The most up-to-date listing of software installed on HPC can be obtained by running
module avail
on a HPC cluster login node. The listing below may not exactly match the output from the above command at any point in time.
Software provided by RedHat
| A | |
|---|---|
armadillo | 8.600.1 |
arpack | 3.1.3 |
atlas | 3.10.1 |
autoconf | 2.69 |
automake | 1.13.4 |
| B | |
bakefile | 0.2.9 |
bash | 4.2.46 |
bc | 1.06.95 |
bla | 3.4.2 |
blas64 | 3.4.2 |
blt | 2.4 |
boost | 1.53.0 |
bwidget | 1.9.0 |
bzip2 | 1.0.6 |
| C | |
cairo | 1.15.12 |
cfitsio | 3.370 |
clipper | 2.1 |
cmake | 2.8.12.2 |
cogl | 1.22.2 |
curl | 7.29.0 |
cvs | 1.11.23 |
| D | |
docker | 1.13.1 |
| D | |
ed | 1.9 |
emacs | 24.3 |
| F | |
fftw | 3.3.3 |
fftw2 | 2.1.5 |
filezilla | 3.7.4.1 |
freexl | 1.0.5 |
| G | |
gawk | 4.0.2 |
gcc | 4.8.5 |
gd | 2.0.35 |
gdal | 1.11.4 |
gdl | 0.9.7 |
ghc | 7.6.3 |
giflib | 4.1.6 |
git | 1.8.3.1 |
glibc | 2.17 |
glpk | 4.52.1 |
gmp | 6.0.0 |
gnuplot | 4.6.2 |
gnutls | 3.3.26 |
GraphicsMagick | 1.3.29 |
graphviz | 2.30.1 |
grass | 6.4.4 |
gsl | 1.15 |
gzip | 1.5 |
| H | |
hdf | 4.2.13 |
hdf5 | 1.8.12 |
| I | |
ImageMagick | 6.7.8.9 |
imake | 1.0.5 |
imlib | 1.9.15 |
imlib2 | 1.4.5 |
| J | |
jasper | 1.900.1 |
| java | 1.8.0 |
| K | |
ksh | 20120801 |
| L | |
lapack | 3.4.2 |
lapack64 | 3.4.2 |
lesstif | 0.95.2 |
libccp4 | 6.4.6 |
libexif | 0.6.21 |
libgeotiff | 1.2.5 |
libjpeg | 1.5.1 |
libjpeg-turbo | 1.2.90 |
libmng | 1.0.10 |
libmpc | 1.0.1 |
libpng | 1.5.13 |
libquadmath | 4.8.5 |
librsvg2 | 4.8.5 |
libtiff | 4.0.3 |
libtool | 2.4.2 |
lzo | 2.06 |
| M | |
make | 3.82 |
maxima | 5.41.0 |
mercurial | 2.6.2 |
motif | 2.3.4 |
mpfr | 3.1.1 |
mpich | 3.0 , 3.2 |
mvapich | 2.0 , 2.2 , 2.3 |
| N | |
nano | 2.3.1 |
ncl | 6.3.0 |
nco | 4.4.4 |
ncurses | 5.9 |
netcdf | 4.3.3.1 |
netpbm | 10.79.00 |
nettle | 2.7.1 |
| O | |
octave | 3.8.2 |
ogdi | 3.2.0 |
openjpeg2 | 2.3.0 |
openmpi | 1.10.7 , 3.0.2 |
openssh | 7.4p1 |
| P | |
p11-kit | 0.23.5 |
p7zip | 16.02 |
pbzip2 | 1.1.12 |
pcre | 8.32 |
pcre2 | 10.23 |
perl | 5.16.3 |
plplot | 5.10.0 |
proj4 | 4.8.0 |
python | 2.7.5 |
| Q | |
qhull | 2003.1 |
qrupdate | 1.1.2 |
qt | 4.8.5 |
qt3 | 3.3.8b |
qt5 | 5.6.2 |
| R | |
rcs | 5.9.0 |
readline | 6.2 |
ruby | 2.0.0.648 |
| S | |
sdl | 1.2.15 |
sed | 4.2.2 |
singularity | 2.6.0 |
snappy | 1.1.0 |
sqlite | 3.7.17 |
subversion | 1.7.14 |
suitesparse | 4.0.2 |
superlu | 5.2.0 |
| T | |
tar | 1.26 |
tcl | 8.5.13 |
tclx | 8.4.0 |
tcsh | 6.18.01 |
tix | 8.4.3 |
tk | 8.5.13 |
