0 Emboss Biology, multi-tool suite
espresso 3.0, 3.2.2, 4.0.4, 5.0 Espresso Modeling, Physics
Exonerate 2.2 Exonerate Biology, Genomics
FAR 2.15 FAR Biology, Genomics
FASTA 34.26.5 FASTA Biology, Genomics
fastx_toolkit 0.0.13.1 Fastx Tolkit Biology, NGS
FastQC 0.9.6, 0.10.0 FastQC Biology, NGS
fftw 2.1.5, 3.1.2 FFTW Gaussian Math, Library, C++
fluent 6.3.26 ANSYS FLUENT Simulation
FragGeneScan 1.16 FragGeneScan Biology, NGS
FreeBayes 0.9.4 FreeBayes Biology,
gadget 2.0.4, 2.0.5 Atlassian Gadgets Software Development
gamess 11-Aug11 GAMESS Quantum Chemistry
garli 2.0 GARLI Biology, Phylogenetics
GATK 1.4.30 GATK Biology, NGS
gulp 4.0.3 GULP Modeling/simulation, Computational Chemistry
gaussian E01, G03, G09-A.02, G09-C.01 Gaussian Modeling, Computational Chemistry
Geneid 1.4 geneid Biology, Genomics, Annotation
GeneMark 2012.04 GeneMark Biology, Genomics, Metagenomics
Genewise 2.2.3 Wise2 Biology, Genomics, Annotation
GMAP 20070928, 20120111, 20120323, 20120427, 20120524, 20120612 GMAP Biology, Genomics
Grace 5.1.22 Grace Graphics, plotting, 2D
Gromacs 4.0.4, 4.0.7 Gromacs Physics, Modeling
HDF5 1.8.7, 1.8.8 HDF5 Library, Data
HMMER3 3.0 HMMER3 Biology, Genomics
HTSeq 0.5.3p3 HTSeq Biology, NGS
HugeSeq 1.0.1 HugeSeq Biology, NGS, Genomics
hypre 2.8.0 HYPRE Library, Math, Physics
IM and IMa 2009.12.17 IM&IMa Biology, Population
IMa2 8.26.11 IMa2 Biology, Population
Inelastica 1.1 (python/2.7.2) Inelastica Quantum Chemistry
IE3D 15.1 IE3D Simulation, Design
JDK 1.6.0_12, 1.7.0 Oracle JDK Java Development Kit
Khmer 20120321 Khmer Biology, NGS, Utilities
Kmer r1909 Kmer package Biology, NGS, genome alignment
lammps 17-Sept11 LAMPPS Simulation
Last 193 Last Biology, Sequence alignment
libxc 1.1.0 libxc Math, funtionals
MACS 1.4.1 MACS Biology, ChIP-Seq
madness 1769 MADNESS Math, DIff. Equation solving
mafft 6.859 MAFFT Biology, Multiple sequence alignment
Maker 2.10 Maker Biology, Annotation, Genomics
MapSplice 1.15.2 MapSplice Biology, Genomics
Matlab 2009b MathWorks Math, Simulation, Programming
MATS 2.1.0 MATS BIology, NGS
Mauve 2.3.1 Mauve Biology, Multiple genome alignments
MCL 11-335 MCL Biology, Genomics, Clustering
meme 3.0.13, 4.3.0 MEME Biology, Motifs, Sequence analysis
MetaPhyler 1.13 MetaPhyler Biology, Metagenomics
metis 4.0 Metis Math, Graph partitioning
Migrate-n 3.2.16 Migrate-n Biology, Population
mira 3.2.0, 3.4.0.1 MIRA Biology, NGS
mosaik 1.1.0021 MOSAIK Biology,NGS
MPIBlast 1.6.0 MPIBlast Biology, Sequence alignment
MrBayes 3.1.2,3.2.1 MrBayes Biology, Phylogenetics
MUMmer 3.22 MUMmer Biology, Genomics
MUSCLE 3.8.31 MUSCLE Biology, Genomics
NAMD 2.7b2 NAMD Simulation, Chemistry, Biology
NCO 4.0.9 NCO Data exchange tools
netcdf 3.6.3, 4.1.2, 4.1.3 NetCDF Data exchange, Tools
NetLogo 4.1.3 NetLogo Modeling
Newbler 2.5.3, 2.6 Newbler Biology, NGS
NFFT 3.1.3 nfft NDFT, library, math
Novoalign 2.07.15 Novoalign Biology, NGS
NWChem 6.0 NWChem Simulation, Chemistry
Oases 0.2.04 Oases Biology, NGS
OpenFOAM 1.7.1 OpenFoam Molecular Dynamics
