Graphical Software
Command-line Software on SCINet Clusters
Each SCINet cluster has software preinstalled on it. Some general software is available in the global environment but most specialized scientific software is managed by the Module system. This software can be loaded with a command like
or a specific version can be selected with
module load bamtools/2.5.1
Available modules are listed below in the section Ceres Command-line Software Managed by the Module System.
The command-line software I need is not on the list!
No problem. You have two options: 1) you can install the software yourself or 2) you can request the software be installed for you.
Option 1: Install the software yourself
The easiest way to do this is to use a conda environment. Often times installing the software you need is as easy as typing
conda create --name my_environment my_program
Thousands of biological packages and their dependencies can be installed with a single command using the Bioconda repository for the Conda package manager. You can also install a package directly from Github or elsewhere and compile it yourself. For more on installing Conda see User-installed Software on Ceres with Conda.
You can also install and or compile software manually in your $HOME or $PROJECT directories. This is the fastest and easiest way to get your software.
Option 2: Request a new module be installed
If you need software that you think will be useful to many SCINet users you can request that the software be installed as a module. Doing this requires an agency-level security review and takes a few weeks. Modules can be requested with the software request form (eAuthentication required, non-ARS users should contact their sponsor):
Software Request Form
Ceres Command-line Software Managed by the Module System
List updated October 9, 2020. To generate this list run module avail.
| Application |
Version(s) |
|
TBB
|
4.4 |
|
a5_miseq
|
20160825--pl5.22.0_0 |
|
abricate
|
0.5 |
|
abyss
|
2.0.2 |
|
ace
|
1 |
|
admixture
|
1.3.0 |
|
agbase
|
1.0.0 |
|
agbase_interproscan
|
5.36-75.0_0 |
|
allmaps
|
1.0 |
|
allpathslg
|
52488 |
|
alphaimpute
|
1.9.2 |
|
amap
|
2.2 |
|
amos
|
3.1.0 |
|
amphora
|
2.0.0 |
|
antismash
|
4.2.0 |
|
antlr
|
2.7.7 |
|
anvio
|
6.2 |
|
arcs
|
1.0.0 |
|
argtable2
|
2.13 |
|
arrowgrid
|
1.0.0 |
|
augustus
|
