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Preinstalled Software

Graphical Software

Software Information
Galaxy Server SCINet Runs its own Galaxy Server.  Galaxy is an open source, web-based platform for data intensive bioinformatic research.
CLC Server SCINet has a license key to CLC Server
Geneious SCINet has a license key to Geneious
Rstudio SCINet runs a R studio Server
Jupyter  Project Jupyter notebooks and Lab can be run on Ceres

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

module load bamtools

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 December 30, 2024. To generate this list run module avail.
Application Version(s)
TBB 2021.7.0
abricate 1.0.1
abyss 2.3.5
admixture 1.3.0
allmaps 1.1.11--py36h4f025d9_1
alphafold 2.2.0, 2.3.2
alphaimpute 1.9.8
alphapulldown 1.0.4
amber 22-gpu, 22
amptk 1.5.5--pyh7cba7a3_0, 1.6.0--pyhdfd78af_0
annif 0.60.0
antismash 6.1.1, 7.0.0, 7.1.0
antlr 2.7.7-1
anvio 6.2, 7.1, 8
apptainer 1.3.1
arcs 1.2.5
argtable2 2.13
armadillo 11.4.3
arrowgrid 1.0.0
augustus 3.5.0
autoconf 2.71
bamtools 2.5.2
barrnap 0.9
bayestraits 4.0.0
bazel 6.0.0
bbtools 39.01
bcftools 1.16, 1.2
bcl2fastq 2.20.0.422
beagle-geno 5.4
beagle 4.0.0
beast 1.8.4, 1.10.4
beast2 2.7.3
bedops 2.4.41
bedtools 2.30.0
beopest 14.02
bigscape latest, 1.1.9
binutils 2.4
bio_polyploid_tools 1.1.2
bismark 0.24.0
blasr 47.3
blast+ 2.13.0, 2.15.0
blobtools 4.3.6
blupf90 20190531, 20230629, 20240722
boost 1.81.0, 1.85.0
bowtie 1.3.1
bowtie2 2.5.1, 2.5.2
bracken 2.8
braker 2.1.6, 3.0.3
breakdancer 1.4.5
btllib 1.4.10
busco5 5.4.5, 5.7.1
bwa 0.7.17
bwa_mem2 2.2.1_7aa5ff6
bzip2 1.0.6
cactus 2.4.1, 2.6.11, 2.7.2
canu 2.2
cap3 3
card 3.2.6
cd-hit 4.8.1
cdna_cupcake 29.0.0--py310h79ef01b_0
censor 4.2.29
centrifuge 1.0.4
checkm 1.2.2
checkm2 1.0.1
circos 0.69.9
cisa 2014.03.04
clark 1.2.6.1
clustalomega 1.2.4
cmake 3.25.2
cnvnator 0.4.1
code_server 4.9.1
combine_gafs 1.0.0, 1.1
cometgazer 1
concoct 1.1.0--py38h7be5676_2, 1.1.0
consensuscore 1.1.1
cpat 3.0.4
crl_scripts 1
crystal 1.0.1
cuda 12.0.0
cufflinks 2.2.1--py36_2
curl 7.87.0
cutadapt 4
daligner 2022.12.15
damapper 2021.03.30
damasker 2021.03.30
dascrubber 2021.03.30
dastool 1.1.6
datamash 1.8
dazz_db 2022.12.15, 2023.03.25
delly 1.2.6, 1.3.1
dentist 4.0.0
diamond 2.1.2, 2.1.8
discovar 52488
dna_3d 201008
dorado 0.4.2, 0.8.3
eautils 1.04.807
edirect 17.3.20220713
effectorp2 2.0.1
effectorp3 3
egapx 0.1.0-alpha, 0.1.2-alpha, 0.2-alpha, 0.3.0-alpha, 0.3.1-alpha
eig 8.0.0
eigen 3.4.0
emboss 6.6.0
esmfold 2.0.0
evm 2.0.0
exonerate 2.4.0
express 1.5.3
fargene 0.1--py27h21c881e_4, 0.1
fasta 36.3.8i
