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list-of-software

List of Software

In general you can use the command module avail to show you the list of available software and their versions. Sometimes there are other software packages installed which aren't listed via the modules system; if you're curious you can look around in /export/apps to see if you can find what you're looking for.

Otherwise, here is a feeble attempt to list the software we have installed at ILRI, their versions, and (possibly) anyone who has experience running it. We will attempt to keep this list updated as the One True List™.

Name Latest version How to load Contact
abyss2.0.2module load abyss/2.0.2
abacas1.3.1module load abacas/1.3.1
ACT13.0.0module load act/13.0.0
admixture1.3.0module load admixture/1.3.0
AdapterRemoval1.5.4module load AdapterRemoval/1.5.4
aliview1.17.1module load aliview/1.17.1
Apache Ant1.10.1module load ant/1.10.1
amber suite12module load amber/12
ampssemblergit-51f0081module load ampssembler/git-51f0081
amos3.1.0module load amos/3.1.0
angsd0.910module load angsd/0.910
annovar2016-02-01module load annovar/2016-02-01
apt1.14.3module load apt/1.14.3
arb6.0.3module load arb/6.0.3
artemis16.0.0module load act/16.0.0
augustus3.2.3module load augustus/3.2.3
bam-readcount0.8.0module load bam-readcount/0.8.0
bamtools2.4.0module load bamtools/2.4.0
bayescan2.1module load bayescan/2.1
bcftools1.3.1module load bcftools/1.3.1
beagle2.1.2module load beagle/2.1.2
beast1.8.3module load beast/1.8.3
bedops2.4.29module load bedops/2.4.29
bedtools2.25.0module load bedtools/2.25.0
binpacker1.0module load binpacker/1.0
bitseq0.7.5module load bitseq/0.7.5
blasrsmrtanalysis-4.0.0module load blasr/smrtanalysis-4.0.0
blast2.6.0+module load blast/2.6.0+
blobtools0.9.19.3module load blobtools/0.9.19.3
blat06-Aug-2013module load blat/06-Aug-2013
bowtie1 1.1.1module load bowtie/1.1.1
bowtie2 2.3.3module load bowtie2/2.3.3
brig0.95module load brig/0.95
BUSCO 3.0.2module load BUSCO/3.0.2
bwa0.7.15module load bwa/0.7.15
cangs1.1module load cangs/1.1
canu1.6module load canu/1.6
cap3latestmodule load cap3/latest
cd-hit4.6.6module load cd-hit/4.6.6
cegmav2.5module load cegma/v2.5
celera-wgs6.1module load celera-wgs/6.1
censor4.2.28module load censor/4.2.28
changeo0.3.5module load changeo/0.3.5
circos0.67module load circos/0.67
clonalframe1.2module load clonalframe/1.2
clonalframeml1.0module load clonalframeml/1.0
clustalo1.2.3module load clustalo/1.2.3
clustalw2.1module load clustalw/2.1
CNVnator0.3.3module load CNVnator/0.3.3
consed20.0module load consed/20.0
COPEread1.1.2module load coperead/1.1.2
corset1.06module load corset/1.06
cufflinks2.2.1module load cufflinks/2.2.1
cutadaptv1.8.1module load cutadapt/v1.8.1
dendroscope2.7.4module load dendroscope/2.7.4
diamond0.9.9module load diamond/0.9.9
ea-utils1.1.2module load ea-utils/1.1.2
eigenstrat3.0module load eigenstrat/3.0
emboss6.6.0module load emboss/6.6.0
easer1.7.0module load easer/1.7.0
est2unilatestmodule load est2uni/latest
exabayes1.4.1module load exabayes/1.4.1
express1.5.1module load express/1.5.1
fastPHASE1.4.8module load fastPHASE/1.4.8
fastqc0.11.5module load fastqc/0.11.5
fastSTRUCTURE1.0module load fastSTRUCTURE/1.0
fastx_toolkit0.0.13module load fastx_toolkit/0.0.13
figtree1.4.0module load figtree/1.4.0
firefox 33.1.1module load firefox/33.1.1
flapjack 1.17.07.26module load flapjack/1.17.07.26
flash 1.2.11module load FLASH/1.2.11
flash2git-64826f45module load flash2/git-64826f45
