Software-old: Difference between revisions

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| [[pagan]] || 0.39 || Bioinformatics || zcluster ||  ||  
| [[pagan]] || 0.39 || Bioinformatics || zcluster ||  ||  
|-
|-
| [[PAML]] || 4.4 || Bioinformatics || zcluster || working, JKP ||  
| [[PAML]] || 4.4 || Bioinformatics || zcluster || working, JKP || clear, YH
|-
|-
| [[pandaseq]] || 2.0 || Bioinformatics || zcluster || JKP ||  
| [[pandaseq]] || 2.0 || Bioinformatics || zcluster || JKP || clear, YH
|-
|-
| [[Papara_nt]] || 2.1.2 || Bioinformatics || zcluster || JKP ||  
| [[Papara_nt]] || 2.1.2 || Bioinformatics || zcluster || JKP || clear, YH
|-
|-
| [[PASHA]] || 1.0.6 || Bioinformatics || zcluster || JKP ||  
| [[PASHA]] || 1.0.6 || Bioinformatics || zcluster || JKP || clear, YH
|-
|-
| [[PeakSplitter]] || 1.0 || Bioinformatics || zcluster || JKP ||  
| [[PeakSplitter]] || 1.0 || Bioinformatics || zcluster || JKP || clear, YH
|-
|-
| [[pebl]] || 1.01 ||  || zcluster ||  ||  
| [[pebl]] || 1.01 ||  || zcluster ||  ||  
Line 353: Line 353:
| [[pfam]] || 26.0 || Database || zcluster ||  ||  
| [[pfam]] || 26.0 || Database || zcluster ||  ||  
|-
|-
| [[Pfam_scan]] || 04282012 || Bioinformatics || zcluster || JKP ||  
| [[Pfam_scan]] || 04282012 || Bioinformatics || zcluster || JKP || clear, YH
|-
|-
| [[pftools]] || 2.3.5 || Bioinformatics || zcluster || JKP ||  
| [[pftools]] || 2.3.5 || Bioinformatics || zcluster || JKP || clear, YH
|-
|-
| [[PGDBG]] || 12.10 || Debugger || zcluster || working, SHT ||
| [[PGDBG]] || 12.10 || Debugger || zcluster || working, SHT ||
Line 361: Line 361:
| [[PGPROF]] || 12.10 || Profiler || zcluster || working, SHT ||
| [[PGPROF]] || 12.10 || Profiler || zcluster || working, SHT ||
|-
|-
| [[phred/phrap/conced]] ||  || Bioinformatics || zcluster || JKP, not enough information ||  
| [[phred/phrap/conced]] ||  || Bioinformatics || zcluster || JKP, not enough information || clear, YH
|-
|-
| [[PhyloBayes]] || 3.3b || Bioinformatics || zcluster || JKP ||  
| [[PhyloBayes]] || 3.3b || Bioinformatics || zcluster || JKP || clear, YH
|-
|-
| [[PHYML]] || 20110919 ||  Bioinformatics || zcluster || JKP ||  
| [[PHYML]] || 20110919 ||  Bioinformatics || zcluster || JKP || clear, YH
|-
|-
| [[picard]] || 1.62 || Bioinformatics || zcluster || JKP ||  
| [[picard]] || 1.62 || Bioinformatics || zcluster || JKP || clear, YH
|-
|-
| [[pileup]] || 0.6 || Bioinformatics || zcluster ||  ||  
| [[pileup]] || 0.6 || Bioinformatics || zcluster ||  || clear, YH
|-
|-
| [[prank]] || 100802 || Bioinformatics || zcluster || JKP ||  
| [[prank]] || 100802 || Bioinformatics || zcluster || JKP || clear, YH
|-
|-