3.2.3, 3.3.2 |
|
bamm
|
1.7.3 |
|
bamm_groopm_checkm_refinem
|
latest |
|
bamtools
|
2.4.0, 2.5.1 |
|
barrnap
|
0.8 |
|
bayestraits
|
2.0 |
|
bazel
|
0.4.5 |
|
bbtools
|
36.92, 37.02, 38.79 |
|
bcftools
|
1.2, 1.4.1, 1.9 |
|
bcl2fastq
|
2.2 |
|
beagle-geno
|
4.1, 5.0 |
|
beagle
|
2.1.2, 3.1.1 |
|
beast
|
1.8.2, 1.10.4 |
|
beast2
|
2.5.2, 2.6.2 |
|
bedtools
|
2.25.0 |
|
beopest
|
14.02 |
|
bigscape
|
latest |
|
binutils
|
2.25 |
|
bio_polyploid_tools
|
1.1.2 |
|
bismark
|
0.16.2 |
|
blast+
|
2.2.31, 2.6.0, 2.9.0 |
|
blast
|
2.2.26 |
|
blat
|
35, 36 |
|
blobtools
|
1.0.1, 1.1.1 |
|
blupf90
|
20190531 |
|
boost
|
1.62.0 |
|
bowtie
|
1.1.2 |
|
bowtie2
|
2.2.6, 2.3.4 |
|
braker
|
2.1.2, 2.1.5 |
|
braker1
|
1.9 |
|
breakdancer
|
1.4.5 |
|
busco
|
1.1b1 |
|
busco2
|
2.0.1 |
|
busco3
|
3.0.2, 3.1.0 |
|
busco4
|
4.0.2 |
|
bwa
|
0.7.12, 0.7.17 |
|
bzip2
|
1.0.6 |
|
cDNA_cupcake
|
5.8.0 |
|
cactus
|
2019.03.01--py27hdbcaa40_1 |
|
canu
|
latest, 1.6, 1.6.0, 1.7.0, 1.7.1_0828, 1.7.1_0830, 1.7.1, 1.8, 1.9, 2.0, 2.1 |
|
canu16
|
1.6.0 |
|
cap3
|
3 |
|
card
|
1.1.3 |
|
cd-hit
|
4.6.4 |
|
censor
|
4.2.29 |
|
centrifuge
|
1.0.4-beta |
|
cfncluster
|
1.3.1 |
|
checkm
|
v1.0.11, 1.1.2 |
|
circlator
|
1.5.0 |
|
circos
|
0.69.6 |
|
cisa
|
2014.03.04 |
|
clark
|
1.2.3.2, 1.2.5.1 |
|
clustalomega
|
1.2.3, 1.2.4 |
|
cmake
|
3.10.0 |
|
cnvnator
|
v0.3.3, 0.4.1 |
|
cogent
|
2.1 |
|
combine_gafs
|
1.0 |
|
cometgazer
|
1.0 |
|
concoct
|
latest, 1.0.0--py36h88e4a8a_5, 1.1.0--py36h88e4a8a_0 |
|
consensuscore
|
1.0.0 |
|
crl_scripts
|
1.0 |
|
cuda
|
9.2, 10.0 |
|
cudnn
|
7.4.1, 7.5.0.56 |
|
cufflinks
|
2.2.1 |
|
curl
|
7.54.0 |
|
cutadapt
|
1.16 |
|
daccord
|
0.0.17 |
|
daligner
|
2020.01.15, 2020.05.04, 2020.07.27 |
|
damapper
|
2020.05.04 |
|
damasker
|
2020.05.04 |
|
dascrubber
|
1.1 |
|
dastool
|
1.1.0, 1.1.1 |
|
dazz_db
|
2020.05.04 |
|
delly
|
0.8.1 |
|
dentist
|
1.0.0-beta.1, 1.0.0-beta.3 |
|
diamond
|
0.8.29, 0.9.18, 0.9.28 |
|
discovar
|
52488 |
|
discovardenovo
|
52488 |
|
dna_3d
|
1.0.0, 180922 |
|
eautils
|
1.04.807 |
|
eccodes
|
2.7.3 |
|
edirect
|
11.7 |
|
eigen
|
3.2.6, 3.3.7 |
|
emboss
|
6.6.0 |
|
envi
|
5.5 |
|
epic
|
0810 |
|
esmf
|
7.1.0 |
|
evm
|
1.1.1 |
|
exabayes
|
1.4.1 |
|
exonerate
|
2.2.0 |
|
express
|
f845cab |
|
falcon
|
0.3.0, 0.4.2 |
|
fargene
|
1.0.0 |
|
fasta
|
36.3.8e |
|
fastaindex
|
0.11c |
