Software availability

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
`blas`	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`	1.0.6
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
`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-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
`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_toolkit`	0.0.14
`ffmpeg`	4.3.1
`flye`	2.7 , 2.8.3
`freebayes`	1.3.5
`freexl`	1.0.6
G
`gatk`	3.8
`gatk4`	4.1.7.0 , 4.2.0.0
`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`	20210528
`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
`metawrap‑mg`	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
`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
`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

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