NERSCPowering Scientific Discovery Since 1974
Login
My NERSC | Site Map
For Users

Passwords &
Account Support

https://nim.nersc.gov
accounts@nersc.gov
1-800-66-NERSC,  option 2
or 510 486-8612

Consulting

http://help.nersc.gov
consult@nersc.gov
1-800-66-NERSC, option 3
or 510 486-8611

Off-Hours Status &
Passwords

1-800-66-NERSC, option 1

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
ABYSS applications/ bioinformatics 1.3.2 Abyss/1.3.2 2012-04-03 2012-04-03
acml libraries/ math 5.1.0 acml/5.1.0 2012-07-07
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
AMOS applications/ bioinformatics 3.1.0 AMOS/3.1.0 2012-04-04 2012-04-04
ant applications/ programming 1.8.4 ant/1.8.4 2012-07-27 2012-07-27
arb applications/ bioinformatics 5.3 arb/5.3 2012-07-23 2012-07-23
atlas libraries/ math 3.10.0 atlas/3.10.0 2012-07-18 2012-07-18
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
BAMTOOLS applications/ bioinformatics 20120308 bamtools/20120308 2012-04-04 2012-04-04
bio++ applications/ bioinformatics 20120823 biopp/20120823 2012-08-24
biopython applications/ bioinformatics 1.60 biopython/1.60 2012-07-21 2012-07-21
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 libraries/ general 1.42.0 boost/1.42.0 2012-07-14
boost 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 libraries/ general 1.50.0 boost/1.50.0 2012-07-02 2012-07-03
bowtie applications/ bioinformatics 0.12.8 bowtie/0.12.8 2012-07-25 2012-07-25
bowtie2 applications/ bioinformatics 2.0.0-beta7 bowtie2/2.0.0-beta7 2012-07-25 2012-07-25
BWA applications/ bioinformatics 0.6.2 BWA/0.6.2 2012-07-31 2012-07-31
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
CIRCOS applications/ bioinformatics 0.52 circos/0.52 2012-04-03 2012-04-03
CLUSTALO applications/ bioinformatics 1.0.3 clustalo/1.0.3 2012-04-04 2012-04-04
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 2012-09-07
CONSED applications/ bioinformatics 21.00 consed/21.00 2012-04-04 2012-04-04
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
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
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
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
EAGLEVIEW applications/ bioinformatics 2.1 eagleview/2.1 2012-04-03 2012-04-03
eigen libraries/ general 3.1.0 eigen/3.1.0 2012-07-03
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 1.0 emirge/1.0 2012-09-11 2012-09-11
erlang-OTP applications/ programming R15B01 erlang-OTP/R15B01 2012-07-28 2012-07-28
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
FastQC applications/ bioinformatics 0.10.1 fastqc/0.10.1 2012-08-02 2012-08-02
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
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
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
gdb applications/ programming 7.5 gdb/7.5 2012-09-23 2012-09-23
GHC compilers/ programming 7.0.3 ghc/7.0.3 2012-04-03 2012-04-03
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
glib applications/ programming 2.24.2 glib/2.24.2 2012-07-18 2012-07-18
glimmer applications/ bioinformatics 3.02 glimmer/3.02 2012-08-09 2012-08-09
GMAP applications/ bioinformatics 2011-11-14 gmap/2011-11-14 2012-04-03 2012-04-03
GNU Scientific Library libraries/ math 1.15 gsl/1.15 2012-07-30 2012-08-08
GNUPLOT applications/ general 4.2.2 gnuplot/4.2.2 2012-04-04 2012-04-04
GNUPLOT applications/ general 4.4.3 gnuplot/4.4.3 2012-04-04
GRAPHVIZ applications/ general 2.26.3 graphviz/2.26.3 2012-04-03 2012-04-03
GTK+ libraries/ programming 2.24.11 gtk/2.24.11 2012-08-08 2012-08-08
HASKELL applications/ programming 2011.2.0.1 haskell/2011.2.0.1 2012-04-03 2012-04-03
HDF5 applications/ bioinformatics 1.8.7 hdf5/1.8.7 2012-04-04 2012-04-04
hdf5 libraries/ general 1.8.9 hdf5/1.8.9 2012-07-19 2012-07-19
HMMER applications/ bioinformatics 3.0 hmmer/3.0 2012-03-19 2012-03-19
htop applications/ general 1.0.1 htop/1.0.1 2012-07-20 2012-07-20
infernal applications/ bioinformatics 1.1rc1 infernal/1.1rc1 2012-08-13 2012-08-13
IPERF applications/ general 2.0.5 iperf/2.0.5 2012-04-03 2012-04-03
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 1.1.5 jellyfish/1.1.5 2012-08-09 2012-08-09
jgi-python-packages applications/ bioinformatics 1.0 jgi-python-packages/1.0 2012-08-30 2012-08-30
kcachegrind applications/ programming 0.7.1 kcachegrind/0.7.1 2012-09-28 2012-09-28
libgmp libraries/ math 5.0.5 gmp/5.0.5 2012-06-17
libhmsbeagle libraries/ bioinformatics 1.0 libhmsbeagle/1.0 2012-06-10
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 applications/ programming 0.10.1 libzip/0.10.1 2012-07-20 2012-07-20
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
m4 applications/ programming 1.4.16 m4/1.4.16 2012-07-16 2012-07-16
MAFFT applications/ bioinformatics 6.864b MAFFT/6.864b 2012-04-03 2012-04-03
maven applications/ programming 3.0.4 maven/3.0.4 2012-07-27 2012-07-27
