Current software
Tip
Contact Secretariat System Administrators with HPC Questions!
vshanka@clemson.edu,jopoole@clemson.edu,madonay@clemson.edu
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ihgcores@clemson.edu
This is a table of the modularized software on Secretariat.
Attention
This list is updated only periodically. For a full, current list, log in to Secretariat and run the command module avail. For more information on software modularization, see the Software modularization page.
Software |
Version |
|---|---|
abblast |
3.0 |
afterqc |
0.9.7 |
adios |
1.13.1 |
argweaver |
50bbd3c |
augustus |
3.3.3 |
autotools |
|
bamtools |
1.0 |
bbmap |
38.73 |
bedops |
2.4.40 |
bedtools2 |
2.29.2 |
blast |
2.9.0 |
bowtie1 |
1.2.0-py27_0 |
bowtie2 |
2.2.5 |
busco |
2.0.1 |
bwa |
0.7.17 |
cd-hit |
4.8.1 |
cellranger |
3.1.0, 7.0.1 |
cellranger-arc |
2.0.2 |
centos_compat |
1.0.0 |
charliecloud |
0.9.2, 0.15 |
cmake |
3.12.2, 3.21.3 |
conda |
2.0.1 |
cufflinks |
2.2.1 |
cutadapt |
1.18 |
delly |
0.8.3 |
dorado |
0.9.1 |
easybuild |
3.7.1 |
EasyBuild |
4.5.0 |
exonerate |
2.4.0 |
fastp |
0.21.0 |
fastqc |
0.11.9 |
fastqvalidator |
0.1.1 |
ffmpeg |
N-99555-g00772ef |
fftw |
3.3.8 |
flash |
1.2.11 |
gatk |
4.1.4.1 |
gcc |
10.1.0, 12.2.0 |
gcta |
1.93.2, 1.94.1 |
gdc-client |
1.6.1 |
gemma |
0.98.5 |
genometools |
1.5.9 |
gffcompare |
0.11.2 |
gffread |
0.11.6, 0.12.7 |
gmap_gsnap |
2019.09.12 |
gsl |
2.5, 2.7 |
gsutil |
4.47 |
hdf5 |
1.10.3, 1.10.8 |
hisat2 |
2.1.0 |
hmmer |
3.1b2 |
htop |
3.0.5 |
htseq |
0.11.2 |
hwloc |
1.11.10, 2.5.0 |
iribo |
carvunislab |
java_jdk |
1.8.231, 11.0.2 |
lemma |
1.0.0 |
libStatGen |
1.0.5 |
libboost |
1.72.0 |
libfabric |
1.13.0 |
libiconv |
1.17 |
likwid |
4.3.2, 5.0.1 |
linearpartition |
1.0 |
ltr_retriever |
2.6 |
mafft |
7.453 |
maker |
2.31.9, 2.31.10 |
mauve |
2.4.0 |
mauvealigner |
1.2.0 |
mfem |
3.4, 4.3 |
metis |
5.1.0 |
mpiP |
3.4.1 |
mpich |
3.2.1, 3.4.2-ofi |
mvapich2 |
2.3, 2.3.6 |
multiqc |
1.7 |
netcdf |
4.6.1, 4.7.4 |
netcdf-cxx |
4.3.0, 4.3.1 |
netcdf-fortran |
4.4.4, 4.5.3 |
ninja |
0.95_co |
nvidia/cuda |
12.5.0 |
ohpc |
|
openblas |
0.3.0, 0.3.7, 0.3.10 |
opencoarrays |
2.2.0, 2.9.2 |
openmpi3 |
3.1.2 |
openmpi4 |
4.1.1 |
pdtoolkit |
3.25, 3.25.1 |
papi |
5.6.0, 5.7.0 |
pbmm2 |
1.2.1 |
pbsv |
2.3.0 |
picard |
2.21.7 |
plink |
1.90b6.20 |
plasma |
2.8.0 |
pmix |
2.1.4 |
prun |
1.2, 2.2 |
python2.7-fm |
2.7.18 |
python3.8 |
3.8.4 |
py2-numpy |
1.15.1 |
py2-mpi4py |
3.0.0 |
py2-scipy |
1.1.0 |
py3-mpi4py |
3.0.0, 3.0.3 |
py3-numpy |
1.15.1, 1.19.5 |
py3-scipy |
1.1.0, 1.5.1 |
readline |
8.0 |
recon |
1.08 |
regtools |
0.5.0 |
repeatmasker |
4.1.0 |
repeatscout |
1.0.6 |
rmblast |
2.9.0-p2 |
rmtgenenet |
1.0 |
R |
3.5.0, 3.6.1, 4.0.3, 4.1.2, 4.2.1, 4.2.3, 4.3.0 |
rnastructure |
6.2, 6.5 |
rsem |
1.3.2 |
samtools |
1.9, 1.10 |
scalapack |
2.0.2, 2.1.0 |
scalasca |
2.4, 2.5 |
shapeit2 |
2.0.0 |
shapemapper |
2.1.5, 2.2.0 |
shapewarp |
1.0 |
sionlib |
1.7.2, 1.7.4 |
singularity |
2.6.0, 3.7.1 |
snap |
11.29.2013 |
sra |
2.11.0 |
stack |
2.3.3 |
star |
2.7.3a-0, 2.7.10a |
stringtie |
2.0 |
subread |
1.6.4 |
superfold |
1.0 |
superlu |
5.2.1 |
superlu_dist |
5.4.0, 6.4.0 |
texlive |
53254-2019.12.29 |
tophat |
2.1.1 |
trf |
4.0.9 |
trimmomatic |
0.39-1 |
trilinos |
12.12.1, 13.2.0 |
trinity |
2.1.1-6 |
trinotate |
3.2.0 |
tau |
2.27.1, 2.29 |
ucx |
1.11.2 |
valgrind |
3.13.0, 3.18.1 |
vbt |
1.1 |
vcftools |
0.1.16 |
viennarna |
2.4.18 |
xclip |
0.13 |
yasm |
1.2.0 |
List last updated: 11 November 2025.