NERSCPowering Scientific Discovery Since 1974

Software

NERSC/JGI Supported Software in Modules

NERSC is actively building a new tree of software for genepool accessible through the modules system.  For software not yet migrated into modules, please see the legacy /jgi/tools installations below.

PackageCategoryVersionModuleInstall DateDate Made Default
7zip applications/ general 9.20.1 7zip/9.20.1 2013-01-14 2013-01-14
ABYSS applications/ bioinformatics 1.3.2 Abyss/1.3.2 2012-04-03 2012-04-03
ABySS applications/ bioinformatics 1.3.4 ABySS/1.3.4 2012-11-26 2012-11-26
ABySS applications/ bioinformatics 1.3.6 ABySS/1.3.6 2014-05-06
ABySS applications/ bioinformatics 1.5.0 ABySS/1.5.0 2014-05-06
acml libraries/ math 5.1.0 acml/5.1.0 2012-07-07
ALE applications/ bioinformatics 20120918-2-g28da522 ALE/20120918-2-g28da522 2013-01-24 2013-01-24
ALE applications/ bioinformatics 20130717 ALE/20130717 2013-07-17 2013-07-17
ALLPATHS applications/ bioinformatics 34900 allpaths/34900 2012-04-03
ALLPATHS applications/ bioinformatics 35973 allpaths/35973 2012-04-03 2012-04-03
allpaths-lg applications/ bioinformatics 39750 allpaths-lg/39750 2012-09-24
allpaths-lg applications/ bioinformatics 42816 allpaths-lg/42816 2012-09-24 2012-09-24
allpaths-lg applications/ bioinformatics 44008 allpaths-lg/44008 2013-01-17 2013-01-17
allpaths-lg applications/ bioinformatics 44849 allpaths-lg/44849 2013-01-28 2013-02-22
allpaths-lg applications/ bioinformatics 46513 allpaths-lg/46513 2013-06-07
allpaths-lg applications/ bioinformatics 46652 allpaths-lg/46652 2013-06-12 2013-06-28
allpaths-lg applications/ bioinformatics 47710 allpaths-lg/47710 2013-10-22 2013-12-04
allpaths-lg applications/ bioinformatics 49403 allpaths-lg/49403 2014-04-10
AMOS applications/ bioinformatics 3.1.0 AMOS/3.1.0 2012-04-04 2012-04-04
amqpLogger applications/ programming 0.10 amqpLogger/0.10 2013-07-15 2013-07-15
amqpLogger applications/ programming 1.0 amqpLogger/1.0 2013-10-03 2013-10-11
ant applications/ programming 1.8.4 ant/1.8.4 2012-07-27 2012-07-27
ant applications/ programming 1.9.3 ant/1.9.3 2014-01-13
antismash applications/ bioinformatics 1.2 antismash/1.2 2012-10-31
antismash applications/ bioinformatics 2.0.2 antismash/2.0.2 2014-03-03
arb applications/ bioinformatics 5.3 arb/5.3 2012-07-23 2012-07-23
arb applications/ bioinformatics 5.5 arb/5.5 2013-04-25 2013-04-25
argtable pe_libraries/ general 2.13 argtable/2.13 2012-12-07 2012-12-07
atlas pe_libraries/ math 3.10.0 atlas/3.10.0 2012-07-18 2012-07-18
atsas applications/ bioinformatics 2.5.1-1 atsas/2.5.1-1 2013-04-25 2013-04-25
AUTOCONF applications/ programming 2.68 autoconf/2.68 2012-04-03 2012-04-03
autoconf applications/ programming 2.69 autoconf/2.69 2012-07-16 2012-07-16
AUTOMAKE applications/ programming 1.11.3 automake/1.11.3 2012-04-03 2012-04-03
automake applications/ programming 1.12 automake/1.12 2012-07-16 2012-07-16
BAMTOOLS applications/ bioinformatics 2.1.1 bamtools/2.1.1 2012-08-23 2012-08-23
BBMap applications/ bioinformatics v29 bbmap/v29 2013-10-30 2013-10-30
bbtools applications/ bioinformatics bb31.18 bbtools/bb31.18 2014-02-03
bbtools applications/ bioinformatics dev bbtools/dev 2013-11-14
bbtools applications/ bioinformatics prod bbtools/prod 2013-11-14 2013-11-14
BBTools applications/ bioinformatics v29 bbtools/v29 2013-10-30 2013-10-30
bcbb applications/ bioinformatics v0.6.0-62-gc460408 bcbb/v0.6.0-62-gc460408 2013-11-11 2013-11-11
bcl2fastq applications/ bioinformatics 1.8.4 bcl2fastq/1.8.4 2014-07-02
beagle applications/ bioinformatics 3.2.1 beagle/3.2.1 2013-07-16
beagle applications/ bioinformatics 4r1099 beagle/4r1099 2013-07-16 2013-07-16
beagle_utilities applications/ bioinformatics 05Feb13 beagle_utilities/05Feb13 2013-07-16 2013-07-16
bedtools applications/ bioinformatics 2.17.0 bedtools/2.17.0 2013-09-24 2013-09-24
bedtools applications/ bioinformatics 2.19.0 bedtools/2.19.0 2014-02-11
bio++ applications/ bioinformatics 20120823 biopp/20120823 2012-08-24 2013-06-28
Bio-SamTools applications/ general 1.38_0.1.19 perl-BioSamTools/1.38_0.1.19 2013-08-12 2013-08-12
biopython applications/ bioinformatics 1.60 biopython/1.60 2012-07-21 2012-07-21
biopython applications/ bioinformatics 1.61 biopython/1.61 2013-06-02 2013-06-18
biostudio applications/ bioinformatics 1.0 biostudio/1.0 2014-03-06
biotoolbox applications/ bioinformatics 20130305 biotools/20130305 2013-03-05 2013-03-05
biotoolbox applications/ bioinformatics 20130305 biotoolbox/20130305 2013-03-05 2013-03-05
bison applications/ general 3.0 bison/3.0 2013-11-01 2013-11-01
bittornado applications/ programming 0.3.18 bittornado/0.3.18 2012-08-14 2012-08-14
blat applications/ bioinformatics 3.4 blat/3.4 2012-08-01 2012-08-01
boost pe_libraries/ general 1.42.0 boost/1.42.0 2012-07-14
boost pe_libraries/ general 1.47.0 boost/1.47.0 2012-07-03
boost libraries/ general 1.47.0 boost_mpi/1.47.0 2012-08-24
boost pe_libraries/ general 1.50.0 boost/1.50.0 2012-07-02 2012-07-03
boost pe_libraries/ general 1.52.0 boost/1.52.0 2013-02-10
boost pe_libraries/ general 1.53.0 boost/1.53.0 2013-02-10
boost pe_libraries/ general 1.54.0 boost/1.54.0 2013-07-03
boost pe_libraries/ general 1.55.0 boost/1.55.0 2013-11-19
bowtie applications/ bioinformatics 0.12.8 bowtie/0.12.8 2012-07-25 2012-07-25
bowtie applications/ bioinformatics 0.12.9 bowtie/0.12.9 2013-02-19
bowtie2 applications/ bioinformatics 2.0.0-beta7 bowtie2/2.0.0-beta7 2012-07-25 2012-07-25
bowtie2 applications/ bioinformatics 2.0.2 bowtie2/2.0.2 2012-11-11 2012-11-11
bowtie2 applications/ bioinformatics 2.0.6 bowtie2/2.0.6 2013-02-19
breakdancer applications/ bioinformatics 1.1.2 breakdancer/1.1.2 2013-08-02 2013-08-02
BWA applications/ bioinformatics 0.5.9 BWA/0.5.9 2013-08-30
BWA applications/ bioinformatics 0.6.2 BWA/0.6.2 2012-07-31 2013-08-30
BWA applications/ bioinformatics 0.7.4 BWA/0.7.4 2013-07-08
BWA applications/ bioinformatics 0.7.5a bwa/0.7.5a 2014-01-31
BWA applications/ bioinformatics 0.7.6a bwa/0.7.6a 2014-01-31
cap3 applications/ bioinformatics 20080617 cap3/20080617 2012-12-19 2012-12-19
casava applications/ bioinformatics 1.8.2 casava/1.8.2 2013-08-28 2013-08-28
ccp4 applications/ bioinformatics 6.3.0 ccp4/6.3.0 2012-09-26 2012-09-26
cctools applications/ programming 3.5.1 cctools/3.5.1 2012-07-28 2012-07-28
