Available programs (Iceberg)

WARNING

The list of software below is outdated. To get a list of installed programs, libraries, R packages, and Perl modules (including versions), please use the command:

 softrepo

 


 

programfoldercurrent versionother versionsnotes
ABCtoolboxABCtoolbox2014-04-08
ABySSabyss2.0.21.9.0compiled for multiple max k-mer sizes: 32, 64, 96, 128; a wrapper automatically selects the right version; an example for running it is at: /usr/local/extras/Genomics/submit_scripts/abyss_pe_hybrid4.sh
AdapterRemovaladapterremoval2.2.0
AGREPagrep3.412
alleleEstalleleEst0.1b0.1
ANGSDangsd0.9170.538, 0.57, 0.588, 0.612a,0.911
Apache Antant1.9.3
Arlequinarlequin3.5
ASTRALastral4.10.12
ATLASatlas is a python module1.0.4 Requires using anaconda python 3.5 with the command: source activate py35
Point to databases (downloaded on 28/03/2017) with: --database-dir /usr/local/extras/Genomics/db/atlas
Augustusaugustus3.2.22.5.5, 3.2.1
AutoClassautoclass3.3.6parallel version using autoclass-p (see link)
BAMMbamm2.5.0
Bayenvbayenv2.0.0
BayesAssbayesass3.0.3
BayeScanbayescan2.1.1
BayesTraitsbayestraits2.0
BCFtoolsbcftools1.3.1dev-0.2.0, 0.1.19,1.2,1.3
bcl2fastqbcl2fastq2.17.1.14
BEAST 2beast2.4.52.0.2, 2.1.0, 2.1.1, 2.1.2, 2.1.3, 2.3.1, 2.3.2, 2.4.0,2.4.2All add-ons available on 28/04/2017 installed
BEAST 1beast1.8.41.7.5, 2014-03-14, 1.8.0,1.8.3
bedtoolsbedtools2.24.0
bgcbgc1.03
biopybiopy is a python module0.1.9Documentation. Requires using anaconda python 2.7 with the command: source activate py27
Bismarkbismark0.16.1
BLASRblasr2015-08-19
Blatblat35
Blatblat35
Bowtiebowtie1.21.1.1
Bowtie 2bowtie22.2.92.1.0, 2.2.3, 2.2.7
BP&Pbpp2.2
Bridgerbridgerr2014-12-01
BUSCObusco2-201611291.1b1,1.21,1.22
BWAbwa0.7.5a
CAP3cap321-12-07
CD-HITcd-hit4.6.44.6.1
CEGMAcegma2.4.010312
CLUMPPclumpp1.1.2
Clustal Wclustalw2.1
coalevolcoalevol7.3.5
COLONYcolony2.0.6.32010-01-13
CONSELconsel0.2
cortex_varcortex_var1.0.5.2
Cufflinkscufflinks2.1.1
cutadaptcutadapt1.2.1
dadidadi is a python module1.7.0-2015-12-27Documentation. Requires using anaconda python 2.7 with the command: source activate py27
DCRAWdcraw9.26
DELLYdelly0.6.7
DendroPydendropy is a python module4.1.0Documentation. Requires using anaconda python 2.7 with the command: source activate py27
DETONATEdetonate1.11
DetSexdetsex1
DISCOVARdiscovar52488
DISCOVAR de novodiscovardenovo52488
distructdistruct1.1
DIYABCdiyabc2.1.0
DSRCdsrc2.0.2
ecoPCRecopcr0.8.0