tkinter | 2.7.5 |
| U | |
udunits2 | 2.2.20 |
units | 2.01 |
unzip | 6.0 |
| V | |
vim | 7.4.160 |
| W | |
wavpack | 4.60.1 |
| X | |
xfig | 3.2.5 |
xz | 5.2.2 |
| Z | |
zlib | 1.2.7 |
zsh | 5.0.3 |
Conda Environments
| A | |
|---|---|
abyss | 2.2.4 . 2.3.1 |
ac-diamond | 1.0 |
admixtools | 6.0 , 7.0.1 |
admixture | 1.3.0 |
angsd | 0.931 , 0.935 |
assembly‑scan | 0.3.0 |
assembly‑stats | 1.0.1 |
astral | 5.7.3 |
augustus | 3.3.3 , 3.4.0 |
| B | |
bamm | 1.7.3 |
bamtools | 2.5.1 |
bayescan | 2.0.1 |
bazel | 2.1.0 , 4.1.0 |
bcftools | 1.9 , 1.12 |
beast | 1.10.4 |
beast2 | 2.6.3 |
bedtools | 2.30.0 |
biopython | 1.70 , 1.78 |
bismark | 0.22.3 , 0.23.0 |
blast | 2.9.0 , 2.11.0 |
blat | 36 |
boost-cpp | 1.76.0 |
bowtie2 | 2.4.1 , 2.4.3 |
busco | 3.0.2 , 5.1.3 |
bwa | 0.7.17 |
| C | |
cairocffi | 1.2.0 |
canu | 1.4 , 2.1.1 |
cap3 | 10.2011 |
cd-hit | 4.8.1 |
checkm‑genome | 1.1.3 |
cloog | 0.18.0 |
corset | 1.09 |
coverm | 0.5.0 , 0.6.1 |
cufflinks | 2.2.1 |
cutadapt | 2.8 , 3.4 |
| D | |
dadi | 2.1.1 |
das_tool | 1.1.2 |
diamond | 2.0.9 |
diamond_add_taxonomy | 0.1.2 |
dlcpar | 1.0 |
| dmd | 2.065.0 |
drep | 2.6.2 , 3.2.0 |
| E | |
emboss | 6.6.0 |
enrichm | 0.5.0 , 0.6.3 |
exonerate | 2.4.0 |
| F | |
fasta3 | 36.3.8 |
fastai | 2.3.1 |
fastme | 2.1.5 |
fastp | 0.20.1 |
fastqc | 0.11.9 |
faststructure | 1.0 |
fastx | 0.0.14 |
ffmpeg | 4.3.1 |
flye | 2.7 , 2.8.3 |
freebayes | 1.3.5 |
freexl | 1.0.6 |
| G | |
gatk | 3.8ls |
gatk4 | 4.1.7.0 , 4.2.2.0 |
gblocks | 0.91b |
gdal | 3.0.4 , 3.3.0 |
gdc | 2.0 |
glpk | 4.65 |
gmap | 2021.03.08 |
gmsh | 4.5.3 , 4.8.4 |
gnuplot | 5.4.1 |
gradle | 6.2.2 , 7.0.2 |
graftm | 0.13.1 |
graftm_genome | |
gtdbtk | 1.5.0 |
| H | |
hdf4 | 4.2.15 |
hdf5 | 1.10.6 . 1.12.0 |
hisat2 | 2.2.1 |
hmmer | 3.3 , 3.3.2 |
hmmer2 | 2.3.2 |
| I | |
iqtree | 2.1.2 |
itsx | 1.1.3 |
| J | |
jags | 4.3.0 |
jellyfish | 2.2.10 |
julia | 1.0.3 , 1.1.1 |
| K | |
kmer-jellyfish | 2.3.0 |
kraken | 1.1.1 |
kraken2 | 2.0.8 , 2.1.2 |
krakenuniq | 0.5.8 |
krona | 2.7.1 , 2.8 |
| L | |
lastz | 1.0.4 |
libgdal | 3.3.0 |
libnetcdf | 4.8.0 |
| M | |
mafft | 7.475 |
mapdamage2 | 2.2.1 |
maxbin2 | 2.2.7 |
mcl | 14.137 |
medaka | 1.0.3 , 1.3.3 |
megahit | 1.2.9 |
metabat2 | 2.15 |
metawrap‑ng | 1.3.2 |
metis | 5.1.0 |
mfqe | 0.5.0 |
migrate-n | 3.6.11 |
minimap2 | 2.17 , 2.20 |
mirdeep2 | 2.0.1.2 |
mrbayes | 3.2.7 |
multiqc | 1.9 , 1.10.1 |
muscle | 3.8.1551 |
| N | |
netcdf4 | 1.5.6 |
netcdf-cxx4 | 4.3.1 |
netcdf‑fortran | 4.5.2 |
nettle | 3.4.1 , 3.7 |
