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list-of-software

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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 endeavor to keep this list updated as the One True List™.

Name Latest version How to load Contact
abyss2.1.4module load abyss/2.1.4
abacas1.3.1module load abacas/1.3.1
ace1.01module load ace/1.01
ACT13.0.0module load act/13.0.0
admixture1.3.0module load admixture/1.3.0
AdapterRemoval1.5.4module load AdapterRemoval/1.5.4
aegean0.16.0module load aegean/0.16.0
aliview1.17.1module load aliview/1.17.1
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
augustus3.3module load augustus/3.3
awscli1.17.9module load awscli/1.17.9
bam-readcount0.8.0module load bam-readcount/0.8.0
bamtools2.5.1module load bamtools/2.5.1
barrnap0.9module load barrnap/0.9
bayescan2.1module load bayescan/2.1
bbmap38.67module load bbmap/38.67
bcftools1.8module load bcftools/1.8
beagle3.1.2module load beagle/3.1.2
beast1.10.4module load beast/1.10.4
bedops2.4.29module load bedops/2.4.29
bedtools2.29.0module load bedtools/2.29.0
binpacker1.0module load binpacker/1.0
bioperl1.7.2module load bioperl/1.7.2
bitseq0.7.5module load bitseq/0.7.5
blasrsmrtanalysis-4.0.0module load blasr/smrtanalysis-4.0.0
blast2.10.0+module load blast/2.10.0+
blobtools0.9.19.3module load blobtools/0.9.19.3
blat06-Aug-2013module load blat/06-Aug-2013
bowtie1 1.2.3module load bowtie/1.2.3
bowtie2 2.3.4.1module load bowtie2/2.3.4.1
brig0.95module load brig/0.95
BUSCO 4.0.6module load BUSCO/4.0.6
bwa0.7.17module load bwa/0.7.17
cafe4.1module load cafe/4.1
cangs1.1module load cangs/1.1
canu1.8module load canu/1.8
cap3latestmodule load cap3/latest
cd-hit4.6.8module load cd-hit/4.6.8
cegmav2.5module load cegma/v2.5
celera-wgs6.1module load celera-wgs/6.1
censor4.2.28module load censor/4.2.28
changeo1.0.0module load changeo/1.0.0
checkm1.1.2module load checkm/1.1.2
circos0.69-9module load circos/0.69-9
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
cutadapt1.18module load cutadapt/1.18
dextractorgit-a7f50c52module load dextractor/git-a7f50c52
dendroscope2.7.4module load dendroscope/2.7.4
diamond0.9.9module load diamond/0.9.9
drep2.5.4module load drep/2.5.4
ea-utils1.04.807module load ea-utils/1.04.807
edirect 7.80 module load edirect/7.80
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
fastANI1.3module load fastANI/1.3
fastPHASE1.4.8module load fastPHASE/1.4.8
fastqc0.11.7module load fastqc/0.11.7
fastSTRUCTURE1.0module load fastSTRUCTURE/1.0
fasttree2.1.11module load fasttree/2.1.11
fastx_toolkit0.0.13module load fastx_toolkit/0.0.13
figtree1.4.0module load figtree/1.4.0
flapjack 1.18.04.23-betamodule load flapjack/1.18.04.23-beta
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
flye2.4.2module load flye/2.4.2
frappe1.1module load frappe/1.1
FragGeneScan 1.30module load fraggenescan/1.30
FreeBayes 1.0.2module load freebayes/1.0.2
GassFlow 1.0module load gassflow/1.0
GATK 4.0.10.1module load gatk/4.0.10.1
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
graphmap0.5.2module load graphmap/0.5.2
grom-rd1.0module load grom-rd/1.0
gromacs2018.2module load gromacs/2018.2
groovy2.4.9module load groovy/2.4.9
GSEA2.2.3module load gsea/2.2.3
gtdbtk1.1.1module load gtdbtk/1.1.1
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
hmmer3.3module load hmmer/3.3
hpg-variant1.0module load hpg-variant/1.0
hisat22.1.0module load hisat2/2.1.0
htseq0.9.1module load htseq/0.9.1
htslib1.9module load htslib/1.9
idba1.1.2module load idba/1.1.2
igblast1.10.0module load igblast/1.10.0
