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Software preinstalled on Ceres

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 Workbench SCINet has a license key to CLC Workbench
Geneious SCINet has a license key to Geneious
Rstudio SCINet runs a R studio Server
Jupyter Project Jupyter notebooks, Lab, and Hub 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).

Ceres Command-line Software Managed by the Module System

List updated February 20, 2020. To generate this list run module avail.

Software available through the Module system on Ceres
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
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
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
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
bedtools 2.25.0
beopest 14.02
bigscape latest
binutils 2.25
bismark 0.16.2
blast+ 2.2.31, 2.6.0, 2.9.0
blast 2.2.26
blat 35
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
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
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
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
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
dastool 1.1.0, 1.1.1
delly 0.8.1
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
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
faststructure latest, 1.0
fasttreemp 2.1.8
fastx 0.0.14
flexbar 2.5.0
flye 2.5, 2.6
fraggenescan 1.3.0
frc_align 1.0.0
freebayes 1.1.0, 1.2.0
funannotate 1.5.3
gapcloser 1.12
garli 2.01
gatk 3.6, 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
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
gmp 6.1.0
gnuplot 4.6.7
goanna 2.0
google_cloud_sdk 211.0.0
grib-api 1.26.1
groopm 1.7.3
gsl 2.3
gtdbtk 0.3.2
guppy-cpu 3.1.5
guppy-gpu 3.1.5
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
hmmer3 3.1b2, 3.2.1
htslib 1.10
htstream 1.0.0
humann2 0.11.1
idba 1.1.2
infernal 1.1.2
intarna 3.1.3--h176a8bc_0
intel 2017.3
interproscan 5.24-63.0
iq_tree 1.5.3, 1.5.5-omp, 1.6.8, 1.6.10, 1.6.12
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 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
ldt 7.2r
libevent 2.0.22
libexpat 2.2.0
libgd 2.2.3
libgtextutils 0.7
libpng 1.6.28
lis 7.2r
llvm 5.0.0
lordec 0.8
lumpy 0.2.13
mafft 7.307, 7.429
maker-mpich 2.31.10
maker 2.31.10
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
mcl 14-137
mcscanx 1.0.0
mdust 1.0
mecat 1.0.0
mecat2 2019.03.04
med-foes 0.6
megahit 1.1.1
megan 6.17.0, 6.18.4
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
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 latest
nek5000-intel 1.0.0
nek5000 1.0.0
netcdf-fortran 4.4.3
netcdf 4.3.3.1
newick_utils 1.0
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
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
phylosift 1.0.1
phyml 20151014
picard 64, 64
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
protexcluder 1.2
provean 1.1.5
pspp 1.0.1
pullseq 1.0.2
purge_dups 1.0
pyscaf 0.12a4
python36 2-alpine3.6
python_2 2.7.10, 2.7.12, 2.7.13, 2.7.14
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
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
raxml 8.2.3, 8.2.12
recon 1.08
redundans latest
refinem 1.7.3
repeatmasker 4.0.6, 4.0.7
repeatmodeler 1.0.8
repeatscout 1.0.5
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
salmon 0.9.1, 0.10.0, 0.10.1
salsa 2.0.0, 2.2
samtools 1.4.1, 1.9
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
smrtsv 1.0.0
snap 1.0beta.18
snap_ucdavis 2013.11.29
sniffles 1.0.8
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
sparsehash 2.0.3
speedseq 0.1.2
sqlite3 3.2.0
sratoolkit 2.5.8, 2.9.0, 2.9.6
stacks 1.44
star 2.5.2b, 2.7.2b
stringtie 1.3.3b
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
trinotate 2.0.2, 3.1.1
trnascanse 1.3.1, 1.23
uclust 1.2.22
udunits 2.2.24
unicycler 0.4.4, 0.4.7
usearch 11.0.667
vcftools 0.1.15
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