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
armadillo8.600.1
arpack3.1.3
atlas3.10.1
autoconf2.69
automake1.13.4
B
bakefile 0.2.9
bash 4.2.46
bc 1.06.95
blas3.4.2
blas64 3.4.2
blt 2.4
boost1.53.0
bwidget1.9.0
bzip21.0.6
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
docker1.13.1
D
ed1.9
emacs24.3
F
fftw 3.3.3
fftw2 2.1.5
filezilla 3.7.4.1
freexl 1.0.6
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
hdf4.2.13
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
java1.8.0
K
ksh 20120801
L
lapack3.4.2
lapack643.4.2
lesstif 0.95.2
libccp4 6.4.6
libexif 0.6.21
libgeotiff 1.2.5
libjpeg-turbo 1.2.90
libmng 1.0.10
libmpc 1.0.1
libpng 1.5.13
libquadmath 4.8.5
librsvg2 2.40.20
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
octave3.8.2
ogdi3.2.0
openjpeg22.3.0
openmpi 1.10.7 , 3.0.2
openssh7.4p1
P
p11-kit 0.23.5
p7zip16.02
pbzip2 1.1.12

pcre

8.32

pcre2

10.23
perl 5.16.3
plplot 5.10.0
proj44.8.0
python2.7.5
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
sdl1.2.15
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
udunits22.2.20
units2.01
unzip 6.0
V
vim 7.4.160
W
wavpack4.60.1
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
admixtools6.0 , 7.0.1
admixture1.3.0
angsd 0.931 , 0.935
assemblyscan 0.3.0
assemblystats 1.0.1
astral5.7.3
augustus 3.3.3 , 3.4.0
B
bamm 1.7.3
bamtools 2.5.1
bayescan2.0.1
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
blast2.9.0 , 2.11.0
blat 36
boost-cpp1.76.0
bowtie22.4.1 , 2.4.3
busco 3.0.2 , 5.1.3
bwa0.7.17
C
cairocffi1.2.0
canu 1.4 , 2.1.1
cap310.2011
cd-hit4.8.1
checkmgenome 1.1.3
cloog0.18.0
corset1.09
coverm 0.5.0 , 0.6.1
cufflinks 2.2.1
cutadapt 2.8 , 3.4
D
dadi2.1.1
das_tool 1.1.2
diamond2.0.9
diamond_add_taxonomy0.1.2
dlcpar 1.0
dmd2.065.0
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_toolkit 0.0.14
ffmpeg 4.3.1
flye2.7 , 2.8.3
freebayes 1.3.5
freexl 1.0.6
G
gatk 3.8
gatk4 4.1.7.0 , 4.2.0.0
gblocks0.91b
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_genome20210528
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 10.4
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
metawrapmg 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
netcdf41.5.6
netcdf-cxx4 4.3.1
netcdffortran 4.5.2
nettle 3.4.1 , 3.7
newick_utils1.6
nlopt 2.6.1 , 2.7.0
O
orfm1.3
orthofinder2.2.6 , 2.5.2
P

pal2nal

14.1

paml

4.9

pandoc

2.9.2 , 2.13

parallel

20210422
pblat 2.5

pcre

8.44

pcre2

10.31 , 10.36

pear

0.9.6

petsc

3.12.4 , 3.15.0

phyluce

1.7.0
picard2.22.0 , 2.25.5
pipits2.5 , 2.7
plink1.90b6.21
pplacer1.1a19
prodigal 2.6.3
proj8.0.1
proj4 6.1.1
proteinortho 6.0.14 , 6.0.30
purge_haplotigs 1.1.1
pyfasta 0.5.2
pyfastaq 3.17.0
pyfastx0.6.7 , 0.8.3
pyproj2.6.1 , 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
slim3.3.2 , 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
trinity2.9.1 , 2.12.0
trinotate 3.2.1
U
ucsc-blat 377
V
vcflib1.0.2
vcftools0.1.16
velvet1.2.10
vsearch2.14.2 , 2.17.0



Custom Software Installations

A
abyss 2.0.3
admb 12.0
anaconda2 2019.10
angsd 0.920
armadillo10.1.0
augustus 3.3
automake1.14.1
B
bamm 2.5.0
bamaddrg20180316
bamtools 2.4.1
bayesass 3.04
bayescan2.1
bayescenv1.1
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
boost1.73.0
bowtie 1.2.2
bowtie22.3.4.1
C
cd-hit4.6.8
cloog0.18.4
cmake 3.13.4
colony2 20170630
conda3 2019.10
corset1.07
curl 7.58.0
D
diamond0.9.22
dmd2.079.0 , 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
gblocks0.91b
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
java1.6.0 , 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
netcdffortran 4.4.4
netphos 1.0
nettle 3.4
NGSadmix 32
nlopt 2.4.2
O
onedrive2.4.11
openblas0.3.10
opencoarrays2.9.2
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
picard2.18.1
pipits1.5.0
proj4.9.3 , 6.1.1
psort 2
python2.7.14
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 / SLiM3.3
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
units2.16
V
vcflib1.0.0
vcftools0.1.13
velvet20140816
vsearch2.7.1
W
wolfpsort0.2
wxWidgets3.1.1
X
xz 5.2.3
Y
yasm 1.3.0
Z
zeromq 4.2.3
zlib 1.2.11