|
fastme
|
2.1.6.1 |
|
fastqc
|
0.11.5, 0.11.9 |
|
faststructure
|
latest, 1.0 |
|
fasttreemp
|
2.1.8 |
|
fastx
|
0.0.14 |
|
flexbar
|
2.5.0 |
|
flye
|
2.5, 2.6, 2.7 |
|
fraggenescan
|
1.3.0, 1.31 |
|
frc_align
|
1.0.0 |
|
freebayes
|
1.1.0, 1.2.0, 1.3.1 |
|
funannotate
|
1.5.3, 1.7.4 |
|
gapcloser
|
1.12 |
|
garli
|
2.01 |
|
gatk
|
3.6, 3.8-1, 4.0.8.1 |
|
gcc
|
5.3.0, 8.1.0, 9.1.0 |
|
gdal
|
2.4.2 |
|
geant4
|
10.1.2, 10.4.0 |
|
gemma
|
0.96 |
|
geneious
|
11.1.5, 11.1.5 |
|
genemark
|
4.33, 4.59 |
|
genomestrip
|
2.00.1685 |
|
genometools
|
1.5.9 |
|
genomicconsensus
|
1.0.0 |
|
gensel
|
4.90 |
|
get_homologues
|
3.2.3 |
|
git
|
2.7.1 |
|
glimmer3
|
3.02 |
|
glpk
|
4.55 |
|
gmap_gsnap
|
2017-03-17, 2020-04-08 |
|
gmp
|
6.1.0 |
|
gnuplot
|
4.6.7 |
|
goanna
|
2.0 |
|
google_cloud_sdk
|
211.0.0, 308.0.0 |
|
grib-api
|
1.26.1 |
|
groopm
|
1.7.3 |
|
gsl
|
2.3 |
|
gtdbtk
|
0.3.2, 1.2.0 |
|
guppy-cpu
|
3.1.5, 3.6.1 |
|
guppy-gpu
|
3.1.5, 3.6.1 |
|
gzip
|
1.9 |
|
h2o
|
3.2.0.3 |
|
h5py
|
2.5.0 |
|
haplomerger2
|
20180603 |
|
hawk
|
0.9.8 |
|
hdf5
|
1.8.9, 1.8.16, 1.8.19 |
|
hgtector
|
0.2.1 |
|
hisat2
|
2.0.5, 2.2.0 |
|
hmmer3
|
3.1b2, 3.2.1 |
|
htslib
|
1.10 |
|
htstream
|
1.0.0 |
|
humann2
|
0.11.1 |
|
idba
|
1.1.2 |
|
igvtools
|
2.8.2 |
|
infernal
|
1.1.2 |
|
intarna
|
3.1.3--h176a8bc_0 |
|
intel
|
2017.3 |
|
interproscan
|
5.24-63.0, 5.42-78.0, 5.44-79.0 |
|
iq_tree
|
1.5.3, 1.5.5-omp, 1.6.8, 1.6.10, 1.6.12, 2.0-rc1 |
|
isescan
|
1.5.4.3 |
|
itasser
|
5.0 |
|
itsx
|
1.1b |
|
java
|
1.7.0_80, 1.8.0_121, 11.0.2 |
|
java_8_sdk
|
1.8.0_121 |
|
jellyfish
|
1.1.11 |
|
jellyfish2
|
2.2.9 |
|
jemalloc
|
4.0.4 |
|
juicer
|
latest, 1.6.2 |
|
kaiju
|
1.5.0, 1.6.0, 1.6.3, 1.7.2 |
|
kallisto
|
0.42.4 |
|
kentutils
|
302 |
|
kineros2
|
2.0 |
|
kobas
|
3.0.3_0 |
|
kraken
|
0.10.5-beta, 1.1 |
|
kraken2
|
2.0.7-beta, 2.0.8-beta |
|
ksnp3
|
3.021 |
|
kstat
|
0.0.1 |
|
ldt
|
7.2r |
|
libevent
|
2.0.22 |
|
libexpat
|
2.2.0 |
|
libgd
|
2.2.3 |
|
libgtextutils
|
0.7 |
|
libmaus2
|
2.0.717, 2018.11.29 |
|
libpng
|
1.6.28 |
|
lis
|
7.2r |
|
llvm
|
5.0.0 |
|
lordec
|
0.8 |
|
lumpy
|
0.2.13, 0.3.0 |
|
mafft
|
7.307, 7.429 |
|
maker-mpich
|
2.31.10 |
|
maker
|
2.31.10 |
|
maker3
|
3.01.03 |
|
maker_centos7
|
3.00.0-beta |
|
manta
|
1.1.1 |
|
mariadb
|
10.1 |
|
masurca
|
3.1.3, 3.2.4, 3.3.1, 3.3.6 |
|
matlab_runtime