flexbar2.7.0module load flexbar/2.7.8
flux-capacitor1.6.1module load flux-capacitor/1.6.1
frappe1.1module load frappe/1.1
FragGeneScan 1.19module load fraggenescan/1.19
FreeBayes 1.0.2module load freebayes/1.0.2
GassFlow 1.0module load gassflow/1.0
GATK 3.7.0module load gatk/3.7.0
gapfiller1.10module load gapfiller/1.10
geneid1.4.4module load geneid/1.4.4
genscanlatestmodule load genscan/latest
gffread0.9.6module load gffread/0.9.6
glimmer3.02module load glimmer/3.02
glu1.0b3-prerelease4module load glu/1.0b3-prerelease4
gmap2015-12-31module load gmap/2015-12-31
grom-rd1.0module load grom-rd/1.0
groovy2.4.9module load groovy/2.4.9
GSEA2.2.3module load gsea/2.2.3
guidance2.02module load guidance/2.02
hapflk1.4module load hapflk/1.4
hapmix2.0module load hapmix/2.0
hdf51.8.19module load hdf5/1.8.19
hmmer3.1b2module load hmmer/3.1b2
hpg-variant1.0module load hpg-variant/1.0
hisat22.0.5module load hisat2/2.0.5
htseq0.6.1module load htseq/0.6.1
htslib1.6module load htslib/1.6
igblast1.6.0module load igblast/1.6.0
igrec3.0.0module load igrec/3.0.0
igvtools2.3.90module load igvtools/2.3.90
interproscan5.13module load interproscan/5.13
i-tasserlatestmodule load i-tasser/latest
java1.8module load java/1.8
jellyfish2.2.6module load jellyfish/2.2.6
jMHC1.5.0929module load jMHC/1.5.0929
juliav0.1.2module load julia/v0.1.2
kaiju1.4.4module load kaiju/1.4.4
kallisto0.43.0module load kallisto/0.43.0
kat2.3.4module load kat/2.3.4
kmergenie1.7038module load kmergenie/1.7038
kmer-ssrgit-4043c0e7module load kmer-ssr/git-4043c0e7
kraken0.10.5module load kraken/0.10.5
krona2.4module load krona/2.4
lamp2.5module load lamp/2.5
lava0.1module load lava/0.1
ldhat2.1module load ldhat/2.1
libsvm3.20module load libsvm/3.20
lucy1.19pmodule load lucy/1.19p
mafft6.861module load mafft/6.861
make4.1module load make/4.1
mapsplice2.2.0module load mapsplice/2.2.0
mauve2.3.1module load mauve/2.3.1
masurca2.3.2module load masurca/2.3.2
maximus0.2module load maximus/0.2
megahitgit-02102e1bmodule load megahit/git-02102e1b
megan4.70.4module load megan/4.70.4
metabat2.12.1module load metabat/2.12.1
metis5.1.0module load metis/5.1.0
migec1.2.4amodule load migec/1.2.4a
migmap1.0.2module load migmap/1.0.2
MinPath1.0.2module load MinPath/1.2
mira 4.0.2module load mira/4.0.2
mitools1.4module load mitools/1.4
mixcr2.0.1module load mixcr/2.0.1
mkatari-ilrilatestmodule load mkatari-ilri/latest
modeller9.17module load modeller/9.17
mothur1.39.1module load mothur/1.39.1
mothur-kronagit-87499a0module load mothur-krona/git-87499a0
mpiblast1.6.0module load mpiblast/1.6.0
mrbayes3.2.2module load mrbayes/3.2.2
muscle3.8.31module load muscle/3.8.31
MUMmer3.23module load MUMmer/3.23
netmhcpan2.8module load netmhcpan/2.8
nextclip1.3.1module load nextclip/1.3.1
ntCard1.0.0module load ntCard/1.0.0
ngsqctoolkit2.3.3module load ngsqctoolkit/2.3.3
novacraft3.02.07module load novacraft/3.02.07
oases0.2.08module load oases/0.2.08
ocaml 4.02.1module load ocaml/4.02.1
opam 1.2.0module load opam/1.2.0
orthomcl2.0.3module load orthomcl/2.0.3
pagan0.61module load pagan/0.61
pairfq0.14.4module load pairfq/0.14.4
paml4.9amodule load paml/4.9a
pandaseq2.8.1module load pandaseq/2.8.1
peargit-2c309dcmodule load pear/git-2c309dc
pbsuite15.8.24module load pbsuite/15.8.24
perl5.22.3module load perl/5.22.3
PGDSpider2.1.1.0module load pgdspider/2.1.1.0
phrap1.080812module load phrap/1.080812
phred0.990722.fmodule load phred/0.990722.f
phylip3.696module load phylip/3.696
phyml20120412module load phyml/20120412