cd-hit applications/ bioinformatics 4.6.1 cd-hit/4.6.1 2012-11-11 2012-11-11
cdbfasta applications/ bioinformatics 0.99 cdbfasta/0.99 2012-11-11 2012-11-11
CGAL libraries/ math 4.4 CGAL/4.4 2014-06-24 2014-06-24
ciftools applications/ bioinformatics 30032012 ciftools/30032012 2013-06-18 2013-06-18
circos applications/ bioinformatics 0.64 circos/0.64 2013-06-28 2013-06-28
clang applications/ programming 3.2 clang/3.2 2013-06-06 2013-06-06
clang 3 series Programming Environment meta-module applications/ programming 3.2 PrgEnv-clang/3.2 2013-06-06
clustal-omega applications/ bioinformatics 1.1.0 clustal-omega/1.1.0 2012-12-10 2012-12-10
CLUSTALO applications/ bioinformatics 1.0.3 clustalo/1.0.3 2012-04-04 2012-04-04
clustalw applications/ bioinformatics 2.1 clustalw/2.1 2012-12-10 2012-12-10
clustalx applications/ bioinformatics 2.1 clustalx/2.1 2012-12-10 2012-12-10
cmake applications/ programming 2.8.11 cmake/2.8.11 2013-06-02 2013-06-02
cmake applications/ programming 2.8.12.2 cmake/2.8.12.2 2014-01-28 2014-01-28
CMAKE applications/ programming 2.8.4 cmake/2.8.4 2012-04-03 2012-04-03
cmake applications/ programming 2.8.8 cmake/2.8.8 2012-07-11
cmake applications/ programming 2.8.9 cmake/2.8.9 2012-09-07 2014-01-28
cns applications/ bioinformatics 1.3 cns/1.3 2013-02-28 2013-02-28
CONSED applications/ bioinformatics 16.0 consed/16.0 2013-06-28
CONSED applications/ bioinformatics 17.0 consed/17.0 2013-06-28
CONSED applications/ bioinformatics 17.44 consed/17.44 2013-06-28
CONSED applications/ bioinformatics 18.00 consed/18.00 2013-06-28
CONSED applications/ bioinformatics 19.00 consed/19.00 2013-06-28
CONSED applications/ bioinformatics 19.47 consed/19.47 2013-06-28
CONSED applications/ bioinformatics 19.54 consed/19.54 2013-06-28
CONSED applications/ bioinformatics 20.00 consed/20.00 2013-06-28
CONSED applications/ bioinformatics 21.00 consed/21.00 2012-04-04 2012-04-04
CONSED applications/ bioinformatics 22.00 consed/22.00 2013-06-28
CONSED applications/ bioinformatics 22.01 consed/22.01 2013-06-28
CONSED applications/ bioinformatics 23.54 consed/23.54 2013-06-28
CONSED applications/ bioinformatics 23.79beta consed/23.79beta 2013-06-28
CONSED applications/ bioinformatics 23.90beta consed/23.90beta 2013-06-28 2013-06-28
CONSED applications/ bioinformatics 24.00 consed/24.00 2013-06-28
CONSED applications/ bioinformatics 25.0 consed/25.0 2014-06-11
convey applications/ bioinformatics current convey/current 2013-05-24 2013-10-01
convey applications/ bioinformatics prod convey/prod 2013-10-01
convey-hc2 applications/ bioinformatics current convey-hc2/current 2013-05-24
crass applications/ bioinformatics 0.1.8 crisprtools/0.1.8 2014-01-22 2014-01-22
crass applications/ bioinformatics v0.3.7 crass/v0.3.7 2013-12-18 2013-12-18
ctemplate pe_libraries/ general 1.0 ctemplate/1.0 2013-07-02
ctemplate pe_libraries/ general 2.2 ctemplate/2.2 2013-07-02 2013-07-02
cufflinks applications/ bioinformatics 2.0.1 cufflinks/2.0.1 2012-07-03
cufflinks applications/ bioinformatics 2.0.2 cufflinks/2.0.2 2012-07-16 2012-07-16
cufflinks applications/ bioinformatics 2.1.1 cufflinks/2.1.1 2013-05-01
cufflinks applications/ bioinformatics 2.1.1_1 cufflinks/2.1.1_1 2013-08-30
cufflinks applications/ bioinformatics 2.2.1 cufflinks/2.2.1 2014-05-16
CURL applications/ general 7.19.7 curl/7.19.7 2012-04-03 2012-04-03
curl applications/ programming 7.26.0 curl/7.26.0 2012-07-07 2012-09-23
cutadapt applications/ bioinformatics 1.1 cutadapt/1.1 2012-09-12 2013-09-09
cvsps applications/ programming 2.1 cvsps/2.1 2012-10-22
Cytoscape applications/ bioinformatics 2.8.3 cytoscape/2.8.3 2012-11-11 2012-11-11
dadi applications/ bioinformatics 1.6.3 dadi/1.6.3 2012-11-08 2012-11-08
DBD::mysql applications/ general 4.023 perl-dbdmysql/4.023 2013-06-03 2013-06-03
decypher applications/ bioinformatics 8.0.4 decypher/8.0.4 2012-04-04
decypher applications/ bioinformatics 8.5.1.11 decypher/8.5.1.11 2012-04-04 2012-04-04
decypher applications/ bioinformatics 8.7.0 decypher/8.7.0 2013-07-08 2013-07-08
decypher applications/ bioinformatics 9.0.0.65 decypher/9.0.0.65 2013-10-30
DIALIGN-TX applications/ bioinformatics 1.0.2 dialign-tx/1.0.2 2013-07-02 2013-07-02
disovar applications/ bioinformatics 46339 discovar/46339 2013-05-12 2013-05-12
disovar applications/ bioinformatics 46367 discovar/46367 2013-05-14 2013-05-14
disovar applications/ bioinformatics 46449 discovar/46449 2013-05-22 2013-05-22
disovar applications/ bioinformatics 47449 discovar/47449 2013-09-03 2013-10-22
disovar applications/ bioinformatics 47682 discovar/47682 2013-10-09
DMTCP libraries/ general 1.2.4 dmtcp/1.2.4 2012-07-15
DMTCP libraries/ general 1.2.5 dmtcp/1.2.5 2012-07-15 2012-07-15
DMTCP libraries/ general 1.2.7 dmtcp/1.2.7 2013-06-19
duk applications/ bioinformatics 1.05 duk/1.05 2013-08-06 2013-08-06
DustMasker applications/ bioinformatics 1.0 DustMasker/1.0 2013-09-04 2013-09-04
ea-utils applications/ bioinformatics 1.1.2-537 ea-utils/1.1.2-537 2013-04-08 2013-04-08
EAGLEVIEW applications/ bioinformatics 2.1 eagleview/2.1 2012-04-03 2012-04-03
ecj applications/ general 4.3.1 ecj/4.3.1 2013-11-04 2013-11-04
eigen libraries/ general 3.1.0 eigen/3.1.0 2012-07-03
eigensoft applications/ bioinformatics 4.2 eigensoft/4.2 2013-03-05 2013-03-05
EMACS applications/ programming 23.2 emacs/23.2 2012-04-03 2012-04-03
EMBOSS applications/ bioinformatics 6.4.0 EMBOSS/6.4.0 2012-04-04 2012-09-04
EMBOSS applications/ bioinformatics devel_20120828 EMBOSS/devel_20120828 2012-09-04
emirge applications/ bioinformatics 0.60 emirge/0.60 2013-07-29
emirge applications/ bioinformatics 20130614 emirge/20130614 2013-06-14
emirge applications/ bioinformatics 20131014 emirge/20131014 2013-10-14
erange applications/ bioinformatics 4.0a erange/4.0a 2014-01-27 2014-01-27
erlang-OTP applications/ programming R15B01 erlang-OTP/R15B01 2012-07-28 2012-07-28
esom applications/ bioinformatics 1.1 esom/1.1 2013-10-01 2013-10-01
ESTmapper applications/ bioinformatics 1919 sim4db/1919 2013-10-03 2013-10-03
ESTmapper applications/ bioinformatics 1969 estmapper/1969 2013-10-03 2013-10-03
ESTmapper applications/ bioinformatics 1969 sim4db/1969 2013-10-03
ExaML applications/ bioinformatics 20130412 ExaML/20130412 2013-04-12 2013-04-12