|
R2017b |
|
mauve
|
2015-02-13 |
|
maxbin
|
2.2.5, 2.2.7 |
|
mcl
|
14-137 |
|
mcscanx
|
1.0.0 |
|
mdust
|
1.0 |
|
mecat
|
1.0.0 |
|
mecat2
|
2019.03.04, 20190314, 20200228 |
|
med-foes
|
0.6 |
|
megahit
|
1.1.1, 1.2.9 |
|
megan
|
6.17.0, 6.18.4 |
|
merqury
|
1.0 |
|
meryl
|
1.0 |
|
metabat
|
0.32.4, 2.12.1 |
|
metabgc
|
1.1.0, 1.2 |
|
metagenemark
|
3.26 |
|
metaphian2
|
2.6.0 |
|
metavelvet
|
1.2.02 |
|
metawrap
|
1.1--0, 1.2--0 |
|
methpipe
|
3.4.3 |
|
metis
|
5.1.0 |
|
minced
|
0.3.0 |
|
miniasm
|
0.3 |
|
miniconda
|
3.6, 4.7.12 |
|
minimac4
|
latest |
|
minimap2
|
2.6, 2.16 |
|
minpath
|
1.2 |
|
mira
|
4.9.6 |
|
miranda
|
aug2010 |
|
mitehunter
|
11-2011 |
|
mocat2
|
2.0.0 |
|
mothur
|
1.39.5, 1.40.1, 1.44.2 |
|
mpc
|
1.0.3 |
|
mpfr
|
3.1.3 |
|
mpich
|
3.2 |
|
mrbayes
|
3.2.5 |
|
mstmap
|
1.0 |
|
mugsy
|
1.2.3 |
|
mummer
|
3.23, 4.0.0beta2 |
|
muscle
|
3.8.31 |
|
nanopolish
|
latest |
|
nanopolish_500kbp
|
0.11.1, 0.12.5--h7185e64_0 |
|
necat
|
2020.01.19 |
|
nek5000-intel
|
1.0.0 |
|
nek5000
|
1.0.0 |
|
netcdf-fortran
|
4.4.3 |
|
netcdf
|
4.3.3.1 |
|
newick_utils
|
1.0 |
|
nextflow
|
20.07.1 |
|
ngmlr-avx2
|
0.2.7 |
|
nseg
|
1.0 |
|
octave
|
4.2.1 |
|
openblas
|
0.2.15 |
|
opendronemap
|
latest |
|
openmpi
|
2.0.2, 3.0.0, 3.1.3 |
|
openssl
|
1.1.0c |
|
orthofinder
|
2.2.6, 2.2.7 |
|
pacasus
|
1.1 |
|
papi
|
5.4.1 |
|
parallel
|
20151022 |
|
parsnp
|
1.2 |
|
pasa
|
2.2.0 |
|
paup
|
4a152 |
|
pb-assembly
|
0.0.4--py27_6, 0.0.6, 0.0.8, 0.0.8.1 |
|
pbsuite
|
15.8.24 |
|
pbsuite_new
|
15.8.24 |
|
pbzip2
|
1.1.13 |
|
pcre
|
8.41 |
|
pear
|
0.9.10 |
|
perl
|
5.22.0, 5.24.1, 5.32.0 |
|
pgap
|
2020-07-09.build4716 |
|
phyloflash
|
3.3b4 |
|
phylosift
|
1.0.1 |
|
phyml
|
20151014 |
|
picard
|
2.9.2, 2.22.3 |
|
piggy
|
1.2 |
|
pigz
|
2.3.3 |
|
pilon
|
1.22, 1.23 |
|
pindel
|
1.0 |
|
plasflow
|
1.0.7 |
|
platanus
|
1.2.4 |
|
plink
|
1.07, 1.9, 2.0_avx2, 2.0 |
|
porechop
|
0.2.3 |
|
poretools
|
0.6.0 |
|
postgresql
|
9.6.1 |
|
pplacer
|
v1.1.alpha19 |
|
prodigalorffinder
|
2.6.3 |
|
proj4
|
4.9.2, 4.9.3 |
|
prokka
|
1.12, 1.13, 1.14.0, 1.14.5 |
|
protexcluder
|
1.2 |
|
provean
|
1.1.5 |
|
pspp
|
1.0.1 |
|
pullseq
|
1.0.2 |
|
purge_dups
|
1.0, 1.0.1 |
|
purge_haplotigs
|
1.1.1 |
|
pyscaf
|
0.12a4 |
|
python36
|
2-alpine3.6 |
|
python_2
|
2.7.10, 2.7.12, 2.7.13, 2.7.14, 2.7.18 |
|
python_3
|