newick_utils | 1.6 |
nlopt | 2.6.1 , 2.7.0 |
| O | |
orfm | 1.3 |
orthofinder | 2.2.6 , 2.5.2 |
| P | |
| 14.1 |
| 4.9 |
| 2.9.2 , 2.13 |
| 20210422 |
pblat | 2.5 |
| 8.44 |
| 10.31 , 10.36 |
| 0.9.6 |
| 3.12.4 , 3.15.0 |
| 1.7.0 |
picard | 2.22.0 , 2.25.5 |
pipits | 2.5 , 2.7 |
plink | 1.90b6.21 |
pplacer | 1.1a19 |
prodigal | 2.6.3 |
proj | 8.0.1 |
proj4 | 6.1.1 |
proteinortho | 6.0.14 , 6.0.30 |
purge_haplotigs | 1.1.1 |
pyfasta | 0.5.2 |
pyfastaq | 3.17.0 |
pyfastx | 0.6.7 , 0.8.3 |
pyproj | 2.6.1 , 3.1.0 |
| Q | |
qualimap | 2.2.2d |
quast | 5.0.2 |
| R | |
R | 3.6.1 , 4.0.3 , 4.1.0 |
r-rstan | 2.21.2 |
rcorrector | 1.0.4 |
rdp_classifier | 2.2 , 2.13 |
repeatmodeler | 2.0.1 |
rnastructure | 6.1 |
| S | |
salmon | 1.1.0 , 1.5.0 |
samtools | 1.9 , 1.12 |
scalpel | 0.5.4 |
seqtk | 1.3 |
sga | 0.10.15 |
shannon_cpp | 0.5.0 |
shovill | 0.9.0 , 1.1.0 |
slim | 3.3.2 , 3.6 |
sortmerna | 4.2.0 , 4.3.3 |
spades | 3.14.0 , 3.15.2 |
sparsehash | 2.0.3 |
sra-tools | 2.10.3 , 2.11.0 |
stacks | 2.52 , 2.55 |
star | 2.7.3a , 2.7.9a |
stringtie | 2.1.1 , 2.1.5 |
structure | 2.3.4 |
| T | |
tensorflow | 2.4.1 |
tpp | 5.0.0 |
transdecoder | 5.5.0 |
transrate | 1.0.3 |
treemix | 1.13 |
treeshrink | 1.3.4 , 1.3.9 |
trimal | 1.4.1 |
trim-galore | 0.6.6 |
trimmomatic | 0.39 |
trinity | 2.9.1 , 2.12.0 |
trinotate | 3.2.1 |
| U | |
ucsc-blat | 377 |
| V | |
vcflib | 1.0.2 |
vcftools | 0.1.16 |
velvet | 1.2.10 |
vsearch | 2.14.2 , 2.17.0 |
Custom Software Installations
| A | |
|---|---|
abyss | 2.0.3 |
admb | 12.0 |
anaconda2 | 2019.10 |
angsd | 0.920 |
armadillo | 10.1.0 |
augustus | 3.3 |
automake | 1.14.1 |
| B | |
bamm | 2.5.0 |
bamaddrg | 20180316 |
bamtools | 2.4.1 |
bayesass | 3.04 |
bayescan | 2.1 |
bayescenv | 1.1 |
bazel | 0.15.0 |
bcftools | 1.3 , 1.5 , 1.7 |
beast | 2.4.6 , 2.4.8 , 2.6.0 , 2.6.1 |
bedtools | 2.1.2 |
bedtools2 | 2.25.0 |
bfast | 0.6.5a |
boost | 1.73.0 |
bowtie | 1.2.2 |
bowtie2 | 2.3.4.1 |
| C | |
cd-hit | 4.6.8 |
cloog | 0.18.4 |
cmake | 3.13.4 |
colony2 | 20170630 |
conda3 | 2019.10 |
corset | 1.07 |
curl | 7.58.0 |
| D | |
diamond | 0.9.22 |
| dmd | 2.079.0 , 2.096.0 |
| E | |
exabayes | 1.5 |
exiftool | 10.60 |
| F | |
fasta | 36.3.8g |
fastp | 0.20.0 |
fastqc | 0.11.7 |
fastsimcoal2 | 2.6.0.3 |
faststructure | 20190710 |
fastx | 0.0.14 |
ffmpeg | 3.4.2 |
fpart | 1.0.0 |
freebayes | 1.3.1 |
| G | |
gblocks | 0.91b |
gcc | 8.4 10.1 |
gdal | 2.2.3 , 2.2.4 , 3.0.1 |
gdc | 2.068.2 |
glassfish | 4.1.1 |
glpk | 4.65 |
gmap | 20180311 |
gmp | 6.1.2 |