ExaML applications/ bioinformatics git ExaML/git 2012-10-12 2012-10-12
exonerate applications/ bioinformatics 2.2.0 exonerate/2.2.0 2012-10-22 2013-09-04
fastbit applications/ bioinformatics 1.3.1 fastbit/1.3.1 2012-08-17
fastbit applications/ bioinformatics 1.3.2 fastbit/1.3.2 2012-09-05 2012-11-16
fastbit applications/ bioinformatics 1.3.4 fastbit/1.3.4 2012-11-16 2012-11-26
fastbit applications/ bioinformatics 1.3.6 fastbit/1.3.6 2013-03-28 2013-04-08
FastQC applications/ bioinformatics 0.10.1 fastqc/0.10.1 2012-08-02 2012-08-02
fasttree applications/ bioinformatics 2.1.5 fasttree/2.1.5 2012-11-11 2012-11-11
FASTX applications/ bioinformatics 0.0.13.2 fastx/0.0.13.2 2013-07-23 2013-07-23
fftw pe_libraries/ math 3.3.3 fftw/3.3.3 2013-09-12 2013-09-12
Firefox applications/ general 13.0.1 firefox/13.0.1 2012-07-13 2012-08-15
Firefox applications/ general 14.0.1_32bit firefox/14.0.1_32bit 2012-08-22
Firefox applications/ general 14.0.1_64bit firefox/14.0.1_64bit 2012-08-22 2012-08-22
Firefox applications/ general 17.0_32bit firefox/17.0_32bit 2012-11-27
Firefox applications/ general 17.0_64bit firefox/17.0_64bit 2012-11-27 2012-11-27
Firefox applications/ general 19.0.2_32bit firefox/19.0.2_32bit 2013-03-20
Firefox applications/ general 19.0.2_64bit firefox/19.0.2_64bit 2013-03-20 2013-03-20
Firefox applications/ general 19.0_32bit firefox/19.0_32bit 2013-02-19
Firefox applications/ general 19.0_64bit firefox/19.0_64bit 2013-02-19 2013-02-19
Firefox applications/ general 22.0_32bit firefox/22.0_32bit 2013-06-28 2013-06-28
Firefox applications/ general 22.0_64bit firefox/22.0_64bit 2013-06-28
Firefox applications/ general 23.0_32bit firefox/23.0_32bit 2013-08-08 2013-08-08
Firefox applications/ general 23.0_64bit firefox/23.0_64bit 2013-08-08
Firefox applications/ general 24.0_32bit firefox/24.0_32bit 2013-10-18
Firefox applications/ general 24.0_64bit firefox/24.0_64bit 2013-10-18
Firefox applications/ general 26.0_32bit firefox/26.0_32bit 2013-12-12
Firefox applications/ general 26.0_64bit firefox/26.0_64bit 2013-12-12 2013-12-12
Firefox applications/ general 27.0.1_32bit firefox/27.0.1_32bit 2014-02-20
Firefox applications/ general 27.0.1_64bit firefox/27.0.1_64bit 2014-02-20 2014-02-20
flash applications/ bioinformatics 1.0.2 flash/1.0.2 2012-09-11
flash applications/ bioinformatics 1.0.3 flash/1.0.3 2012-09-04 2012-09-04
flash applications/ bioinformatics 1.2.6 flash/1.2.6 2013-06-12
flex applications/ general 2.5.37 flex/2.5.37 2013-07-02
fltk libraries/ general 1.3.2 fltk/1.3.2 2013-10-16
gaemr applications/ bioinformatics 1.0.1 gaemr/1.0.1 2013-03-04 2013-03-04
gam-ngs applications/ bioinformatics 20130603 gam-ngs/20130603 2013-06-03 2013-06-03
Garli applications/ bioinformatics 2.0 garli/2.0 2012-10-15
GATK applications/ bioinformatics 2.2-16 GATK/2.2-16 2012-12-10 2012-12-10
GATK applications/ bioinformatics 2.5-2 GATK/2.5-2 2013-06-17
GATK applications/ bioinformatics 2.6-3 GATK/2.6-3 2013-06-24
GATK applications/ bioinformatics 2.6-5 GATK/2.6-5 2013-08-02
GATK applications/ bioinformatics 2.7-2 GATK/2.7-2 2013-09-09
GATK applications/ bioinformatics 2.8-1 GATK/2.8-1 2014-01-07
GATK applications/ bioinformatics 3.1-1 GATK/3.1-1 2014-04-16
GATKQueue applications/ bioinformatics 2.6-4 GATKQueue/2.6-4 2013-07-08 2013-07-08
Gblocks applications/ bioinformatics 0.91b Gblocks/0.91b 2013-06-12 2013-06-12
GBS applications/ bioinformatics 20130905_gpint06 gbs/20130905_gpint06 2013-09-06
gcc applications/ programming 2013.1.117 intel/2013.1.117 2013-06-13 2013-06-13
gcc applications/ programming 4.6.3 gcc/4.6.3 2012-06-17 2012-07-15
gcc applications/ programming 4.7.1 gcc/4.7.1 2012-07-10 2012-07-10
gcc applications/ programming 4.7.2 gcc/4.7.2 2013-03-20
gcc applications/ programming 4.7.3 gcc/4.7.3 2013-04-25
gcc applications/ programming 4.8.0 gcc/4.8.0 2013-04-25
gcc applications/ programming 4.8.1 gcc/4.8.1 2013-06-02
gcc 4.6 series Programming Environment meta-module applications/ programming 4.6 PrgEnv-gnu/4.6 2013-06-02 2013-06-02
gcc 4.7 series Programming Environment meta-module applications/ programming 4.7 PrgEnv-gnu/4.7 2013-06-02
gcc 4.8 series Programming Environment meta-module applications/ programming 4.8 PrgEnv-gnu/4.8 2013-06-02
gdb applications/ programming 7.5 gdb/7.5 2012-09-23 2012-09-23
gdb applications/ programming 7.6 gdb/7.6 2014-05-05
gdb applications/ programming 7.7 gdb/7.7 2014-05-05
genometools applications/ bioinformatics 1.5.1 genometools/1.5.1 2014-02-11 2014-02-11
genome_assembly_group applications/ bioinformatics 1.0 gaag/1.0 2012-12-19 2012-12-19
genome_assembly_group applications/ bioinformatics 1.0 genedesign/1.0 2012-12-19 2012-12-19
genome_assembly_group applications/ bioinformatics 1.0 qaqc/1.0 2013-07-08 2013-07-08
GHC compilers/ programming 7.0.3 ghc/7.0.3 2012-04-03 2012-04-03
ghc applications/ programming 7.6.1 ghc/7.6.1 2012-11-09 2012-11-09
git applications/ programming 1.7.12 git/1.7.12 2012-07-28 2012-07-28
GIT applications/ programming 1.7.7.3 git/1.7.7.3 2012-03-27
GIT applications/ programming 1.7.9.5 git/1.7.9.5 2012-03-27 2012-03-27
git applications/ programming 1.8.3.1 git/1.8.3.1 2013-06-14
git applications/ programming 2.0.0 git/2.0.0 2014-06-24
glib applications/ programming 2.24.2 glib/2.24.2 2012-07-18 2012-07-18
glimmer applications/ bioinformatics 3.0.2 glimmerhmm/3.0.2 2014-03-03 2014-03-03
glimmer applications/ bioinformatics 3.02 glimmer/3.02 2012-08-09 2012-08-09
GLPK applications/ general 4.52.1 glpk/4.52.1 2013-10-17 2013-10-17
GMAP applications/ bioinformatics 2013-02-15 gmap/2013-02-15 2013-02-26 2013-02-26
GMAP applications/ bioinformatics 2013-02-15_1 gmap/2013-02-15_1 2013-12-19 2013-12-19
GMAP applications/ bioinformatics 2013-09-11 gmap/2013-09-11 2013-09-12
GMAP applications/ bioinformatics 2013-11-27 gmap/2013-11-27 2013-12-19
GMAP applications/ bioinformatics 2014-06-10 gmap/2014-06-10 2014-06-17
GNU Scientific Library pe_libraries/ math 1.15 gsl/1.15 2012-07-30 2012-08-08
GNUPLOT applications/ general 4.2.2 gnuplot/4.2.2 2013-07-16
GNUPLOT applications/ general 4.6.1 gnuplot/4.6.1 2012-12-14 2013-01-23
GNUPLOT applications/ general 4.6.2 gnuplot/4.6.2 2013-03-21 2013-03-21
googletest pe_libraries/ general 1.6.0 googletest/1.6.0 2013-08-10 2013-08-10
