Environment modules for ILRI, Nairobi HPC cluster
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AdapterRemoval
BUSCO
CNVnator
MUMmer
MinPath
R
RAxML
RECON
RSEM
SOAPaligner
SOAPdenovo-Trans
SOAPdenovo2
SOAPsnp
SOAPsplice
SolexaQA++
TransDecoder
abacas
abyss
act
admixture
aegean
aliview
amber
amos
ampssembler
angsd
annovar
apt
arb
artemis
augustus
bam-readcount
bamtools
bayescan
bcftools
beagle
beast
bedops
bedtools
biana
binpacker
bioperl
bitseq
blasr
blast
blat
blobtools
bowtie
bowtie2
brig
bwa
cafe
cangs
canu
cap3
casava
cd-hit
cegma
celera-wgs
censor
changeo
circos
clonalframe
clonalframeml
clustalo
clustalw
cmake
consed
coperead
corset
cufflinks
cutadapt
cytoscape
dendroscope
diamond
ea-utils
easer
edirect
eigenstrat
emboss
est2uni
exabayes
exonerate
express
fastPHASE
fastSTRUCTURE
fastqc
fastx_toolkit
figtree
flapjack
flash
flash2
flexbar
flux-capacitor
fraggenescan
frappe
freebayes
gapfiller
gassflow
gatk
geneid
geneious
genscan
gffread
glimmer
glu
gmap
grom-rd
gromacs
groovy
gsea
guidance
hapflk
hapmix
hdf5
hisat2
hmmer
hpg-variant
htseq
htslib
i-tasser
igblast
igrec
igv
igvtools
ilri
interproscan
jMHC
java
jellyfish
julia
kaiju
kallisto
kat
kmer-ssr
kmergenie
kraken
krona
lamp
lava
ldhat
libsvm
lucy
mafft
maker
mapsplice
mash
masurca
matrix2png
mauve
maximus
mcl
megahit
megan
metabat
metis
migec
migmap
mira
mitools
mixcr
mkatari-ilri
modeller
mothur
mothur_krona
mpiblast
mrbayes
multiqc
muscle
netmhcpan
nextclip
ngsqctoolkit
novacraft
ntcard
oases
ocaml
opam
opencv
openmpi
oracle-jdk
orthomcl
pagan
pairfq
paml
pandaseq
pbsuite
pear
perl
pgdspider
phrap
phred
phylip
phyml
picard
picrust
platanus
plink
polyphen
prank
presto
primer3
prokka
provean
python
qdd
qiime
qiime2
quast
quorum
rapsearch
ratt
ray
rdp-classifier
repeatmasker
repeatmodeler
repeatscout
rmblast
root
rrnaselector
rsa-tools
rseqc
rstudio-server
rstudio
rtax
ruby
sailfish
salmon
samtools
scipio
scythe
seq_crumbs
seqkit
seqqs
seqtk
shannon
sickle
sift
sistr
smalt
snap
snowhite
snp-pipeline
snpeff
snpmeta
soap2
sourcetracker
sourmash
spades
speedseq
splitstree
spread
sratoolkit
sspace-longread
sspace
stacks
staden
star
stringtie
structure
svmlight
tabix
tablet
tassel
tmiseq
tophat
tophat2
tracer
transrate
trf
trimmomatic
trinity
trinotate
twinscan
umi-tools
usearch
varscan
vcflib
vcftools
velvet
vep
virusdetect
vntrseek
vsearch
w2rap-contigger
w2rap
whatshap
wise
454
COPYING
README.md
estscan
seqclean
tagdust
tgicl

README.md

ILRI HPC Environment Modules

This repo contains Environment Modules used in ILRI's research computing infrastructure.

For a full list of software, including build and usage instructions, see the list of software on ILRI's HPC wiki.

Assumptions

These modules load and unload programs installed in the /export/apps/$SOFTWARE/$SOFTWARE_VERSION directory.

For example, in our infrastructure, NCBI BLAST 2.2.30+ is installed in /export/apps/blast/2.2.30+.

License

Copyright (C) 2015–2018 International Livestock Research Institute (ILRI)

The contents of this repository are free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.