picard2.8.2module load picard/2.8.2
picrust1.0.0module load picrust/1.0.0
platanus1.2.1module load platanus/1.2.1
plink1.9module load plink/1.9
polyphen2.2.2module load polyphen/2.2.2
prank150803module load prank/150803
presto0.5.3module load presto/0.5.3
primer32.3.6module load primer3/2.3.6
prokka1.11module load prokka/1.11
python3.6.2module load python/3.6.2
qdd3_betamodule load qdd/3_beta
qiime1.9.1module load qiime/1.9.1
quast4.5module load quast/4.5
Quorum1.1.1module load quorum/1.1.1
R3.3.2module load R/3.3.3
rmblast2.2.28module load rmblast/2.2.28
rstudiov0.97.551module load rstudio/v0.97.551
rapsearch2.10module load rapsearch/2.10
RATTr18module load ratt/r18
RAxML8.2.0module load RAxML/8.2.0
ray2.3.1module load ray/2.3.1
RDP Classifier2.11module load rdp-classifier/2.11
repeatmasker3.3.0module load repeatmasker/3.3.0
root6.08.06module load root/6.08.06
rRNASelector1.1module load rrnaselector/1.1
RSEM1.2.21module load RSEM/1.2.21
rseqc2.6.4module load rseqc/2.6.4
ruby2.2.3module load ruby/2.2.3
samtools1.3.1module load samtools/1.3.1
sailfish0.9.2module load sailfish/0.9.2
salmon0.7.2module load salmon/0.7.2
scipio1.4.1module load scipio/1.4.1
scythe0.994-betamodule load scythe/0.994-beta
seq_crumbs0.1.8module load seq_crumbs/0.1.8
seqqsgit-3d053750module load seqqs/git-3d053750
shannon0.0.2module load shannon/0.0.2
sift4.0.3bmodule load sift/4.0.3b
sickle1.33module load sickle/1.33
smalt0.7.6module load smalt/0.7.6
snowhite1.1.4module load snowhite/1.1.4
SnpEff & SnpSift4.1gmodule load snpeff/4.1g
snpmeta2.0module load snpmeta/2.0
SOAPdenovo2r240module load SOAPdenovo2/r240
SOAPaligner2.21module load SOAPaligner/2.21
SOAPsplice1.10module load SOAPsplice/1.10
SOAPdenovo-Trans1.03module load SOAPdenovo-Trans/1.03
SolexaQA++3.1.3module load SolexaQA++/3.1.3
spades3.6.0module load spades/3.6.0
sourmash1.0module load sourmash/1.0
speedseq0.1.2module load speedseq/0.1.2
splitstree4.11.3module load splitstree/4.11.3
spread1.0.6module load spread/1.0.6
sratoolkit2.8.2module load sratoolkit/2.8.2
sspace3.0module load sspace/3.0
sspace-longread1.1module load sspace-longread/1.1
stacks1.24module load stacks/1.24
staden2.0.0b8module load staden/2.0.0b8
star2.5.2bmodule load make/2.5.2b
structure2.3.4module load structure/2.3.4
stringtie1.0.4module load stringtie/1.0.4
svmlightV6.02module load svmlight/V6.02
tabixgit-76b4bbdfmodule load tabix/git-76b4bbdf
tablet1-15.09.01module load tablet/1-15.09.01
tassel4.0module load tassel/4.0
tmiseq2016-01-31module load tmiseq/2016-01-31
tophat2.1.0module load tophat2/2.1.0
tracer1.6module load tracer/1.6
TransDecoder2.0.1module load TransDecoder/2.0.1
Transrate1.0.3module load transrate/1.0.3
trf4.0.4module load trf/4.0.4
trimmomatic0.33module load trimmomatic/0.33
trinityv2.1.1module load trinity/v2.1.1
trinotate2.0.2module load trinotate/2.0.2
twinscan3.5module load twinscan/3.5
umi-tools module load umi-tools/0.2.3
usearch module load usearch/v7.0.1090
varscan2.4.2module load varscan/2.4.2
vcflibgit-7f1575emodule load vcflib/git-7f1575e
vcftools0.1.14module load vcftools/0.1.14
velvet1.2.10-kmer111module load velvet/1.2.10-kmer111
vep87module load vep/87
vntrseek1.08module load vntrseek/1.08
w2rapgit-60781b6cmodule load w2rap/git-60781b6c
w2rap-contiggergit-a43f5a05module load w2rap-contigger/git-a43f5a05
wise2.4.1module load wise/2.4.1

The source code for all environment modules can be found in ILRI's GitHub repository.

list-of-software.txt · Last modified: 2017/11/09 17:52 by aorth