| [[Primer3]] || 2.3.4 || Bioinformatics || zcluster || JKP ||  
| [[Primer3]] || 2.3.4 || Bioinformatics || zcluster || JKP || clear, YH
|-
|-
| [[pysam]] || 0.6 || Bioinformatics || zcluster || JKP ||  
| [[pysam]] || 0.6 || Bioinformatics || zcluster || JKP || clear, YH
|-
|-
| [[PyTables]] || 2.3.1 || Other || zcluster ||  ||  
| [[PyTables]] || 2.3.1 || Other || zcluster ||  ||  
Line 381: Line 381:
| [[Python]] || 2.4.3, 2.7.2, 3.3.0 || Programming Language || zcluster || Done, SHT ||
| [[Python]] || 2.4.3, 2.7.2, 3.3.0 || Programming Language || zcluster || Done, SHT ||
|-
|-
| [[Qiime]] || 1.6.0 || Bioinformatics || zcluster || JKP ||  
| [[Qiime]] || 1.6.0 || Bioinformatics || zcluster || JKP || clear, YH
|-
|-
| [[QTL Cartographer]] || 1.17j || Bioinformatics || zcluster || JKP ||  
| [[QTL Cartographer]] || 1.17j || Bioinformatics || zcluster || JKP || clear, YH
|-
|-
| [[quake]] || 0.3.4 || Bioinformatics || zcluster || JKP ||  
| [[quake]] || 0.3.4 || Bioinformatics || zcluster || JKP || clear, YH
|-
|-
| [[Quantum Espresso]] || 5.0.2 || Chemistry || zcluster ||  ||  
| [[Quantum Espresso]] || 5.0.2 || Chemistry || zcluster ||  ||  

Revision as of 15:35, 8 February 2013

Installed Software List

Last updated 2013-02-08.

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

Software Template

Name Version Category Cluster Notes Reviewed By
00-Skipped Page 0.0 Work Log GACRC YH Created
3D_DOCK 2.0 Chemistry pcluster Ignored by SMW, YH reviewed, need SHT review
454 Software Bioinformatics zcluster Done, SMW clear, YH
aaarf 1.0.0 Bioinformatics zcluster Done, SMW clear, YH
ABINIT 6.12.1 Chemistry zcluster Done, SMW
ABySS 1.3.4 Bioinformatics zcluster Done, SMW clear, YH
ALLPATHS-LG 44254 Bioinformatics zcluster Contains Dead Links, SMW clear, YH
AMBER 11, 12 Chemistry zcluster Done, SHT
AMBER-pcluster 8 Chemistry pcluster
amos 3.1.0 Bioinformatics zcluster Done, SMW clear, YH
ARB 5.3 Bioinformatics zcluster ?, Please Review Running Program Section, SMW clear, YH
AUGUSTUS 2.5.5 Bioinformatics zcluster Please verify Documentation Section, SMW clear, YH
bam2fastq 1.1.0 Bioinformatics zcluster Done, SMW clear, YH
BEAST 1.7.2 Bioinformatics zcluster Done, with Dead Links, SMW clear, YH 2/7 8:30 am YH
BEDTools 2.16.2 Bioinformatics zcluster Done, SMW clear, YH
BEST Bayesian 2.3.1 Bioinformatics zcluster Done, SMW clear, YH
BioPerl 1.61 Bioinformatics zcluster Done, SMW clear, YH
BioPython 1.58 Bioinformatics zcluster Done, SMW clear, YH
Bismark Bisulfite Mapper 0.7.6 Bioinformatics zcluster Done, SMW clear, YH
BiSS 0.0.1 Bioinformatics zcluster Done, SMW clear, YH
BLAS 3.0.37 Math Library zcluster working, SHT
Blat 3.5 Bioinformatics zcluster Done, SMW clear, YH