GRAPHVIZ applications/ general 2.26.3 graphviz/2.26.3 2012-04-03 2012-04-03
graphviz applications/ programming 2.30.1 graphviz/2.30.1 2013-07-28 2013-07-28
GTK+ libraries/ programming 2.24.11 gtk/2.24.11 2012-08-08 2012-08-08
gts pe_libraries/ programming 0.7.6 gts/0.7.6 2013-10-11 2013-10-11
HASKELL applications/ programming 2011.2.0.1 haskell/2011.2.0.1 2012-04-03 2012-04-03
hbar-dtk applications/ bioinformatics 20130329 hbar-dtk/20130329 2013-03-29 2013-03-29
hbar-dtk applications/ bioinformatics 20130417 hbar-dtk/20130417 2013-04-17 2013-04-17
hdf5 pe_libraries/ general 1.8.10-patch1 hdf5/1.8.10-patch1 2013-03-28 2013-04-08
hdf5 pe_libraries/ general 1.8.11 hdf5/1.8.11 2013-06-11
hdf5 pe_libraries/ general 1.8.12 hdf5/1.8.12 2014-01-14
hdf5 pe_libraries/ general 1.8.4-patch1 hdf5/1.8.4-patch1 2013-04-17
HDF5 applications/ bioinformatics 1.8.7 hdf5/1.8.7 2012-04-04 2012-04-04
hdf5 pe_libraries/ general 1.8.9 hdf5/1.8.9 2012-07-19 2012-07-19
hdf5 libraries/ general 4.10.2 rpm/4.10.2 2013-01-24 2013-01-24
hdf5-parallel pe_libraries/ general 1.8.11 hdf5-parallel/1.8.11 2014-02-04
hdf5-parallel pe_libraries/ general 1.8.12 hdf5-parallel/1.8.12 2014-02-04 2014-02-04
HGAp applications/ bioinformatics 0.1.0_2 HGAp/0.1.0_2 2013-01-11 2013-01-11
HGAp applications/ bioinformatics 0.1.0_3 HGAp/0.1.0_3 2013-01-18 2013-01-18
HMMER applications/ bioinformatics 3.0 hmmer/3.0 2012-03-19 2012-03-19
HMMER applications/ bioinformatics 3.0_mpi hmmer/3.0_mpi 2012-10-15
HMMER applications/ bioinformatics 3.1b1 hmmer/3.1b1 2013-06-24
HMMER applications/ bioinformatics 3.1b1_mpi hmmer/3.1b1_mpi 2014-01-08
htop applications/ general 1.0.1 htop/1.0.1 2012-07-20 2012-07-20
hwloc applications/ general 1.8 hwloc/1.8 2013-11-25 2013-11-25
idba_ud applications/ bioinformatics 1.0.9 idba_ud/1.0.9 2012-12-14 2012-12-14
idba_ud applications/ bioinformatics 1.1.0 idba/1.1.0 2013-09-18
idba_ud applications/ bioinformatics 1.1.1 idba/1.1.1 2013-09-18 2013-09-18
IGV - Integrative Genomics Viewer applications/ bioinformatics 2.2.8 igv/2.2.8 2013-03-15 2013-03-15
IGV - Integrative Genomics Viewer applications/ bioinformatics 2.3.25 igv/2.3.25 2014-01-13
Illumina Off-Line Basecaller applications/ bioinformatics 1.9.4 olb/1.9.4 2013-09-09 2013-09-09
ImageMagick libraries/ programming 6.8.0-10 ImageMagick/6.8.0-10 2012-12-18 2012-12-18
infernal applications/ bioinformatics 1.1rc1 infernal/1.1rc1 2012-08-13 2012-08-13
intel 13 series Programming Environment meta-module applications/ programming 13 PrgEnv-intel/13 2013-06-13 2013-06-13
IPERF applications/ general 2.0.5 iperf/2.0.5 2012-04-03 2012-04-03
isolasso applications/ bioinformatics 2.6.1 isolasso/2.6.1 2014-06-24 2014-06-24
itagqc applications/ bioinformatics dev itagqc/dev 2013-11-25 2013-11-25
itagqc applications/ bioinformatics prod itagqc/prod 2014-03-06 2014-03-06
JAMO - JGI Archive Metadata Organizer applications/ general dev jamo/dev 2013-11-19
JAMO - JGI Archive Metadata Organizer applications/ general prod jamo/prod 2013-09-12 2013-09-12
jazz_trim applications/ bioinformatics 20080206 jazz_trim/20080206 2013-10-23 2013-10-23
JDK applications/ programming 1.6.0_26 jdk/1.6.0_26 2012-04-03
JDK applications/ programming 1.7.0_02 jdk/1.7.0_02 2012-04-03 2012-04-03
jellyfish applications/ bioinformatics 1.1.10 jellyfish/1.1.10 2013-04-19
jellyfish applications/ bioinformatics 1.1.5 jellyfish/1.1.5 2012-08-09 2012-08-09
jellyfish applications/ bioinformatics 1.2.8 amplicon/1.2.8 2013-04-25 2013-04-25
jgi-auto-qc applications/ bioinformatics dev auto-qc/dev 2014-05-15
jgi-auto-qc applications/ bioinformatics prod auto-qc/prod 2014-05-15 2014-05-15
jgi-database-contamination applications/ bioinformatics prod db-contamination/prod 2014-05-19 2014-05-19
jgi-fastq-metrics applications/ bioinformatics dev fastq-metrics/dev 2014-05-08
jgi-fastq-metrics applications/ bioinformatics prod fastq-metrics/prod 2014-05-08 2014-05-08
jgi-gaag applications/ bioinformatics dev gaag/dev 2014-07-14
jgi-gaag applications/ bioinformatics prod gaag/prod 2014-07-14 2014-07-14
jgi-library-metrics applications/ bioinformatics dev library-metrics/dev 2014-05-07 2014-05-07
jgi-library-metrics applications/ bioinformatics prod library-metrics/prod 2014-05-16 2014-05-16
jgi-perl-packages applications/ bioinformatics 1.0 jgi-perl-packages/1.0 2012-10-15
jgi-perl-packages applications/ bioinformatics 1.1 jgi-perl-packages/1.1 2012-11-14 2012-11-14
jgi-python-packages applications/ bioinformatics 1.0 jgi-python-packages/1.0 2012-08-30 2012-08-30
jgi-qaqc applications/ bioinformatics dev qaqc/dev 2013-12-03
jgi-qaqc applications/ bioinformatics prod qaqc/prod 2013-12-03 2014-01-14
JGIBIO applications/ bioinformatics dev jgibio/dev 2013-02-05
JGIBIO applications/ bioinformatics prod jgibio/prod 2013-02-05 2013-02-05
JGIsynbio applications/ bioinformatics 1.0 jgisynbio/1.0 2013-07-31 2013-07-31
JGITOOLS applications/ bioinformatics 1.2.0 jgitools/1.2.0 2013-07-10
JGI_iTagger applications/ bioinformatics 1.0 itagger/1.0 2013-10-15
JGI_iTagger applications/ bioinformatics 1.1 itagger/1.1 2014-05-16
JGI_iTagger applications/ bioinformatics dev itagger/dev 2013-10-15 2013-10-15
jigsaw applications/ bioinformatics 2.3.2 jigsaw/2.3.2 2014-02-24 2014-04-22
julia applications/ programming v0.2.1 julia/v0.2.1 2014-05-31 2014-05-31
kcachegrind applications/ programming 0.7.1 kcachegrind/0.7.1 2012-09-28 2012-09-28
khmer applications/ bioinformatics 20130504 khmer/20130504 2013-05-04 2013-05-04
kmernator applications/ bioinformatics dev kmernator/dev 2013-06-14
kmernator applications/ bioinformatics prod kmernator/prod 2013-06-14 2013-06-14
kraken applications/ bioinformatics 0.10.4-beta kraken/0.10.4-beta 2014-07-08 2014-07-08
lapinpy applications/ bioinformatics dev lapinpy/dev 2013-12-05
lapinpy applications/ bioinformatics prod lapinpy/prod 2013-12-04 2013-12-04
libcrispr pe_libraries/ general 1.0.1 libcrispr/1.0.1 2013-12-18 2013-12-18
libgmp libraries/ math 5.0.5 gmp/5.0.5 2012-06-17
libhmsbeagle libraries/ bioinformatics 1.0 libhmsbeagle/1.0 2012-06-10 2013-04-08
libmpc libraries/ math 0.9 mpc/0.9 2012-06-17
libmpfr libraries/ math 3.1.0 mpfr/3.1.0 2012-06-17
libsigc++ applications/ programming 2.2.10 libsigc++/2.2.10 2012-07-20 2012-07-20