igdiscover0.12.3module load igdiscover/0.12.3
igrec3.0.0module load igrec/3.0.0
igsimulatorgit-c3778b74module load igsimulator/git-c3778b74
igv2.4.5module load igv/2.4.5
igvtools2.3.98module load igvtools/2.3.98
infernal1.1.2module load infernal/1.1.2
interproscan5.13module load interproscan/5.13
i-tasserlatestmodule load i-tasser/latest
jellyfish2.2.9module load jellyfish/2.2.9
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
karect1.0module load karect/1.0
kat2.3.4module load kat/2.3.4
kmc3.0.0module load kmc/3.0.0
kmergenie1.7038module load kmergenie/1.7038
kmer-ssrgit-4043c0e7module load kmer-ssr/git-4043c0e7
kraken2.0.8-betamodule load kraken/2.0.8-beta
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
lighter1.1.2module load lighter/1.1.2
lordec0.9module load lordec/0.9
lucy1.19pmodule load lucy/1.19p
mafft7.313module load mafft/7.313
mapsplice2.2.0module load mapsplice/2.2.0
marginaligngit-2369dafdmodule load marginalign/git-2369dafd
marginpolish1.0.0module load marginpolish/1.0.0
mash2.2module load mash/2.2
masurca3.3.1module load masurca/3.3.1
mauve2.3.1module load mauve/2.3.1
maxbin22.2.7module load maxbin2/2.2.7
maximus0.2module load maximus/0.2
mcl14-137module load mcl/14-137
MECATgit-d04bfa84module load MECAT/git-d04bfa84
medaka0.8.2module load medaka/0.8.2
megahit1.1.4module load megahit/1.1.4
megan4.70.4module load megan/4.70.4
megax10.0.5module load megax/10.0.5
metabat2.12.1module load metabat/2.12.1
metaphlan22.9.5module load metaphlan2/2.9.5
metis5.1.0module load metis/5.1.0
migec1.2.4amodule load migec/1.2.4a
migmap1.0.2module load migmap/1.0.2
miniasm0.3module load miniasm/0.3
minimap22.13module load minimap2/2.13
MinPath1.0.2module load MinPath/1.2
mira4.0.2module load mira/4.0.2
mirdeep20.1.3module load mirdeep2/0.1.3
mitools1.4module load mitools/1.4
mixcr3.0.11module load mixcr/3.0.11
mkatari-ilrilatestmodule load mkatari-ilri/latest
modeller9.17module load modeller/9.17
mothur1.44.1module load mothur/1.44.1
mothur-kronagit-87499a0module load mothur-krona/git-87499a0
mpiblast1.6.0module load mpiblast/1.6.0
mrbayes3.2.2module load mrbayes/3.2.2
multiqc1.4module load multiqc/1.4
muscle3.8.1551module load muscle/3.8.1551
MUMmer3.23module load MUMmer/3.23
nanopolish0.10.2module load nanopolish/0.10.2
netmhcpan2.8module load netmhcpan/2.8
nextclip1.3.1module load nextclip/1.3.1
nextflow20.04.1module load nextflow/20.04.1
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
ocaml4.02.1module load ocaml/4.02.1
opam1.2.0module load opam/1.2.0
orthomcl2.0.3module load orthomcl/2.0.3
Oyster River Protocol2.2.8module load orp/2.2.8
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
pastad939adb2module load pasta/d939adb2
pear0.9.6module load pear/0.9.6
pblat2.1module load pblat/2.1
pbsuite15.8.24module load pbsuite/15.8.24
perl5.28.2module load perl/5.28.2
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
phyml3.3.20180621module load phyml/3.3.20180621
picard2.17.0module load picard/2.17.0
picrust1.0.0module load picrust/1.0.0
pilon1.23module load pilon/1.23
platanus1.2.1module load platanus/1.2.1
plink2.00-alphamodule load plink/2.00-alpha
polyphen2.2.2module load polyphen/2.2.2
porechop0.2.4module load porechop/0.2.4
pplacer1.1.alpha19module load pplacer/1.1.alpha19
prank170427module load prank/170427
presto0.5.13module load presto/0.5.13
primer32.3.6module load primer3/2.3.6
prinseq0.20.4module load prinseq/0.20.4
prodigal2.6.3module load prodigal/2.6.3
prokka1.14.6module load prokka/1.14.6
provean1.1.5module load provean/1.1.5
python3.7.7module load python/3.7