BMGE 1.1 Bioinformatics zcluster Done, SMW clear, YH
Boost 1.47.0, 1.48.0 Library zcluster working, SHT
bowtie 0.12.8 Bioinformatics zcluster Done, SMW clear, YH
bowtie2 2.0.0-beta7 Bioinformatics zcluster Done, SMW clear, YH
breakdancer 1.1_2011_02_21 Bioinformatics zcluster Done, SMW clear, YH
brownie 2.1.2 Bioinformatics zcluster Done, SMW clear, YH
BS Seeker Dec 113 Bioinformatics zcluster Done, SMW clear, YH
Burrows-Wheeler Aligner (BWA) 0.6.2 Bioinformatics zcluster Done, SMW clear, YH
cd-hit 4.5.6 Bioinformatics zcluster Done, SMW clear, YH
cdbfasta 04282012 Bioinformatics zcluster Done, SMW clear, YH
CEAS 1.0.2 Bioinformatics zcluster Done, SMW clear, YH
CEGMA 2.4.010312 Bioinformatics zcluster Done, SMW clear, YH
circos 0.62 Bioinformatics zcluster Done, SMW clear, YH
ClustalW 2.1 Bioinformatics zcluster Done, SMW clear, YH
Coding Potential Calculator 0.9-r2 Bioinformatics zcluster Done, SMW clear, YH
CONSEL v0.20 Bioinformatics zcluster
cortex_con 0.04c Bioinformatics zcluster
cortex_var 1.0.5.3 Bioinformatics zcluster
Count 2010-04-02 Bioinformatics zcluster
CREST 1.0 Bioinformatics zcluster
ctrax 0.3.2 Other zcluster
cufflinks 2.0.2 Bioinformatics zcluster
cutadapt 1.1 Bioinformatics zcluster
ddRADseq Bioinformatics zcluster
DLCoal 1.0 Bioinformatics zcluster
drmma 0.5 Other zcluster
ea-utils 1.1.2-537 Bioinformatics zcluster
edena 3Dev120626 Bioinformatics zcluster
EMBOSS 6.2.0 Bioinformatics zcluster clear, YH
emmix 1.3 Bioinformatics zcluster
ESTscan 3.0.3 Bioinformatics zcluster Done, YH clear, YH
evm (EVidenceModeler) r2012-06-25 Bioinformatics zcluster
ExaML 315576 Bioinformatics zcluster
exonerate 2.2.0 Bioinformatics zcluster
FAR 2.15 Bioinformatics zcluster
FASTA 36 Bioinformatics zcluster
FastQC 0.10.1 Bioinformatics zcluster
fasttree 2.1.4 Bioinformatics zcluster
FastX 0.0.13, 0.0.13.2 Bioinformatics zcluster
FIRE 1.1 Bioinformatics zcluster
FitModel 0.5.3 Bioinformatics zcluster
FFTW 2.1.5, 3.3.0, 3.3.2 Math Library zcluster working, SHT
FLASH 1.0.3 Bioinformatics zcluster
GAMESS May2012R1 with XMVB 2.0. Chemistry zcluster
GAMESS-pcluster 2007 R6 Chemistry pcluster
GapFiller 1.11 Bioinformatics zcluster
gatk 2.2-2-gf44cc4e Bioinformatics zcluster
GAUSSIAN03 03 Chemistry pcluster
GAUSSIAN94 94 Chemistry pcluster
Gblocks 0.91b Bioinformatics zcluster
GDB 7.0.1 Debugger zcluster working, SHT
GeneMark genemark-ES 2.3e gGeneMark version 2.5m Bioinformatics zcluster
Genome Phred version: 0.071220.c Bioinformatics zcluster
GenomeMapper 0.4.3 (Version for SHORE/WMD3) Bioinformatics zcluster
GenomeTools 1.3.9 Bioinformatics zcluster
git 1.7.4.1, 1.7.9 Others zcluster
Glimmer 3.0.2 Bioinformatics zcluster