libtool applications/ programming 2.4.2 libtool/2.4.2 2012-04-03 2012-08-11
libzip pe_libraries/ programming 0.10.1 libzip/0.10.1 2012-07-20 2012-07-20
libzip applications/ programming 04252013 liblam/04252013 2013-04-25 2013-04-25
libzip1 pe_libraries/ programming 0.9.3 libzip1/0.9.3 2013-07-02 2013-07-02
lua applications/ general 5.1.5 lua/5.1.5 2013-04-25
lua applications/ general 5.2.1 lua/5.2.1 2012-08-08 2012-08-08
LUCY applications/ bioinformatics 1.19p lucy/1.19p 2012-04-04 2012-04-04
LUCY applications/ bioinformatics 1.20p lucy/1.20p 2013-07-02 2013-07-02
lzo2 libraries/ general 2.06 lzo2/2.06 2013-03-22 2013-03-22
m4 applications/ programming 1.4.16 m4/1.4.16 2012-07-16 2012-07-16
macs applications/ bioinformatics 1.4.2-1 macs/1.4.2-1 2013-06-24 2013-06-24
MAFFT applications/ bioinformatics 7.047 MAFFT/7.047 2013-06-28 2013-06-28
MAFFT applications/ bioinformatics 7.047_1 MAFFT/7.047_1 2013-12-16
maq applications/ bioinformatics 0.7.1 maq/0.7.1 2014-03-11 2014-03-11
MaSuRCA applications/ bioinformatics 2.0.0 MaSuRCA/2.0.0 2013-06-04 2013-06-04
maven applications/ programming 2.0.11 maven/2.0.11 2014-01-13
maven applications/ programming 2.2.1 maven/2.2.1 2014-01-13
maven applications/ programming 3.0.4 maven/3.0.4 2012-07-27 2012-07-27
maven applications/ programming 3.0.5 maven/3.0.5 2014-01-13
maven applications/ programming 3.1.1 maven/3.1.1 2014-01-13
mcl applications/ bioinformatics 12-135 mcl/12-135 2013-09-13 2013-09-13
mdasim applications/ bioinformatics 1.2 mdasim/1.2 2014-06-26
MEGAN applications/ bioinformatics 3.9 MEGAN/3.9 2013-11-04
MEGAN applications/ bioinformatics 4.69.4 MEGAN/4.69.4 2013-11-04
MEGAN applications/ bioinformatics 4.70.4 MEGAN/4.70.4 2013-11-04 2013-11-04
MEGAN applications/ bioinformatics 5.0.80_beta MEGAN/5.0.80_beta 2013-11-04
meraculous applications/ bioinformatics 2.0.2 meraculous/2.0.2 2014-07-10 2014-07-10
meraculous applications/ bioinformatics dev meraculous/dev 2014-05-07 2014-05-07
mercurial applications/ programming 2.2.3 mercurial/2.2.3 2012-07-16 2012-07-16
mercurial applications/ programming 2.6.2 mercurial/2.6.2 2013-06-19 2013-06-19
MetaBAT applications/ bioinformatics dev metabat/dev 2013-12-19 2013-12-19
MetaCluster applications/ bioinformatics 3.0 MetaCluster/3.0 2013-07-29
MetaCluster applications/ bioinformatics 4.0.8 MetaCluster/4.0.8 2013-07-29
MetaCluster applications/ bioinformatics 5.0 MetaCluster/5.0 2013-07-29 2013-07-29
MetaCluster applications/ bioinformatics TA MetaCluster/TA 2013-07-29
METAPHYLER applications/ bioinformatics 1.13 MetaPhyler/1.13 2012-04-04 2012-04-04
metawatt applications/ bioinformatics 1.7 metawatt/1.7 2014-01-17 2014-01-17
mira applications/ bioinformatics 3.4.1.1 mira/3.4.1.1 2013-10-22 2013-10-22
mkl libraries/ general 2013.1.117 mkl/2013.1.117 2013-06-13 2013-06-13
mongodb applications/ general 2.4.4 mongodb/2.4.4 2013-06-26 2013-06-26
MOSAIK applications/ bioinformatics 2.1.78 MOSAIK/2.1.78 2013-06-28 2013-06-28
mothur applications/ bioinformatics 1.26.0 mothur/1.26.0 2012-08-02 2012-08-02
mpptest applications/ services 1.5 mpptest/1.5 2013-01-26 2013-01-26
MrBayes applications/ bioinformatics 3.2.1 MrBayes/3.2.1 2012-06-10
multitail applications/ general 5.2.12 multitail/5.2.12 2013-04-09 2013-04-09
MUMmer applications/ bioinformatics 3.23 mummer/3.23 2012-08-02 2012-08-02
muscle applications/ bioinformatics 3.8.31 muscle/3.8.31 2012-07-31 2012-07-31
mysql applications/ services 5.0.96 mysql/5.0.96 2012-07-30 2012-07-30
mysql applications/ services 5.0.96_1 mysql/5.0.96_1 2013-12-06 2013-12-17
mysql applications/ services 5.1.69 mysql/5.1.69 2013-06-03
mysql applications/ services 5.5.25a mysql/5.5.25a 2012-07-30
mysql-workbench applications/ general 5.2.47 mysql-workbench/5.2.47 2013-07-02 2013-07-02
NCBI BLAST applications/ bioinformatics 2.2.26 blast/2.2.26 2012-11-11 2012-11-11
NCBI BLAST+ applications/ bioinformatics 2.2.26 blast+/2.2.26 2012-12-18 2012-12-18
NCBI BLAST+ applications/ bioinformatics 2.2.26_1 blast+/2.2.26_1 2013-05-20 2013-09-26
NCBI BLAST+ applications/ bioinformatics 2.2.27 blast+/2.2.27 2012-12-18
NCBI BLAST+ applications/ bioinformatics 2.2.27_1 blast+/2.2.27_1 2013-05-20
NCBI BLAST+ applications/ bioinformatics 2.2.28 blast+/2.2.28 2013-05-20 2014-01-07
NCBI BLAST+ applications/ bioinformatics 2.2.29 blast+/2.2.29 2014-05-19
NCBI SRA Toolkit applications/ bioinformatics 2.1.16 ncbi-sra-toolkit/2.1.16 2012-10-22
neon pe_libraries/ programming 0.29.6 neon/0.29.6 2012-11-08 2012-11-08
netlib-lapack libraries/ math 3.4.1 netlib-lapack/3.4.1 2012-07-18 2012-07-18
networkx applications/ bioinformatics 1.1 py_networkx/1.1 2014-06-11 2014-06-11
networkx applications/ bioinformatics 1.9rc1 py_networkx/1.9rc1 2014-06-11
newbler applications/ bioinformatics 2.5.3 newbler/2.5.3 2013-05-01
newbler applications/ bioinformatics 2.5.3-01-25-2011-threads newbler/2.5.3-01-25-2011-threads 2013-05-01
newbler applications/ bioinformatics 2.5p1 newbler/2.5p1 2013-05-01
newbler applications/ bioinformatics 2.6 newbler/2.6 2013-05-01
newbler applications/ bioinformatics 2.7 newbler/2.7 2013-05-01
newbler applications/ bioinformatics 2.8 newbler/2.8 2013-05-01 2013-05-01
NOVOCRAFT applications/ bioinformatics 1.05.01 novocraft/1.05.01 2012-04-04 2013-10-22
NOVOCRAFT applications/ bioinformatics 2.08.01 novocraft/2.08.01 2013-10-22
OASES applications/ bioinformatics 0.2.05 Oases/0.2.05 2012-04-04 2012-04-04
oases applications/ bioinformatics 0.2.08 oases/0.2.08 2012-08-01 2012-08-01
OCTAVE applications/ programming 2.9.17 octave/2.9.17 2012-04-04 2012-04-04
octave applications/ general 3.6.4 octave/3.6.4 2013-10-17 2013-10-17
OFED libraries/ programming 1.5.3-3.1.0-Mellanox OFED/1.5.3-3.1.0-Mellanox 2013-01-24 2013-01-24
OFED libraries/ programming 2.0-2.0.5-Mellanox OFED/2.0-2.0.5-Mellanox 2013-08-20 2013-08-20
OFED libraries/ programming 2.0-3.0.0-Mellanox OFED/2.0-3.0.0-Mellanox 2013-11-15 2013-11-15
OFED libraries/ programming 2.1-1.0.0-Mellanox OFED/2.1-1.0.0-Mellanox 2014-07-22
Open MPI libraries/ programming 1.4.5 openmpi-gcc/1.4.5 2012-06-09 2012-06-09
Open MPI libraries/ programming 1.6 openmpi-gcc/1.6 2012-06-09
Open MPI pe_libraries/ programming 1.6.3 openmpi/1.6.3 2012-11-19 2013-02-13
Open MPI pe_libraries/ programming 1.6.4 openmpi/1.6.4 2013-03-28 2013-06-18