ecoPrimers
ecoprimers0.3
embossemboss6.6.0
entropyentropy1.2c2013-10-04, 1.2, 1.2b
estpEMestpEM2014-10-08
EvolveAGeneevolvagene4.0.2
ExaMLexaml3.0.171.0.12-20140423, 1.0.8-20131209, 2.0.0-20140529,2.0.4-20140709
Exonerateexonerate2.2.0
-extractPIRs-
FASTAfasta35.4.12
fastPHASEfastphase1.4.8
FastQCfastqc0.11.50.10.1
fastsimcoalfastsimcoal2.5.2.21
fastStructurefaststructure2014-09-09
FastTreefasttree2.1.7
FASTX-Toolkitfastx-toolkit0.0.13.2
FMAPfmap0.10
fstfst2012-04-25
GARLIgarli2.01
gatkGATK2.5.2
Gblocksgblocks0.91b
GEMMAgemma0.940.93
geneidgeneid1.4.4
GMAP/GSNAPgmap-gsnap2013-06-18
GeneMarkESgmes2.3.e2.3.e
HDF5hdf51.8.151.8.11
HDF-Javahdf-java2.10.0
HMMERhmmer3.1b22012.10.16, 3.1b1
HPG alignerhpg-aligner2015-02-16
HTSeqhtseq is a python module0.6.1Requires using anaconda python 2.7 with the command: source activate py27
HTSlibhtslib1.3.11.2.1,1.3
Hydrahydra0.5.5-2015-10-14
IMa2ima28.27.12
ImageMagickImageMagick7.0.2-26.8.6-8
indel-Seq-Delindel-seq-del2.2.13
InterProScaninterproscan5.20-59.05.2-45.0,5.7-48.0
IQ-TREEiqtree1.5.41.0.1,1.3.13,1.4.3
Java JDKjava1.8.0_65To use it, set JAVA_HOME as:
export JAVA_HOME='/usr/local/extras/Genomics/apps/java/current'
juliajulia0.3.112014-05-13, 2014-08-25_v0.3.0, 2014-09-04_v0.3.0
Kakusan4kakusan4
Kalignkalign2.04
KronaToolskronatools2.7
Ktreedistktreedist1.0
Lazaruslazarus2012-12-17
lbzip2lbzip22.2
lumpylumpy0.2.11
MACSEmacse1.01b
MAFFTmafft7.1647.047, 7.158
MAKERmaker2.28b2.1
MCLmcl14.137
Meraculousmeraculous2.0.5
metaBITmetabit1.0.1
MetaPhlAn2metaphlan22.6.0
MetaPIGAmetapiga3.1
mothurmothur1.35.1
MPICHmpich3.0.4
MrBayesmrbayes3.2.63.2.1, 3.2.2, 3.2.5Compiled with BEAGLE library. To run MPI version, execute:

module add mpi/intel/openmpi/1.10.0
mpirun -np 4 mb_mpi nexus

*4->number of processors (must be the same than number of chains in nexus)

Nexus commands are required to use beagle (set beagle=yes, etc.). See documentation
for more info.
MSMCmsmc2014-09-08Maintained by Martin
Mugsymugsy1r2.3
MUSCLEmuscle3.8.31
MySQLmysql5.6.16
NCBI BLAST+ncbi-blast2.6.02.2.28, 2.2.31,2.4.0,2.5.0
Newblernewbler2.8
NGS QC Toolkitngsqcoolkit2.3.3
ngsToolsngsTools2014-03-122013-09-09
NINJAninja1.2.2
NxTrimnxtrim0.3.2-alpha-8bb986b
Oasesoases0.2.09
OBIToolsobitools1.2.10
Ontologizerontologizer2.1
PAMLpaml4.84.7
GNU Parallelparallel2013-06-22
Parsimonatorparsimonator1.0.3-201407091.0.2-20131211
PartitionFinderpartitionfinder2.1.11.1.1
PASApasa2013-06-05
PBGZIPpbgzip2017-05-16
pbsmrtpipepbsmrtpipe2017-05-11

PBSuite
pbsuite15.8.24To use it, execute 'source pbsuite_load'
PEARpear0.94
Perlperl5.16.35.18CPAN modules can be shown with: 'cpan -l'
PGDSpiderpgdspider2.0.7.4
PHASTphast1.3
PHLAWDphlawd2013-06-25
PHYLIPphylip3.695
PhyloBayesphylobayes3.3f
phylonet-HMMphylonet-HMM0.1-2015-10-30
PhyMLphyml2012-04-12
Picard Toolspicard-tools2.5.01.92A wrapper allows running commands as: picard (there is no need to use java -jar)
pigzpigz2.3
piMASSpimass0.9
Platypusplatypus0.7.9.10.7.8Maintained by Martin
PLINKplink1.07
PLL-DPPDivpll-dppdiv2014-08-22
pmdtoolspmdtools2015-09-07
popoolation2popoolation22014-01-26
Primer3primer32.3.6
PRINSEQprinseq0.20.3
proovreadproovread2.13.8-2015-10-08
ProteinEvolverproteinevolver1.2.0
pyRADpyrad3.0.52.16.1
Python (Anaconda)python-4.0.0, Anaconda (2.6, 2.7, 3.3)To use a particular Anaconda version: 'source activate py27' or 'source activate py33'