3.5.0, 3.6.6 |
|
qiime
|
latest, 1.9.1--np112py27_1 |
|
qiime2
|
latest, 2.2017.12, 2.2018.2, 2019.4, 2019.10, 2020.2, 2020.6 |
|
qiime_vsearch
|
1.9.1 |
|
qtlcart
|
1.17f |
|
quast
|
3.1, 5.0.2 |
|
quickmerge
|
0.2 |
|
r-gcc-9.1.0
|
3.6.1 |
|
r-intel
|
3.6.1 |
|
r
|
3.4.0, 3.4.1, 3.4.3, 3.5.2, 3.6.1 |
|
racon
|
1.3.0, 1.4.3 |
|
ragtag
|
1.0.1 |
|
raxml
|
8.2.3, 8.2.12 |
|
reads2resistome
|
0.0.1 |
|
recon
|
1.08 |
|
redundans
|
latest |
|
refinem
|
1.7.3 |
|
repeatmasker
|
4.0.6, 4.0.7, 4.1.0 |
|
repeatmodeler
|
1.0.8 |
|
repeatscout
|
1.0.5 |
|
revbayes
|
1.3.1 |
|
rgi
|
3.1.1, 4.0.3, 5.1.0--py36hed695b0_0, 5.1.0 |
|
rmblast
|
2.2.28 |
|
roary
|
3.12.0 |
|
rsem
|
1.2.23, 1.3.0 |
|
ruby
|
2.7.1 |
|
salmon
|
0.9.1, 0.10.0, 0.10.1 |
|
salsa
|
2.0.0, 2.2 |
|
samtools
|
1.3, 1.4.1, 1.9, 1.10 |
|
sbt
|
0.13.13 |
|
seqkit
|
0.10.1 |
|
seqtk
|
1.2 |
|
sga
|
0.10.13 |
|
sickle
|
1.33 |
|
smart-bs-seq
|
2.2.7 |
|
smartdenovo
|
1.0.0 |
|
smrtanalysis
|
2.3.0.140936 |
|
smrtlink
|
7.0.0, 8.0.0 |
|
smrtsv
|
1.0.0 |
|
snakemake
|
5.25.0 |
|
snap
|
1.0beta.18 |
|
snap_ucdavis
|
2013.11.29 |
|
sniffles
|
1.0.8 |
|
snoscan
|
0.9.1 |
|
snpeff
|
4.3 |
|
soapdenovo2
|
2.04 |
|
soapdenovotrans
|
1.03, 1.04 |
|
soapindel
|
2.1.7.17 |
|
sortmerna
|
4.0.0 |
|
spades
|
3.7.1, 3.10.1, 3.11.1, 3.12.0, 3.14.0 |
|
sparsehash
|
2.0.3 |
|
speedseq
|
0.1.2 |
|
sqlite3
|
3.2.0 |
|
sratoolkit
|
2.5.8, 2.9.0, 2.9.6, 2.10.7 |
|
stacks
|
1.44 |
|
star
|
2.5.2b, 2.7.2b |
|
stringtie
|
1.3.3b, 2.1.1 |
|
structure
|
2.3.4 |
|
subread
|
1.5.2 |
|
superfocus
|
0.27 |
|
supernova
|
1.2.0, 2.0.0, 2.1.1 |
|
svdetect
|
0.8b |
|
swat
|
627 |
|
swig
|
3.0.12 |
|
symap
|
4.2 |
|
tabix
|
1.3.2 |
|
tassel5
|
5.2.37 |
|
tcltk
|
8.6.6 |
|
tcoffee
|
11.00.8cbe486 |
|
tmux
|
2.1, 3.0-rc5 |
|
toil_vg
|
latest, 1.4.1, 1.6.0a1.dev132, 1.6.0a1 |
|
tophat2
|
2.1.0 |
|
trf
|
4.09 |
|
trim_isoseq_polyA
|
1.0.0 |
|
trimmomatic
|
0.38 |
|
trinityrnaseq
|
2.1.1, 2.5.1, 2.6.6, 2.8.4, 2.10.0, 2.11.0 |
|
trinotate
|
2.0.2, 3.1.1 |
|
trnascanse
|
1.3.1, 1.23, 2.0.5 |
|
uclust
|
1.2.22 |
|
udunits
|
2.2.24 |
|
unicycler
|
0.4.4, 0.4.7 |
|
usearch
|
11.0.667 |
|
vasp
|
5.4.4 |
|
vaspvtst
|
5.4.4 |
|
vcftools
|
0.1.15, 0.1.16 |
|
velvet
|
1.2.10 |
|
vicuna
|
1.0.0 |
|
vsearch
|
2.4.0 |
|
wgs_assembler
|
8.3rc2 |
|
xz
|
5.2.3 |
|
zlib
|
1.2.7 |
|
zorro
|
1.0.0 |