fastaindex 0.11c
fastme 2.1.6.4
fastqc 0.11.9, 0.12.1
faststructure 1.0--py27h6b1b274_5
fasttreemp 2.1.11
fastx 0.0.14
fcs-genome 45140
flexbar 3.5.0
flye 2.9.1, 2.9.4
fraggenescan 1.31
fragpipe 21.1
frc_align 5b3f53e--boost1.64_0
freebayes 1.3.6
funannotate 1.8.13, 1.8.16
gapcloser 1.12
garli 2.1-3-deb_cv1
gatk 4.0.8.1, 4.3.0.0, 4.4.0.0
gcc 12.2.0
gdal 3.6.2, 3.6.4, 3.10.0
gemma 0.98.5
geneious 2024.0.5
genemark 4.71
genemarkS 4.3
genomestrip 2.00.1833
genometools 1.6.2
genomicconsensus 2.3.3
get_homologues 3.5.4
git 2.39.2
glimmer 3.02
glimmer3 3.02
glimpse 2.0.1
glpk 4.6
gmap_gsnap 2023.02.17
gmp 6.2.1
gnuplot 5.4.6, 5.4.8
go 1.4.3, 1.19.5, 1.20.6
goanna 2.3
google_cloud_sdk 308.0.0, 463.0.0
groopm 1.0.0
gsalign 1.0.22
gsl 2.7
gtdbtk 2.2.3, 2.2.4, 2.2.6, 2.3.2, 2.4.0
guppy-gpu 6.0.6, 6.5.7
h5py 3.8.0
hapcut2 1.3.1
haplomerger2 20180603
hawk 1.6.0, 1.7.0-container, 1.7.0
hdf5 1.14.0
hgtector 2.0b3
hifiasm 0.18.9, 0.19.8, 0.23.0
hisat2 2.2.1
hmmer3 3.3.2
htseq 2.0.2
htslib 1.17
htstream 1.3.3, 45225
humann 3.6, 3.8, 3.9_conda, 3.9, 4.0.0a1
idba 1.1.3
igvtools 2.16.0
infernal 1.1.4
instagraal 0.1.6
intel oneapi-2023.1
interproscan 5.60-92.0, 5.64-96.0, 5.66-98.0, 5.67-99.0, 5.68-100.0, 5.69-101.0, 5.71-102.0
iq_tree 2.0.6, 2.2.0
isescan 1.7.2.3--h031d066_2
itagger 2.3
itsx 1.1.3
jasper 2.0.33, 4.2.4
java 1.8.0_361, 1.8.0, 11, 11.0.2, 15, 16.0.2, 17
jellyfish 1.1.11
jellyfish2 2.2.9
jemalloc 5.3.0
juicer 1.6
julia 1.7.0, 1.9.3
jupyterlab 4.0.4
kaiju 1.9.2
kallisto 0.48.0
kentutils 302.1.0, 45210
kobas 3.0.3_3
kraken 1.1.1
kraken2 2.1.2, 2.1.3
krona 2.8.1
ksnp 4.1
ksnp3 4
l_rna_scaffolder 10302015
lammps 2Aug2023_update3
lammps_gpu 2Aug2023_update3
libdb 5.3.28
libevent 2.1.12
libexpat 2.5.0
libgd 2.3.3
libgsl 2.7.1
libgtextutils 0.7
libmaus2 2.0.813
libpng 1.6.39
libtiff 4.5.0
libzbar 0.23.90
lpsolve 5.5.2.11
ltr_retriever 2.9.5
lumpy 0.3.1
lyve_set 1.1.4f
mach_admix 2.0.203
mafft 7.505
mariadb 11.5
mariadb_connector_c 3.3.4
mash 2.3
masurca 4.1.0
matlab_runtime R2022b
mauve 42048
maxbin 2.2.7
mcscanx 1.0.0
mdust 1
mecat2 20200228
megahit 1.2.9
megan 6_25_3
merfin 1.1
merqury 1.3
meryl 1.4
meson 1.0.0
metabat 2.15
metabgc 2.0.0
metaphlan 4.0.6, 4.1.0, 4.1.1
metavelvet 1.2.02
minced 0.4.2
miniasm 0.3
miniconda 24.7.1-2
minimap2 2.24
minpath 1.4
mira 4.9.6
miranda 1.9, 3.3a--h031d066_6
mirdeep2 0.1.3
mitehunter 40848
mocat2 2.0.0
mothur 1.43.0, 1.48.0
mpc 1.3.1
mpfr 4.2.0
mpich 3.4, 4.1.2
mrbayes 3.2.7
mstmap 1
mugsy 1.2.3
multiqc 1.15
mummer 4.0.0rc1
muscle 5.1.0
namd 3.0b6-CUDA, 3.0b6
nanopolish 0.14.0
necat 20200803
nek5000 19
netcdf-intel 4.9.1
netcdf 4.9.1