GlimmerHMM 3.0.1 Bioinformatics zcluster
gmap 2007-09-28 Bioinformatics zcluster
gmap-gsnap 2012-07-20 Bioinformatics zcluster
gnuplot 4.0, 4.6.0 Graphics zcluster Done, SHT
gprof 2.17 Profiler zcluster working, SHT
gpu-blast 1.1 with ncbi-blast-2.2.25+ Bioinformatics zcluster
grace 5.1.22 Other zcluster
Gromacs 4.5.5 Chemistry zcluster Done, SHT
GSL 1.9, 1.15 Math Library zcluster working, SHT
gss Bioinformatics zcluster
HDF5 1.6.4, 1.8.9 Other zcluster
Hmmer 3.0 Bioinformatics zcluster
Homo_sapien Database zcluster
htgs Database zcluster
htseq 0.5.3p3 Bioinformatics zcluster
igb 6.7.3 Bioinformatics zcluster
IGV 2.1.23 Bioinformatics zcluster
IMa May 06 Bioinformatics zcluster
indel-Seq-Gen 2.02 Bioinformatics zcluster
InStruct 3.2.09 Bioinformatics zcluster
iprscan (InterProScan) 5.0 CR2 Bioinformatics zcluster
iscan 1.0.0 Bioinformatics zcluster
Jellyfish 1.1.5 Bioinformatics zcluster
k-link 03 27, 2009 Bioinformatics zcluster
KEGG Database zcluster
LAPACK 3.0.37 Math Library zcluster working, SHT
LASTZ 1.03.02 Bioinformatics zcluster
LDDist 1.3.2 Bioinformatics zcluster
libsequence 1.7.4 Bioinformatics zcluster
LLVM-Clang 3.1 Compiler zcluster
lsa 11182011 Bioinformatics zcluster
macs 1.4.2 Bioinformatics zcluster
mafft 6.864b Bioinformatics zcluster
maize Database zcluster
maker 2.10 Bioinformatics zcluster
Maple-pcluster 10.06 Other pcluster
MAQ 0.7.1 Bioinformatics zcluster
Mathematica 5.2 Other pcluster
MatLab R2012a (7.14.0.739) Other zcluster
MCL 12-135 Bioinformatics zcluster
MEAD 2.2.9 Chemistry zcluster
Medicago Database zcluster
megan 4.67.2 Bioinformatics zcluster
MEME 4.8.1 Bioinformatics zcluster
Migrate 3.0.3 Bioinformatics zcluster
Minia 1.4683 Bioinformatics zcluster
MIRA 3.9.9 Bioinformatics zcluster
MKL 2013 Math Library zcluster working, SHT
MOTECC qmdcp 90 Chemistry zcluster
MOTECC qmdcp pcluster 90 Chemistry pcluster
MOTHUR 1.28.0 Bioinformatics zcluster
mpi4py 1.3 Utilities zcluster
mpiblast 1.6.0 Bioinformatics zcluster
MrBayes 3.1.2 Bioinformatics zcluster
mrfast 2.5.0.4 Bioinformatics zcluster
MSA 3.8.1b Bioinformatics zcluster
MUSCLE 3.8.31 Bioinformatics zcluster
MyScanACE 04232012 Bioinformatics zcluster
NAMD 2.9 Chemistry zcluster
NAMD-pcluster 2.6b2, 2.7b1 Chemistry pcluster
NCBI Blast 2.2.26 Bioinformatics zcluster Done, YH
NCBI Blast + 2.2.26 Bioinformatics zcluster
ncbi blast parsers Bioinformatics zcluster
NCBI_database Bioinformatics zcluster
NETCDF 4.1.3 Other zcluster
NETCDF-pcluster 3.5.1, 3.6.2 Other pcluster
netlogo 5.0 Other zcluster
Newbler 2.6 Bioinformatics zcluster
NH PhyloBayes 0.2.3 Bioinformatics zcluster
nhPhyML 01/2012 Bioinformatics zcluster
NovelSeq 1.0.2 Bioinformatics zcluster