Open MPI pe_libraries/ programming 1.6.5 openmpi/1.6.5 2013-08-20
Open MPI pe_libraries/ programming 1.8.1 openmpi/1.8.1 2014-07-23
OracleJDK applications/ programming 1.6_32bit oracle-jdk/1.6_32bit 2013-06-02
OracleJDK applications/ programming 1.6_64bit oracle-jdk/1.6_64bit 2013-06-02
OracleJDK applications/ programming 1.7_32bit oracle-jdk/1.7_32bit 2013-06-02
OracleJDK applications/ programming 1.7_64bit oracle-jdk/1.7_64bit 2013-06-02
oracle_client applications/ general 11.2.0.3.0 oracle_client/11.2.0.3.0 2012-10-29 2012-10-29
oracle_server applications/ general 11.2.0.1 oracle_server/11.2.0.1 2013-10-04 2013-10-04
PacBio BLASR applications/ bioinformatics 20131205 blasr/20131205 2014-01-14 2014-01-14
PacBio BLASR applications/ bioinformatics 20140325 blasr/20140325 2014-05-22
PacBioPython applications/ bioinformatics 20120918 PacBioPython/20120918 2012-09-18 2012-11-30
PacBioPython applications/ bioinformatics 20121130 PacBioPython/20121130 2012-11-30 2012-11-30
PacBioPython applications/ bioinformatics 20121130_1 PacBioPython/20121130_1 2013-01-11 2013-01-11
PacBioPython applications/ bioinformatics 20130124 PacBioPython/20130124 2013-01-24 2013-01-28
PacBioSMRTAnalysis applications/ bioinformatics 1.3.3 smrtanalysis/1.3.3 2013-01-09 2013-01-09
PacBioSMRTAnalysis applications/ bioinformatics 1.3.3nopy smrtanalysis/1.3.3nopy 2013-04-17
PacBioSMRTAnalysis applications/ bioinformatics 1.3.3syspy smrtanalysis/1.3.3syspy 2013-04-17
PacBioSMRTAnalysis applications/ bioinformatics 1.4.0 smrtanalysis/1.4.0 2013-03-21
PacBioSMRTAnalysis applications/ bioinformatics 1.4.0nopy smrtanalysis/1.4.0nopy 2013-04-17
PacBioSMRTAnalysis applications/ bioinformatics 1.4.0syspy smrtanalysis/1.4.0syspy 2013-04-17
PacBioSMRTAnalysis applications/ bioinformatics 2.0.0 smrtanalysis/2.0.0 2013-04-17
PacBioSMRTAnalysis applications/ bioinformatics 2.0.0nopy smrtanalysis/2.0.0nopy 2013-04-17
PacBioSMRTAnalysis applications/ bioinformatics 2.0.0syspy smrtanalysis/2.0.0syspy 2013-04-17
PacBioSMRTAnalysis applications/ bioinformatics 2.0.1 smrtanalysis/2.0.1 2013-07-02 2013-09-03
PacBioSMRTAnalysis applications/ bioinformatics 2.0.1nopy smrtanalysis/2.0.1nopy 2013-07-02
PacBioSMRTAnalysis applications/ bioinformatics 2.0.1syspy smrtanalysis/2.0.1syspy 2013-07-02
PacBioSMRTAnalysis applications/ bioinformatics 2.1.1 smrtanalysis/2.1.1 2013-12-19
PacBioSMRTAnalysis applications/ bioinformatics 2.1.1nopy smrtanalysis/2.1.1nopy 2013-12-19
PacBioSMRTAnalysis applications/ bioinformatics 2.2.0 smrtanalysis/2.2.0 2014-06-11
PAML applications/ bioinformatics 4.7 paml/4.7 2013-10-07 2013-10-07
pandaseq applications/ bioinformatics 2.5 pandaseq/2.5 2013-09-24 2013-09-24
parallel applications/ programming 20130422 parallel/20130422 2013-04-27 2013-04-27
parsimonator applications/ bioinformatics 1.0.2 parsimonator/1.0.2 2012-10-13 2012-10-13
PASA applications/ bioinformatics r2012-06-25 pasa/r2012-06-25 2012-08-02 2012-08-02
pb-jelly applications/ bioinformatics 12.9.14 pbjelly/12.9.14 2012-11-27
pb-jelly applications/ bioinformatics 14.1.14 pbjelly/14.1.14 2014-05-09 2014-06-24
pBWA applications/ bioinformatics 0.5.9-1.21009 pBWA/0.5.9-1.21009 2012-12-14 2012-12-14
pBWA applications/ bioinformatics alternate-v2 pBWA/alternate-v2 2012-07-31 2012-07-31
PCRE: Perl Compatible Regular Expressions libraries/ general 8.32 pcre/8.32 2013-03-22 2013-03-22
pear applications/ bioinformatics 0.9.0 pear/0.9.0 2014-06-04 2014-06-04
perl applications/ programming 5.10.1 perl/5.10.1 2012-04-12 2012-04-12
perl applications/ programming 5.16.0 jgiperl/5.16.0 2012-11-17
perl applications/ programming 5.16.0 perl/5.16.0 2012-11-16 2012-11-17
PGADMIN3 applications/ general 1.14.0 pgadmin3/1.14.0 2012-04-03 2012-04-03
phenix applications/ bioinformatics 1.8.1-1168 phenix/1.8.1-1168 2012-11-19 2012-11-19
phenix applications/ bioinformatics 1.8.2-1309 phenix/1.8.2-1309 2013-05-02
PHRAP applications/ bioinformatics 20080812 phrap/20080812 2012-04-04 2012-04-04
PHRAP applications/ bioinformatics 20090518 phrap/20090518 2013-07-08
phyldog applications/ bioinformatics 20120823 phyldog/20120823 2012-08-24
phylib applications/ bioinformatics 3.695 phylip/3.695 2013-07-16 2013-07-16
PhyloBayes applications/ bioinformatics 1.4e PhyloBayes/1.4e 2013-04-09 2013-04-09
phylosift applications/ bioinformatics 5.16 phylosift/5.16 2014-04-03 2014-04-03
PhyML applications/ bioinformatics 3.1 PhyML/3.1 2013-06-28 2013-06-28
picard applications/ bioinformatics 1.115 picard/1.115 2014-06-24
picard applications/ bioinformatics 1.74 picard/1.74 2012-08-01 2012-08-01
picard applications/ bioinformatics 1.92 picard/1.92 2013-05-31
pigz applications/ general 2.3 pigz/2.3 2013-05-12 2013-05-12
pigz applications/ general 2.3.1 pigz/2.3.1 2014-02-05
pilon applications/ bioinformatics 1.0 pilon/1.0 2013-06-07 2013-06-07
PLINK applications/ bioinformatics 1.07 PLINK/1.07 2013-04-08
postgresql applications/ services 9.2.3 postgresql/9.2.3 2013-02-14 2013-02-14
primer3 applications/ bioinformatics 2.3.5 primer3/2.3.5 2013-10-16 2013-10-16
prodigal applications/ bioinformatics 2.50 prodigal/2.50 2012-08-14 2012-08-14
prodigal applications/ bioinformatics 2.60 prodigal/2.60 2014-03-17
psmc applications/ bioinformatics 2013-07-17 psmc/2013-07-17 2013-10-16 2013-10-16
python applications/ programming 2.7.3 python/2.7.3 2012-07-05 2012-07-05
python applications/ programming 2.7.3_1 python/2.7.3_1 2012-07-20 2012-07-20
python applications/ programming 2.7.3_2 python/2.7.3_2 2013-01-24 2013-01-27
python applications/ programming 2.7.4 python/2.7.4 2013-04-17 2013-05-21
python applications/ programming 3.2.3_1 python/3.2.3_1 2012-07-28
python-scientific applications/ programming 1.0 python-scientific/1.0 2013-06-13
qaqc_group applications/ bioinformatics 2.3.0 jigsaw/2.3.0 2013-10-10 2013-10-10
qaqc_group applications/ bioinformatics 2.3.1 jigsaw/2.3.1 2013-12-09 2013-12-09
qhull applications/ general 2012.1 qhull/2012.1 2013-10-16 2013-10-16
qiime applications/ bioinformatics 1.7.0 qiime/1.7.0 2013-07-27 2013-07-27
qrupdate applications/ general 1.1.2 qrupdate/1.1.2 2013-10-16 2013-10-16
qsubsafe libraries/ programming 1.0 qsubsafe/1.0 2012-11-17 2012-11-17
qt applications/ programming 4.6.4 qt/4.6.4 2012-07-18 2012-07-18