OrthoMCL 2.0 OrthoMCL Biology, Genomics
PAL2NAL 14 PAL2NAL Biology, bioinformatics, multiple sequence alignment
PAML 4.4e PAML Biology, Phylogenetics
PAPI 4.1.2.1 PAPI CPU API
PASA 20110520 PASA Biology, Genomics
PeakSplitter 1.0 PeakSplitter Biology, Chip-Seq
PDT 3.16 PDT Programming, Profiler
Perl 5.14.1 Perl Programming, Language
PETSc 2.3.3-p8, 3.0.0-p12 PETSc MPI toolkit
Phred 020425 Phred Biology, Genomics, Sequencing
PhyloBayes 3.3b PhyloBayes Biology, Phylogenetics
PhyML 3.0 PhyML Biology, Phylogenetics
Picard 1.54 Picard Biology, NGS
Pindel 0.2.8 Pindel Biology, NGS
PQS 3.3-19 PQS Modeling, Chemistry
Prinseq 0.17 Prinseq Biology, NGS
PyOpenCL 2012.04 PyOpenCL python, parallel programming
python 2.6.5, 2.7.2, 2.7.3 Python Programming, scripting, language
R 2.14.1, 2.14.1-MPI, 2.14.2 R Statistics, Programming
RAxML 7.3.0 RAxML Biology, Phylogenetics
RAxML-Light 1.0.5 RAxML Biology, Phylogenetics
RepeatMasker 3.3.0 Repeat Masker Biology, Genomics
Reptile 1.1, 1.1-omp Reptile Biology, NGS, error correction
riboPicker 0.4.2 riboPicker Biology, Sequence
Rosetta 2.1.1, 2.1.2 Rosetta Biology, Structural, Modeling
Ruby 1.9.3 Ruby Programming, Language, Scripting
RSMToolkit 2961 RSM Math, Modeling, Geometry
samtools 0.1.16, 0.1.18 Samtools Biology, NGS
SAS 9.2, 9.3 SAS Statistics, Graphing
SATe 2.1.0 SATe Biology, Phylogenetics
Scala 2.9.1 Scala Programming, language, java
Segminator 0.0.2 Segminator Biology, NGS
SeqPrep 0.4 SeqPrep Biology, NGS
Siesta 2.0, 2.0.2, 3.0b Siesta Simulation, physics, ab-initio
SOAPdenovo 1.05 SOAPdenovo Biology, NGS
SPARTA+ 2.60 [15] Chemistry
SRA 2.1.7 SRA] biology, NGS
SRNAPredict 3.0 sRNAPredict Biology, Genomics
SRNAScanner 200903 sRNAScanner Biology, Genomics
Staden 2.0.0b9 Staden Biology, Genomics, Sequencing
Stata 10 Stata Statistics, Data analysis
Structure 2.3.3 Structure Biology, Population
TAU 2.20.1 TAU Profiling, Tracing, Programming, Toolkit
tgicl 2.1 TGICL Biology, sequencing, clustering
TRF 4.04 TRF Biology, Genomics
Trimal 1.2 Trimal Biology, NGS
Trinity r20110820, r20120125, r20120317, r20120608 Trinity RNA-Seq Biology, RNA-Seq
Tophat 1.3.0, 1.3.3, 1.4.1 Tophat Biology, NGS
tuxedo The "tuxedo suite" - Bowtie, Tophat, and Cufflinks
Twinscan 3.5,4.1.2 Twinscan Biology, Genomics
usearch 5.0.151,5.1.221 USEARCH Biology, Sequence analysis
VASP 4.6.34,5.2.0 VASP Quantum Chemistry, ab initio
VCFtools 0.1.7, 0.1.9 VCFtools Biology, SNPs
velvet 1.2.06,1.2.02,1.2.01,1.1.05 Velvet Biology, NGS
vmd 1.9 VMD Biology, Visualization
weka 3.6.2 WEKA Data mining algorithms
wgs 6.1, 6.1-20110830 Celera WGS Assembler Biology,Assembler,Genome
wublast 2.0 WU-Blast Biology, Sequence Alignment
  1. ↑ Operating system: CentOS 5 - currently in production at UF HPC
  2. ↑ Operating system: RedHat Enterprise Linux 6 - scheduled for production at UF HPC for the Fall of 2012

To add a documentation page for a new piece of software installed into /apps please go to Add New App Page.

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