NovoAlign 2.07 Bioinformatics zcluster
numexp 1.4.2 Other zcluster
NWCHEM 4.7 Chemistry pcluster
Oases 0.2.02 Bioinformatics zcluster
opal 2.0.0 Bioinformatics zcluster
Open Babel 2.3.1 Chemistry zcluster
OpenBUGS 3.2.2 Statistics zcluster
OpenCV 2.3.1 Other zcluster
OSPREY 2.0 Bioinformatics zcluster
p4 r231 Bioinformatics zcluster
pagan 0.39 Bioinformatics zcluster
PAML 4.4 Bioinformatics zcluster working, JKP clear, YH
pandaseq 2.0 Bioinformatics zcluster JKP clear, YH
Papara_nt 2.1.2 Bioinformatics zcluster JKP clear, YH
PASHA 1.0.6 Bioinformatics zcluster JKP clear, YH
PeakSplitter 1.0 Bioinformatics zcluster JKP clear, YH
pebl 1.01 zcluster
Perl 5.14.1 Programming Language zcluster Done, SHT
pfam 26.0 Database zcluster
Pfam_scan 04282012 Bioinformatics zcluster JKP clear, YH
pftools 2.3.5 Bioinformatics zcluster JKP clear, YH
PGDBG 12.10 Debugger zcluster working, SHT
PGPROF 12.10 Profiler zcluster working, SHT
phred/phrap/conced Bioinformatics zcluster JKP, not enough information clear, YH
PhyloBayes 3.3b Bioinformatics zcluster JKP clear, YH
PHYML 20110919 Bioinformatics zcluster JKP clear, YH
picard 1.62 Bioinformatics zcluster JKP clear, YH
pileup 0.6 Bioinformatics zcluster clear, YH
prank 100802 Bioinformatics zcluster JKP clear, YH
Primer3 2.3.4 Bioinformatics zcluster JKP clear, YH
pysam 0.6 Bioinformatics zcluster JKP clear, YH
PyTables 2.3.1 Other zcluster
Python 2.4.3, 2.7.2, 3.3.0 Programming Language zcluster Done, SHT
Qiime 1.6.0 Bioinformatics zcluster JKP clear, YH
QTL Cartographer 1.17j Bioinformatics zcluster JKP clear, YH
quake 0.3.4 Bioinformatics zcluster JKP clear, YH
Quantum Espresso 5.0.2 Chemistry zcluster
R 2.14.0, 2.15.0, 2.15.2 Statistics zcluster Done, SHT
R-pcluster 1.9.1, 2.1.1, 2.4.0 pcluster
RAxML 04/26/2012 Bioinformatics zcluster JKP clear, YH
RAxML-Light 1.0.5 Bioinformatics zcluster JKP clear, YH
Ray 1.6.1-0 Bioinformatics zcluster skipped, JKP
RCCBatchBlast 5.0 Bioinformatics zcluster JKP clear, YH
RCCBatchBlastPlus 1.0 Bioinformatics zcluster done, YH clear, YH
RECON 1.05 Bioinformatics zcluster JKP clear, YH
Repeatmasker 3.3 Bioinformatics zcluster JKP clear, YH
RepeatScout 1.05 Bioinformatics zcluster JKP clear, YH
riboPicker 0.4.3 Bioinformatics zcluster JKP clear, YH
RMBlast 2.2.27 Bioinformatics zcluster JKP clear, YH
Rmpi 0.5-9 Statistics zcluster
RNAz 2.1 Bioinformatics zcluster JKP clear, YH
rnnotator 2.4.12 Bioinformatics zcluster JKP clear, YH
Roche 2.6 Bioinformatics zcluster JKP, dead link in description clear, YH
RSAT (RSA-tools) 1.0 Bioinformatics zcluster JKP clear, YH
RSEM 1.1.21, 1.2.0 Bioinformatics zcluster JKP clear, YH
RUM 1.11 Bioinformatics zcluster JKP, Verify GACRC Support Form link clear, YH