quast applications/ bioinformatics 2.3 quast/2.3 2014-06-09 2014-06-09
quiver applications/ bioinformatics 20120916 quiver/20120916 2012-09-17
R applications/ programming 2.12.0 R/2.12.0 2012-04-02
R applications/ programming 2.14.1 R/2.14.1 2012-04-02 2012-04-02
R applications/ programming 2.15.0 R/2.15.0 2012-05-14 2012-05-14
R applications/ programming 2.15.1 R/2.15.1 2012-07-07
R applications/ programming 2.15.2 R/2.15.2 2012-11-09 2012-12-18
R applications/ programming 2.15.2_1 R/2.15.2_1 2013-01-28 2013-01-28
R applications/ programming 2.2.26 ncbi/2.2.26 2012-05-14 2012-05-14
R applications/ programming 3.0.1 R/3.0.1 2013-06-08 2013-06-18
rabbitmq-c pe_libraries/ programming 0.4.0 rabbitmq-c/0.4.0 2013-08-20
rabbitmq-c pe_libraries/ programming 0.4.0_nossl rabbitmq-c/0.4.0_nossl 2013-08-20
rabbitmq-c pe_libraries/ programming 20130428 rabbitmq-c/20130428 2013-06-29 2013-06-29
rabbitmq-c pe_libraries/ programming 20130428_nossl rabbitmq-c/20130428_nossl 2013-07-15
RAPSearch2 applications/ bioinformatics 2.19 rapsearch2/2.19 2014-07-21 2014-07-21
RAxML applications/ bioinformatics 7.5.4 RAxML/7.5.4 2013-06-28
RAxML applications/ bioinformatics git RAxML/git 2012-10-13 2012-10-13
RAxML-Light applications/ bioinformatics 1.0.9 RAxML-Light/1.0.9 2012-10-12 2012-10-12
Ray applications/ bioinformatics 2.1.0 Ray/2.1.0 2012-11-26 2012-11-26
Ray applications/ bioinformatics 2.2.0 Ray/2.2.0 2013-05-08
Ray applications/ bioinformatics 2.3.0 Ray/2.3.0 2013-11-05 2013-12-04
RDP_Classifier applications/ bioinformatics 2.5 rdp-classifier/2.5 2012-08-02 2012-08-02
re2 applications/ bioinformatics 20120823 re2/20120823 2012-08-23
readline libraries/ general 6.2 readline/6.2 2012-07-07 2013-03-22
readline libraries/ general 6.2_1 readline/6.2_1 2013-12-04 2013-12-17
REPEATMASKER applications/ bioinformatics 3.2.9 RepeatMasker/3.2.9 2012-04-26 2012-04-26
repeatmasker applications/ bioinformatics 4.0.3 repeatmasker/4.0.3 2013-06-24 2013-06-24
repeatscout applications/ bioinformatics 1.0.5 repeatscout/1.0.5 2013-06-24 2013-06-24
reptyr applications/ general 20130208 reptyr/20130208 2013-04-24 2013-04-24
rnastar applications/ bioinformatics 2.3.0 rnastar/2.3.0 2014-01-28 2014-01-28
ROOT applications/ programming 5.34.05 ROOT/5.34.05 2013-03-20 2013-03-20
rrdtool applications/ general 1.4.8 rrdtool/1.4.8 2013-11-04 2013-11-04
RSeQC applications/ bioinformatics 2.3.2 RSeQC/2.3.2 2012-09-04 2012-09-04
RSeQC applications/ bioinformatics 2.3.6 RSeQC/2.3.6 2013-06-28 2013-06-28
RStudio applications/ general Server0.97_dmj RStudio/Server0.97_dmj 2013-03-11 2013-03-11
RSYNC applications/ general 2.6.8 rsync/2.6.8 2012-04-03 2012-04-03
ruby applications/ programming 1.9.3-p392 ruby/1.9.3-p392 2013-05-22 2013-05-22
SAFECAT applications/ general 1.12-1 safecat/1.12-1 2012-04-03 2012-04-03
SAMTOOLS applications/ bioinformatics 0.1.18 samtools/0.1.18 2012-04-04 2012-04-04
SAMTOOLS applications/ bioinformatics 0.1.19 samtools/0.1.19 2013-03-29 2013-03-30
SAMTOOLS pe_libraries/ bioinformatics 0.1.19_1 samtools/0.1.19_1 2013-08-12 2013-10-09
SAMTOOLS pe_libraries/ bioinformatics 0.1.19_2 samtools/0.1.19_2 2014-01-13
SAMTOOLS applications/ bioinformatics 20130508 samtools/20130508 2013-05-08 2013-10-10
scons applications/ programming 2.1.0 scons/2.1.0 2012-07-15
screen applications/ general 4.0.3 screen/4.0.3 2013-09-11 2013-09-11
screen applications/ general 4.0.3_1 screen/4.0.3_1 2014-01-27
sga applications/ bioinformatics 0.10.10 sga/0.10.10 2013-08-26 2013-08-26
sga applications/ bioinformatics 0.10.13 sga/0.10.13 2014-02-21
sga applications/ bioinformatics 0.9.43 sga/0.9.43 2013-08-26
signalp applications/ bioinformatics 4.1 signalp/4.1 2013-10-17 2013-10-17
SINA applications/ bioinformatics 1.2.11 sina/1.2.11 2014-01-09 2014-01-09
smalt applications/ bioinformatics 0.7.4 smalt/0.7.4 2013-06-07 2013-06-07
snoGPS applications/ bioinformatics 0.2 snoGPS/0.2 2012-12-11 2012-12-11
snoscan applications/ bioinformatics 0.9 snoscan/0.9 2012-12-11 2012-12-11
soapdenovo applications/ bioinformatics 1.05 soapdenovo/1.05 2012-07-25 2012-07-25
soapdenovo2 applications/ bioinformatics 2.04-r240 soapdenovo2/2.04-r240 2013-08-12 2013-08-12
soapec applications/ bioinformatics 2.01 soapec/2.01 2013-09-04 2013-09-04
spades applications/ bioinformatics 2.1.0 spades/2.1.0 2012-07-14 2012-07-14
spades applications/ bioinformatics 2.2.0 spades/2.2.0 2012-07-25
spades applications/ bioinformatics 2.3.0 spades/2.3.0 2012-11-01
spades applications/ bioinformatics 2.4.0 spades/2.4.0 2013-02-19
spades applications/ bioinformatics 2.5.0 spades/2.5.0 2013-07-09
spades applications/ bioinformatics 3.0.0 spades/3.0.0 2014-01-13
spades applications/ bioinformatics 3.0.0_1 spades/3.0.0_1 2014-03-05
spades applications/ bioinformatics 3.1.0 spades/3.1.0 2014-06-02
spanner applications/ bioinformatics 20120823 spanner/20120823 2012-08-23
sparsehash libraries/ general 2.0.2 sparsehash/2.0.2 2012-12-06 2012-12-06
SparseSuite applications/ general 20130425 SparseSuite/20130425 2013-10-16 2013-10-16
SparseSuite applications/ general 20130425 SuiteSparse/20130425 2013-10-16
Sphinx applications/ general 2.0.5 sphinx/2.0.5 2012-08-09 2012-08-09
sqlite3 applications/ general 3.7.14 sqlite3/3.7.14 2012-09-24 2012-09-24
sqlite3 applications/ general 3.8.2 sqlite3/3.8.2 2014-01-24
SSAKE applications/ bioinformatics 3.8 SSAKE/3.8 2012-12-14 2012-12-14
SSPACE applications/ bioinformatics 2.0 SSPACE/2.0 2013-09-04 2013-09-04
stxxl pe_libraries/ general 1.3.1 stxxl/1.3.1 2013-06-30 2013-06-30
subread applications/ bioinformatics 1.4.3 subread/1.4.3 2014-01-28 2014-01-28
subversion applications/ programming 1.6.17 svn/1.6.17 2012-06-18
subversion applications/ programming 1.7.7 svn/1.7.7 2012-11-07 2012-11-07
swift applications/ programming 0.94 swift/0.94 2013-05-02 2013-05-02
swig applications/ programming 2.0.8 swig/2.0.8 2012-09-14 2012-09-14
targetb applications/ bioinformatics 1.1b targetp/1.1b 2013-10-17 2013-10-17
TaskFarmerMQ applications/ general 2.0 taskfarmermq/2.0 2013-01-15 2013-01-15
TaskFarmerMQ applications/ general 2.1 taskfarmermq/2.1 2013-01-18
TaskFarmerMQ applications/ general 2.2 taskfarmermq/2.2 2013-02-13
TaskFarmerMQ applications/ general 2.4 taskfarmermq/2.4 2013-10-18
tassel applications/ bioinformatics 3.0_standalone tassel/3.0_standalone 2013-03-04 2013-03-04