MCL applications/ bioinformatics 11-294 mcl/11-294 2012-04-04 2012-04-04
mercurial applications/ programming 2.2.3 mercurial/2.2.3 2012-07-16 2012-07-16
METAPHYLER applications/ bioinformatics 1.13 MetaPhyler/1.13 2012-04-04 2012-04-04
MIRA applications/ bioinformatics 3.4.0 mira/3.4.0 2012-04-04 2012-04-04
MOSAIK applications/ bioinformatics 1.1.0021 MOSAIK/1.1.0021 2012-04-04 2012-04-04
mothur applications/ bioinformatics 1.26.0 mothur/1.26.0 2012-08-02 2012-08-02
MrBayes applications/ bioinformatics 3.2.1 MrBayes/3.2.1 2012-06-10
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 5.5.25a mysql/5.5.25a 2012-07-30
NCBI BLAST+ applications/ bioinformatics 2.2.6 blast+/2.2.6 2012-07-26 2012-07-26
netlib-lapack libraries/ math 3.4.1 netlib-lapack/3.4.1 2012-07-18 2012-07-18
NOVOCRAFT applications/ bioinformatics 1.05.01 novocraft/1.05.01 2012-04-04 2012-04-04
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
Open MPI libraries/ programming 1.4.5 openmpi-gcc/1.4.5 2012-06-09 2012-06-09
Open MPI libraries/ programming 1.4.5 openmpi/1.4.5 2012-07-26 2012-07-26
Open MPI libraries/ programming 1.6 openmpi-gcc/1.6 2012-06-09
Open MPI libraries/ programming 1.6 openmpi/1.6 2012-07-26
OracleJDK applications/ programming 1.6.0_33 oracle-jdk/1.6.0_33 2012-06-17
OracleJDK applications/ programming 1.6.0_34_32bit oracle-jdk/1.6.0_34_32bit 2012-08-22
OracleJDK applications/ programming 1.6.0_34_64bit oracle-jdk/1.6.0_34_64bit 2012-08-22
OracleJDK applications/ programming 1.7.0_05 oracle-jdk/1.7.0_05 2012-06-17 2012-07-15
OracleJDK applications/ programming 1.7.0_06_32bit oracle-jdk/1.7.0_06_32bit 2012-08-22
OracleJDK applications/ programming 1.7.0_06_64bit oracle-jdk/1.7.0_06_64bit 2012-08-22 2012-08-22
PacBioPython applications/ bioinformatics 20120918 PacBioPython/20120918 2012-09-18 2012-09-18
PAML applications/ bioinformatics 4 paml/4 2012-04-03 2012-04-03
PASA applications/ bioinformatics r2012-06-25 pasa/r2012-06-25 2012-08-02 2012-08-02
pBWA applications/ bioinformatics alternate-v2 pBWA/alternate-v2 2012-07-31 2012-07-31
perl applications/ programming 5.10.1 perl/5.10.1 2012-04-12 2012-04-12
perl applications/ programming 5.16.0 perl/5.16.0 2012-06-19 2012-07-03
PGADMIN3 applications/ general 1.14.0 pgadmin3/1.14.0 2012-04-03 2012-04-03
phenix applications/ bioinformatics 1.8-1069 phenix/1.8-1069 2012-10-02 2012-10-02
PHRAP applications/ bioinformatics 20080812 phrap/20080812 2012-04-04 2012-04-04
phyldog applications/ bioinformatics 20120823 phyldog/20120823 2012-08-24
PHYML applications/ bioinformatics 20120312 PhyML/20120312 2012-04-04 2012-04-04
PHYML applications/ bioinformatics 20120412 PhyML/20120412 2012-09-11 2012-09-11
picard applications/ bioinformatics 1.74 picard/1.74 2012-08-01 2012-08-01
prodigal applications/ bioinformatics 2.50 prodigal/2.50 2012-08-14 2012-08-14
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 3.2.3_1 python/3.2.3_1 2012-07-28
qt applications/ programming 4.6.4 qt/4.6.4 2012-07-18 2012-07-18
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 2.2.26 ncbi/2.2.26 2012-05-14 2012-05-14
RAXML applications/ bioinformatics 7.2.6 RAxML/7.2.6 2012-04-03 2012-04-03
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
REPEATMASKER applications/ bioinformatics 3.2.9 RepeatMasker/3.2.9 2012-04-26 2012-04-26
RSeQC applications/ bioinformatics 2.3.2 RSeQC/2.3.2 2012-09-04 2012-09-04
RSYNC applications/ general 2.6.8 rsync/2.6.8 2012-04-03 2012-04-03
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
scons applications/ programming 2.1.0 scons/2.1.0 2012-07-15
soapdenovo applications/ bioinformatics 1.05 soapdenovo/1.05 2012-07-25 2012-07-25
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
spanner applications/ bioinformatics 20120823 spanner/20120823 2012-08-23
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
subversion applications/ programming 1.6.17 svn/1.6.17 2012-06-18
swig applications/ programming 2.0.8 swig/2.0.8 2012-09-14 2012-09-14
tbl2asn applications/ bioinformatics 10.3 tbl2asn/10.3 2012-08-13
tclap applications/ bioinformatics 1.2.1 tclap/1.2.1 2012-08-23
TIG other/ services 1.0.0 tig/1.0.0 2012-03-27
tophat applications/ bioinformatics 2.0.4 tophat/2.0.4 2012-07-26 2012-07-26
tRNAscan-SE applications/ bioinformatics 1.3.1 tRNAscan-SE/1.3.1 2012-08-03 2012-08-03
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
usg 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
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 1.8.5 ViennaRNA/1.8.5 2012-04-03 2012-04-03
vmatch applications/ bioinformatics 2.1.6 vmatch/2.1.6 2012-09-06 2012-09-06
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
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

Last edited: 2012-08-31 08:47:56

Send us feedback about this page

Logged in users can use our feedback form.You can log in here.

Or you can send email to consult@nersc.gov (click here send).