gmsh | 3.0.6 |
gnuplot | 5.2.2 |
gradle | 4.6 |
graphbin | 1.3 |
grass | 7.4.0 , 7.8.0 |
gsl | 2.4 |
gzip | 1.9 |
| H | |
hdf5 | 1.10.1 , 1.10.5 |
hisat2 | 2.1.0 |
hmmer | 2.3.2 , 3.1b2 |
htslib | 1.3 , 1.5 , 1.7 |
hybpiper | 1.3.1 |
| I | |
interproscan | 5.47 |
iqtree | 1.6.9 , 2.0.8 , 2.1.0 |
isl | 0.18 |
itsx | 1.0.11 |
| J | |
jags | 4.3.0 |
| java | 1.6.0 , 1.7.0 , 1.8.0 , 11.0.1 |
jbigkit | 2.1 |
jellyfish | 2.2.10 |
jpeg | 6b |
julia | 1.2.0 , 1.4.1 , 1.6.1 |
| K | |
kraken | 1.0 |
| L | |
lastz | 1.04.00 |
libcerf | 1.3 |
libffi | 3.2.1 |
libgd | 2.2.5 |
libgeotiff | 1.4.2 |
libgtextutils | 0.7 |
libpng | 1.6.34 |
libtiff | 4.0.9 |
libtasn1 | 4.13 |
lzo | 2.10 |
| M | |
maespa | 20180227 |
mafft | 7.394 |
matlab | 2018a , 2019b , 2020b |
megax | 10.1.8 |
migrate | 3.7.0 |
minimap2 | 2.17 |
molphy | 2.3b3 |
mpc | 1.1.0 |
mpfr | 4.0.1 |
mrbayes | 3.2.7 |
muscle | 3.8.31 |
mvcli | 4.1.13.31 |
| N | |
ncurses | 6.1 |
netbeans | 8.2 |
netcdf | 4.6.0 |
netcdf‑fortran | 4.4.4 |
netphos | 1.0 |
nettle | 3.4 |
NGSadmix | 32 |
nlopt | 2.4.2 |
| O | |
onedrive | 2.4.11 |
openblas | 0.3.10 |
opencoarrays | 2.9.2 |
openmpi | 4.1.1 |
| P | |
parallel | 20180122 |
paup | 4b10 , 4a154 |
pbmpi | 20180308 |
pcre | 8.41 |
pcre2 | 10.31 |
pear | 0.9.10 , 0.9.11 |
perl | 5.26.1 |
petsc | 3.10.0 |
pftools | 2.3 |
pgdspider | 2.1.1.2 |
phyutility | 2.7.1 |
phyx | 1.1 |
| picard | 2.18.1 |
| pipits | 1.5.0 |
| proj | 4.9.3 , 6.1.1 |
psort | 2 |
python | 2.7.14 |
python3 | 3.6.5 |
| Q | |
qgis | 3.12.2 |
| R | |
R | 3.6.1 |
r8s | 1.8.1 |
raxml | 8.2.11 |
rclone | 1.53.1 |
rdp_classifier | 2.12 |
readline | 7.0 |
rnammer | 1.2 |
rsem | 1.3.0 , 1.3.1 |
rstudio | 1.2.5001 |
ruby | 2.5.0 |
| S | |
salmon | 0.9.1 , 0.10.0 , 0.13.1 |
samtools | 1.3 , 1.5 , 1.7 |
secretomep | 1.0 |
SEG | 20180228 |
seqtk | 1.3 |
signalp | 3.2.4.1 |
slim (hydro.) | ? |
slim / SLiM | 3.3 |
SOAPnuke | 2.1.0 |
spades | 3.12.0 |
sparsehash | 2.0.3 |
sratools | 2.9.0 , 2.9.4 |
star | 2.7.0e |
stringtie | 2.0.4 |
structure | 2.3.4 |
swig | 4.0.2 |
| T | |
termcap | 1.3.1 |
tiff | 4.0.9 |
tiger | 202001 |
tmhmm | 2.0c |
tophat | 2.1.1 |
transdecoder | 3.0.0 |
trimal | 1.2 |
trimgalore | 0.5.0 |
trimmomatic | 0.38 |
trinityrnaseq | 2.6.6 |
trinotate | 3.0.1 |
| U | |
units | 2.16 |
| V | |
vcflib | 1.0.0 |
vcftools | 0.1.13 |
velvet | 20140816 |
vsearch | 2.7.1 |
| W | |
wolfpsort | 0.2 |
wxWidgets | 3.1.1 |
| X | |
xz | 5.2.3 |
| Y | |
yasm | 1.3.0 |
| Z | |
zeromq | 4.2.3 |
zlib | 1.2.11 |