tassel applications/ bioinformatics 4.0_standalone tassel/4.0_standalone 2013-08-27
tax2tree applications/ bioinformatics 1.0 tax2tree/1.0 2013-07-27 2013-07-27
tbl2asn applications/ bioinformatics 10.3 tbl2asn/10.3 2012-08-13
tclap applications/ bioinformatics 1.2.1 tclap/1.2.1 2012-08-23
TexLive applications/ programming 2012 texlive/2012 2012-11-14 2012-11-14
tfmq applications/ general dev tfmq/dev 2014-01-23
tfmq applications/ general prod tfmq/prod 2014-01-23 2014-01-23
TIG other/ services 1.0.0 tig/1.0.0 2012-03-27
tmux applications/ general 1.7 tmux/1.7 2013-03-08 2013-03-08
tmux applications/ general 1.7_1 tmux/1.7_1 2013-08-20 2013-08-20
tophat applications/ bioinformatics 1.3.2 tophat/1.3.2 2012-11-09
tophat applications/ bioinformatics 2.0.4 tophat/2.0.4 2012-07-26 2012-07-26
tophat applications/ bioinformatics 2.0.6 tophat/2.0.6 2012-11-09 2012-11-09
tophat applications/ bioinformatics 2.0.7 tophat/2.0.7 2013-02-19
tophat applications/ bioinformatics 2.0.9 tophat/2.0.9 2013-09-30
trans-ABySS applications/ bioinformatics 1.4.8 trans-ABySS/1.4.8 2014-06-24 2014-06-24
tree-puzzle applications/ bioinformatics 5.2 tree-puzzle/5.2 2013-06-12 2013-06-12
trinity applications/ bioinformatics r20131110 trinity/r20131110 2014-04-11 2014-04-11
trinity applications/ bioinformatics r20140413p1 trinity/r20140413p1 2014-04-28
tRNAscan-SE applications/ bioinformatics 1.3.1 tRNAscan-SE/1.3.1 2012-08-03 2012-08-03
uclust applications/ bioinformatics 1.2.22 uclust/1.2.22 2012-11-11
UCSC applications/ bioinformatics kent UCSC/kent 2012-12-17 2012-12-17
usearch applications/ bioinformatics 6.0.152 usearch/6.0.152 2012-07-31 2012-07-31
usearch applications/ bioinformatics 6.0.203 usearch/6.0.203 2012-09-07 2012-09-07
usearch applications/ bioinformatics 6.0.307 usearch/6.0.307 2013-04-19 2013-04-19
usearch applications/ bioinformatics 6.1.544.beta usearch/6.1.544.beta 2013-08-12
usearch applications/ bioinformatics 7.0.959 usearch/7.0.959 2013-08-27 2013-09-03
USeq applications/ bioinformatics 8.4.7 useq/8.4.7 2012-12-17 2012-12-17
USG Default Modules os/ general 1.0 usg-default-modules/1.0 2012-11-08 2012-11-08
USG Default Modules os/ general 1.1 usg-default-modules/1.1 2013-01-25 2013-02-13
USG Default Modules os/ general 1.2 usg-default-modules/1.2 2013-03-20 2013-04-08
USG Default Modules os/ general 1.3 usg-default-modules/1.3 2013-05-21 2013-05-21
USG Default Modules os/ general 1.4 usg-default-modules/1.4 2013-06-17 2013-06-18
USG Environment other/ general 1.1 usg/1.1 2012-08-24 2012-08-24
valgrind applications/ programming 3.7.0 valgrind/3.7.0 2012-09-28 2012-09-28
valgrind applications/ programming 3.9.0 valgrind/3.9.0 2014-05-05
vcftools applications/ bioinformatics 0.1.10 vcftools/0.1.10 2013-06-14 2013-06-14
vcftools applications/ bioinformatics 0.1.11 vcftools/0.1.11 2013-06-14
vcftools applications/ bioinformatics 0.1.8a vcftools/0.1.8a 2012-04-04 2012-04-04
VELVET applications/ bioinformatics 1.2.03 Velvet/1.2.03 2012-04-04 2012-04-04
velvet applications/ bioinformatics 1.2.07 velvet/1.2.07 2012-07-26 2012-07-31
velvet applications/ bioinformatics 1.2.07_1 velvet/1.2.07_1 2012-08-30 2012-08-30
ViennaRNA applications/ bioinformatics 2.1.2 ViennaRNA/2.1.2 2013-06-28 2013-06-28
vim applications/ general 7.3 vim/7.3 2013-03-11
vmatch applications/ bioinformatics 2.1.6 vmatch/2.1.6 2012-09-06 2012-09-06
vmatch applications/ bioinformatics 2.2.0 vmatch/2.2.0 2013-06-25 2013-11-21
vmatch applications/ bioinformatics 2.2.0_test vmatch/2.2.0_test 2014-06-06
Washington University BLAST applications/ bioinformatics 20060510 wublast/20060510 2013-07-08 2013-07-08
WGS/Celera applications/ bioinformatics 20130412 celera/20130412 2013-04-12 2013-04-12
WGS/Celera applications/ bioinformatics 20130415 celera/20130415 2013-04-24 2013-04-24
WGS/Celera applications/ bioinformatics 7.0 celera/7.0 2013-10-15
WGS/Celera applications/ bioinformatics 8.0 celera/8.0 2013-11-13
WGS/Celera applications/ bioinformatics 8.1 celera/8.1 2013-12-19
wgsim applications/ bioinformatics 0.3.0 wgsim/0.3.0 2012-12-14 2012-12-14
Wise2 applications/ bioinformatics 2.2.0 genewise2/2.2.0 2012-10-22
xds applications/ bioinformatics 20120926 xds/20120926 2013-04-25 2013-04-25
xerces-c pe_libraries/ general 3.1.1 xerces-c/3.1.1 2013-08-27 2013-08-27
xiv applications/ general 0.9 xiv/0.9 2013-04-24 2013-04-24
Xpdf applications/ visualization 3.03 xpdf/3.03 2012-05-31 2012-05-31
xz applications/ general 5.0.4 xz/5.0.4 2012-07-18 2012-07-18
yaml pe_libraries/ general 0.1.4 yaml/0.1.4 2013-07-08 2013-07-08
zeromq libraries/ general 2.2.0 zeromq/2.2.0 2012-07-19 2012-07-19

Legacy Software in /jgi/tools

Users can access software in the legacy JGI software in /jgi/tools.  Some of the available tools are listed below for your reference. 

programming languages
perl 5.10.1
R 2.14
python 2.6 and 2.7
ruby 1.9.2 and 1.8.7
java 1.6 and 1.7

other software and tools
abyss http://www.bcgsc.ca/platform/bioinfo/software/abyss
picard
bowtie
igv (Integrated Genomics Viewer from Broad)
gassst
http://bioinformatics.oxfordjournals.org/content/early/2010/08/24/bioinformatics.btq485
samtools
tabix
GATK
Mosaik
bwa
blast+
blastall
vcftools
filo https://github.com/arq5x/filo
velvet http://www.ebi.ac.uk/~zerbino/velvet/
stampy
mercurial http://mercurial.selenic.com/
uclust
usearch
MUMmer
FastTree
emboss
clustalx
clustalo
amos
TopHat
CuffLinks
decypher (Timelogic binaries)
ESTmapper http://sourceforge.net/apps/mediawiki/kmer/index.php?title=Main_Page
MetaCluster
Celera  http://sourceforge.net/projects/wgs-assembler/files/wgs-assembler/wgs-7.0/
jellyfish
Broad's AllPaths http://www.broadinstitute.org/science/programs/genome-biology/crd
Broad's Arachne mira assembler
quake
echo
sga
newbler
megan
fasttree  http://microbesonline.org/fasttree/
smashcell  http://asiago.stanford.edu/SmashCell
tablet  http://bioinf.scri.ac.uk/tablet/index.shtml
hmmer 3.0  http://hmmer.janelia.org/
concavity  http://compbio.cs.princeton.edu/concavity/
sqlite  http://www.sqlite.org/
TagDust  http://bioinformatics.oxfordjournals.org/content/25/21/2839.full
muscle  http://www.drive5.com/muscle/
cd-hit  http://www.bioinformatics.org/cd-hit/
MEGAN Running with Java for tips on running MEGAN on Genepool