qdd3_betamodule load qdd/3_beta
qiime1.9.1module load qiime/1.9.1
qiime22019.10module load qiime2/2019.10
quast5.0.2module load quast/5.0.2
quickmerge0.3module load quickmerge/0.3
Quorum1.1.1module load quorum/1.1.1
R3.6.1module load R/3.6
racon1.3.1module load racon/1.3.1
rmblast2.2.28module load rmblast/2.2.28
rapsearch2.22module load rapsearch/2.22
RATTr18module load ratt/r18
RAxML8.2.12module load RAxML/8.2.12
ray2.3.1module load ray/2.3.1
RDP Classifier2.11module load rdp-classifier/2.11
repeatmasker4.0.5module load repeatmasker/4.0.5
repseqio1.3.3module load repseqio/1.3.3
root6.08.06module load root/6.08.06
rRNASelector1.1module load rrnaselector/1.1
RSEM1.3.1module load RSEM/1.3.1
rseqc2.6.4module load rseqc/2.6.4
ruby2.2.3module load ruby/2.2.3
samtools1.9module load samtools/1.9
sailfish0.9.2module load sailfish/0.9.2
salmon0.9.1module load salmon/0.9.1
scipio1.4.1module load scipio/1.4.1
scythe0.994-betamodule load scythe/0.994-beta
sepp4.3.8module load sepp/4.3.8
seroba1.0.0module load seroba/1.0.0
seq_crumbs0.1.8module load seq_crumbs/0.1.8
seqkit0.11.0module load seqkit/0.11.0
seqqsgit-3d053750module load seqqs/git-3d053750
seqtk1.3module load seqtk/1.3
shannon0.0.2module load shannon/0.0.2
shasta0.4.0module load shasta/0.4.0
sickle1.33module load sickle/1.33
sift4.0.3bmodule load sift/4.0.3b
sistr1.0.2module load sistr/1.0.2
smalt0.7.6module load smalt/0.7.6
smartdenovogit-5cc1356bmodule load smartdenovo/git-5cc1356b
snakemake5.7.0module load snakemake/5.7.0
snowhite1.1.4module load snowhite/1.1.4
SnpEff & SnpSift4.1gmodule load snpeff/4.1g
snpmeta2.0module load snpmeta/2.0
snp-pipeline1.0.1module load snp-pipeline/1.0.1
SOAPdenovo2git-c4d2f5eemodule load SOAPdenovo2/git-c4d2f5ee
SOAPaligner2.21module load SOAPaligner/2.21
SOAPsnp1.03module load SOAPsnp/1.03
SOAPsplice1.10module load SOAPsplice/1.10
SOAPdenovo-Trans1.03module load SOAPdenovo-Trans/1.03
SolexaQA++3.1.3module load SolexaQA++/3.1.3
spades3.13.0module load spades/3.13.0
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
squid1.9gmodule load squid/1.9g
sratoolkit2.10.0module load sratoolkit/2.10.0
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
star2.7.1amodule load star/2.7.1a
structure2.3.4module load structure/2.3.4
stringtie1.3.4dmodule load stringtie/1.3.4d
subread1.6.2module load subread/1.6.2
svmlightV6.02module load svmlight/V6.02
tabixgit-76b4bbdfmodule load tabix/git-76b4bbdf
tablet1.17.08.17module load tablet/1.17.08.17
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
trimmomatic0.38module load trimmomatic/0.38
trinityv2.6.6module load trinity/v2.6.6
trinotate2.0.2module load trinotate/2.0.2
twinscan3.5module load twinscan/3.5
umi-tools 0.2.3 module load umi-tools/0.2.3
unicycler 0.4.7 module load unicycler/0.4.7
usearch v7.0.1090 module load usearch/v7.0.1090
varscan2.4.2module load varscan/2.4.2
vcflibgit-7f1575emodule load vcflib/git-7f1575e
vcftools0.1.15module load vcftools/0.1.15
velvet1.2.10-kmer111module load velvet/1.2.10-kmer111
vep92.1module load vep/92.1
viennarna2.4.14module load viennarna/2.4.14
virusdetect1.7module load virusdetect/1.7
vntrseek1.08module load vntrseek/1.08
vsearch2.8.0module load vsearch/2.8.0
w2rapgit-60781b6cmodule load w2rap/git-60781b6c
w2rap-contiggergit-a43f5a05module load w2rap-contigger/git-a43f5a05
whatshap0.16module load whatshap/0.16
wise2.4.1module load wise/2.4.1
wombat2020-02-07module load wombat/2020-02-07
wtdbg22.4module load wtdbg2/2.4

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

list-of-software.1595847419.txt.gz · Last modified: 2020/07/27 10:56 by aorth