List of modules installed can be obtained with the command: 'pip freeze'

Modules installed (Anaconda py27): biopy 0.1.9, biopython 1.67, Cython 0.24, DendroPy 4.1.0, dadi 1.7.0, numpy 1.11.1, HTSeq 0.6.1, scipy 0.17.1, vcf2networks 1.0.8

Modules installed (Anaconda py33): biopython 1.67, Cython 0.24, dendropy 4.1.0, numpy 1.11.1, scipy 0.15.1, vcf2networks 1.0.8
QDDqdd3.1.2
QualiMapqualimap2.2
QuickTreequicktree1.1
RR3.3.13.0.1, 3.0.2, 3.2.2, 3.2.3This a version compiled using Intel compiler and MKL libraries for improved performance. Installed packages and version can be obtained with the R command:
installed.packages()[,c(1,3:4)]
rainbowrainbow2.0.3
RAPIDNJrapidnj2.3.0.2
RaxMLraxml8.2.107.5.4, 7.9.5, 8.0.3,8.0.20,8.2.9
ReadSeqreadseq2.1.19
REALPHYrealphy1.07
RepeatMaskerrepeatmasker4.0.5
RMBlastrmblast2.2.28

RNAmmer
rnammer1.2
RogueNaRokRogueNaRok1.0-2011-10-25
Roserose1.3
RSEMrsem1.3.01.2.19
Rubyruby2.0.0
Saguarosaguaro2015-10-30
SAMBLASTERsamblaster0.1.21
Samtoolssamtools1.3.1dev-0.2.0, 0.1.19,1.2,1.3
SelEstimSelEstim1.0.51.0.0
Sequence Cleanerseqclean2013-06-19
SeqTKseqtk1.0-r82-2015-06-28
SeqtrimNextseqtrimnext is a Ruby gem2.0.66
shapeitMaintained by Martin
SignalPsignalp4.1
skickaskicka2015-01-13
SNAPsnap2013.02.16
SOAP2soap22.21
SOAP3soap30.01b
SOAPdenovosoapdenovo2.04
SOAPdenovo-transsoapdenovo-trans1.02
SplitsTreesplitstree4.13.1
Squashfssquashfs-tools4.2
SRAtoolkitsratoolkit2.3.2
Stacksstacks1.461.01, 1.12, 1.18, 1.19, 1.20, 1.23, 1.24, 1.29,1.40
Stampystampy1.0.22
Structurestructure2.3.4

Sumaclust
sumaclust1.0.20

Sumatra
sumatra1.0.20
svpropssvprops
2015-09-28
SVToolssvtools2015-08-022015-06-04
tabixtabix0.2.6
Tablettablet1.13.04.22
T-Coffeetcoffee11.00.8cbe486

TMHMM
tmhmm2.0c
TMHMMtmhmm2.0c
TopHattophat2.1.0
Trans-ABySStransabyss1.5.5
TransDecodertransdecoder3.0.0Launch using TransDecoder.LongOrfs and TransDecoder.Predict
Transratetransrate is a Ruby gem1.0.1
treetree1.6.0
TREEFINDERtreefinder2011-03
TreeMixtreemix1.12
treePLtreepl2014-08-23
Tandem Repeats Findertrf407b
Trim Galoretrim_galore0.4.1
Trimmomatictrimmomatic0.360.33,0.35
Trinitytrinity2.0.62013-02-25, 2.0.2
Trinotatetrinotate3.0.12.0.2
USEARCHusearch9.2.647.0.1090,9.0.2132
VariScanvariscan2.0.3jva gui interface is launched with command variscan_gui
VarScanVarScan2.3.6
VCF2Networksvcf2networks is a python module1.0.8Documentation. Requires using anaconda python 2.7 with the command: source activate py27
VCFtoolsvcftools0.1.11
Velvetvelvet1.2.10
velvetkvelvetk2014-03-14
VelvetOptimiservelvetoptimiser2.2.5
Vimvim7.3
VSEARCHvsearch2.4.21.1.13,2.3.0
Celera Assemblerwgs-ca8.3rc2
Wise2wise22.4.1
Zbarzbar0.10
zlibzlib1.2.8
DIAMONDdiamond0.9.6
RAPSearch2rapsearch22.24
SUPER-FOCUSsuperfocus0.27