Sage 3.1.1, 3.4.1 Other zcluster
samtools 0.1.18 Bioinformatics zcluster JKP clear, YH
SAS 9.1 Statistics zcluster
SATé 2.2.4 Bioinformatics zcluster clear, YH
SEQuel 1.0.2 Bioinformatics zcluster JKP clear, YH
SHE-RA 012012 Bioinformatics zcluster JKP, Dead links clear, YH
SHORE 0.8 Bioinformatics zcluster JKP clear, YH
sickle 1.200 Bioinformatics zcluster JKP clear, YH
SiZer 07022012 Bioinformatics zcluster JKP clear, YH
slclust 04282012 Bioinformatics zcluster JKP clear, YH
SNAP 2010-7-28 Bioinformatics zcluster JKP clear, YH
snow 0.3-8 Statistics zcluster
snowhite 1.1.4 Bioinformatics zcluster JKP clear, YH
snpEff 2_0_5d Bioinformatics zcluster JKP clear, YH 2/7 8:30 am YH
SOAPdenovo 1.05 Bioinformatics zcluster JKP clear, YH
SOAPdenovo-trans 1.01 Bioinformatics zcluster JKP clear, YH
SOAPdenovo2 r223 Bioinformatics zcluster JKP clear, YH
SomaticCall 42811 Bioinformatics zcluster JKP clear, YH
spimap 1.1 Bioinformatics zcluster JKP clear, YH
SpliceGrapher 0.2.0 Bioinformatics zcluster JKP clear, YH
SSAHA2 2.5.5 Bioinformatics zcluster JKP clear, YH
SSPACE 2.0 Bioinformatics zcluster JKP clear, YH
stacks 0.9993, 0.9996 Bioinformatics clear, YH
STEM 2.0 Bioinformatics zcluster JKP clear, YH
strauto 0.3.1 Bioinformatics zcluster JKP clear, YH
structure 2.3.3 Bioinformatics zcluster JKP clear, YH
SVDetect r0.7m Bioinformatics zcluster JKP ? clear, YH
SWIG 2.0.5 Utilities zcluster
T-Coffee 9.03.r1318 Bioinformatics zcluster JKP clear, YH
tabix 0.2.5 Bioinformatics zcluster JKP clear, YH
tagdust 1.12 Bioinformatics zcluster JKP ? clear, YH
tassel 4.0 Bioinformatics zcluster JKP clear, YH
tgicl 2.1 Bioinformatics zcluster JKP clear, YH
TIGER 1.02 Bioinformatics zcluster JKP clear, YH
tophat 2.0.5 Bioinformatics zcluster JKP clear, YH
Tracer v 1.5 Bioinformatics zcluster JKP clear, YH
Trinity r2012-10-05 Bioinformatics zcluster JKP clear, YH
UNAFold 3.8 Bioinformatics zcluster JKP ? clear, YH
usearch v6.0.30 Bioinformatics zcluster JKP clear, YH
vcftools 0.1.10 Bioinformatics zcluster Done, JKP clear, YH
velvet 1.2.01 Bioinformatics zcluster JKP clear, YH
VelvetOptimiser 2.2.4 Bioinformatics zcluster JKP clear, YH
ViennaRNA 1.8.5 Bioinformatics zcluster JKP clear, YH
vmatch 2.1.6 Bioinformatics zcluster JKP clear, YH
VMD 1.9.1 Chemistry zcluster
wigToBigWig v 4 Bioinformatics zcluster JKP clear, YH
WISE2 2.2.0 Bioinformatics zcluster JKP clear, YH
WU Blast 2.2.6 Bioinformatics zcluster JKP clear, YH
yasra 2.3 Bioinformatics zcluster JKP clear, YH
Zz-example 0.0 Bioinformatics zcluster example for bioinformatics YH
Zz-template 0.0 Bioinformatics zcluster Template for bioinformatics YH
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