netmhccons 1.1a
nextflow 22.04.3, 22.10.6, 23.04.0, 23.04.3, 23.10.1, 24.04.2, 24.10.1
ninja 1.11.1
ninja_phylo 1.2.2
node 20.11.0
nseg 1.0.1
oases 0.2.09
omegafold 1.1.0
openblas 0.3.21
opendronemap 3.3.0
openmpi 4.1.4, 4.1.5
orthofinder 2.5.5
pangloss 0.9.1
papi 7.0.0
parallel 20230222
parsnp 1.7.4, 2.0.5
pasa 2.5.2
paup 4a168
pb-assembly 0.0.8
pbsuite 15.8.24
pbzip2 1.1.13
pepper r0.8
perl 5.36.0
pgap 2022-12-13.build6494, 2023-05-17.build6771, 2023-10-03.build7061
phylip 3.697
phyloflash 3.4.2
phylosift 1.0.1
phylosnp 0.0.1
phyluce 1.7.2, 1.7.3
phyml 3.3.20220408
phyx 1.1
picard 2.26.2, 3.0.0
picrust2 2.5.1
piggy 1.5
pigz 2.7
pilon 1.24
pindel 0.2.5b9--h84372a0_10
platanus 2.0.2
plink 1.9, 2
porechop 0.2.4
porechop_abi 0.5.0
postgresql 15.2
pplacer v1.1.alpha19
primer3 2.6.1
prodigalorffinder 2.6.3
proj 9.1.1
prokka 1.14.6
proot 5.3.1
provean 1.1.5
pullseq 1.0.2--hbd632db_7
purge_dups 1.2.6
purge_haplotigs 1.1.2
pyscaf 0.12a4
python_3 3.9.18, 3.11.1
qiime2 2023.2, 2023.7
qiime2_amplicon 2024.2
qtlcart 1.17f
qualimap 2.3
quast 5.2.0
quickmerge 0.3
r 4.2.2, 4.2.3, 4.3.0, 4.3.1, 4.4.1
racon 1.5.0
ragtag 2.1.0
randfold 2.0.1
raxml 8.2.12
recon 1.08
repeatmasker 4.1.0, 4.1.3-p1, 4.1.5
repeatmodeler 1.0.8, 2.0.4, 2.0.5
repeatscout 1.0.6
revbayes 1.3.1
rgi 5.1.0, 6.0.2
rmblast 2.11.0, 2.14.0
roary 3.13.0--pl526h516909a_0
rsem 1.3.3
ruby 3.2.0, 3.2.1
run_dbcan 2.0.11, 4.1.1
rust 1.66.1, 1.75.0
salmon 1.10.0
salsa 2.3
samtools 1.16.1, 1.17
sbt 0.13.18
seqkit 2.4.0
seqtk 1.3
shapeit5 5.1.1
sickle 1.33
singularityCE 1.3.1
smartdenovo 1.0.0
smrtlink 10.2.1.143962, 11.1.0.166339, 12.0.0.177059, 13.0.0.207600
snap_ucdavis 2024.03.14
sniffles 2.0.7
snoscan 1
snpeff 5.1d
snphylo 20180901
soapdenovo2 2.04
sortmerna 4.3.6
spades 3.15.5
sparsehash 2.0.4
sqlite3 3.40.1
squashfuse 0.5.2
squid 1.9g
sratoolkit 3.1.1
stacks 2.64
star 2.7.10b
stringtie 2.2.0
structure 2.3.4
subread 2.0.4
superfocus 1.6
supernova 2.1.1
svdetect 0.8b
swat 670
swig 4.1.1
symap 5.3.3
tassel3 3.0.174
tassel5 5.2.89--hdfd78af_0
tatajuba 1.0.4
tcltk 8.6.13
tcoffee 13.45.0.4846264
tetools 1.7
texinfo 7
tmux 3.3a
tophat 2.0.13--py27_2
transdecoder 5.7.0, 5.7.1
trf 4.09
trimgalore 0.6.10
trimmomatic 0.38, 0.39
trinityrnaseq 2.15.1
trinotate 3.2.2
trnascanse 2.0.12
turbomole-huge 6.3.1-mpi, 6.3.1-smp, 6.3.1
turbomole 6.3.1-mpi, 6.3.1-smp, 6.3.1, 7.6.0-mpi, 7.6.0-smp, 7.6.0
udunits 2.2.28
unicycler 0.5.0
usearch 11.0.667
vasp 5.4.4
vaspvtst 5.4.4
vcftools 0.1.16
velvet 1.2.10
vicuna 1.0.0
viennarna 2.5.1
virtualenv virtualenv
vsearch 2.22.1
wgs_assembler 8.3rc2
xz 5.4.1
yaggo 1.5.10
zlib 1.2.13
zorro 1.0.0