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Available HPC Tools

Available Tufts HPC Tools

There are a number of modules available on the Tufts HPC. Here we link out to the NIH's documentation for these tools, which will provide descriptions and how to create a batch script to use that tool.

Note about NIH HPC Documentation

Note that this will not perfectly line up with how to use this tool on the HPC as we have different reservation, node, and partition names. However, it is a good start to get you going on how to use the tool in a batch script.

For more information on how to create a batch script to work with the Tufts Cluster, check out the following tutorial: How to Create a Batch Script

Link To Documentation Versions
ABySS https://hpc.nih.gov/apps/abyss.html ABySS/1.5.2
afni https://hpc.nih.gov/apps/afni.html afni/2014-01-28(default)
amber https://hpc.nih.gov/apps/AMBER.html amber/12(default), amber/12.gpu, amber/14, amber/22-cuda, amber/22-mpi, amber/22-omp, amber/22-serial
anaconda https://hpc.nih.gov/apps/python.html anaconda/2, anaconda/3, anaconda/2020.02, anaconda/2021.05, anaconda/2021.11, anaconda/bio35
ancestrymap https://hpc.nih.gov/apps/AncestryMap.html ancestrymap/6210
ant https://hpc.nih.gov/apps/ANTs.html ant/1.8.2
aspera https://hpc.nih.gov/docs/transfer.html aspera/3.5.4
ATLAS https://hpc.nih.gov/development/ATLAS.html ATLAS/3.9.78
autoconf https://hpc.nih.gov/development/autotools.html autoconf/2.69
bcftools https://hpc.nih.gov/apps/samtools.html bcftools/1.2, bcftools/1.12
bcl2fastq https://hpc.nih.gov/apps/bcl2fastq.html bcl2fastq/2.19
beagle https://hpc.nih.gov/apps/Beagle.html beagle/1.0-cuda, beagle/3.1.2
BEAST https://hpc.nih.gov/apps/BEAST.html BEAST/1.10.1(default), BEAST/1.10.4, BEAST/1.8.4
bedtools https://hpc.nih.gov/apps/bedtools.html bedtools/2.17.0, bedtools/2.19.1, bedtools/2.26.0(default)
binutils https://hpc.nih.gov/apps/python.html binutils/2.29.1
blacs https://hpc.nih.gov/docs/svis.html blacs/1.1
BLAS https://hpc.nih.gov/apps/Blast.html BLAS/1.0, BLAS/3.5.0, OpenBLAS/0.2.19
blast https://hpc.nih.gov/apps/Blast.html blast/2.2.24, blast/2.2.31, blast/2.3.0, blast/2.8.1, blast-plus/2.11.0, ncbi-magicblast/1.5.0
blat https://hpc.nih.gov/apps/blat.html blat/20140708(default)
bowtie https://hpc.nih.gov/apps/bowtie.html bowtie/0.12.7(default), bowtie/1.0.1, bowtie/1.1.2, bowtie/2.1.0, bowtie2/2.2.3(default)
bowtie2 https://hpc.nih.gov/apps/bowtie2.html bowtie2/2.2.3(default)
bwa https://hpc.nih.gov/apps/bwa.html bwa/0.7.17, bwa/0.7.9a
caffe https://hpc.nih.gov/development/caffe.html caffe/20161026, caffe/20170201, caffe/20170227, caffe_unet/16.04.10.7, matcaffe/1.0
cellranger https://hpc.nih.gov/apps/cellranger.html cellranger/2.1.1, cellranger/3.0.2, cellranger-atac/1.2.0
chimera64 https://hpc.nih.gov/apps/Chimera.html chimera64/1.6.2, chimera64-osmesa/1.4.2577
chimera64-osmesa https://hpc.nih.gov/apps/Chimera.html chimera64-osmesa/1.4.2577
CirSeq https://hpc.nih.gov/apps/VIRTUS.html CirSeq/3
comsol https://hpc.nih.gov/apps/Comsol.html comsol/4.3b1, comsol/4.4, comsol/5.0, comsol/5.1, comsol/5.2(default), comsol/5.2a, comsol/5.3, comsol/5.3a, comsol/5.4, comsol/5.5, comsol/5.6, comsol/6.0
cuda https://hpc.nih.gov/docs/deep_learning.html beagle/1.0-cuda, cuda/10.0, cuda/10.2, cuda/11.0, cuda/4.2.9, cuda/5.0.35, cuda/6.5.14, cuda/7.5.18, cuda/8.0.44, cuda/9.0, amber/22-cuda, cuda/11.6, cuda/11.7
cudnn https://hpc.nih.gov/development/cuDNN.html cudnn/5.1, cudnn/7.1, cudnn/8.0.4-11.0
cufflinks https://hpc.nih.gov/apps/cufflinks.html cufflinks/0.8.3, cufflinks/2.0.0, cufflinks/2.0.2(default), cufflinks/2.1.1, cufflinks/2.2.1
Cytoscape https://hpc.nih.gov/apps/Cytoscape.html Cytoscape/2.8.3
eclipse https://hpc.nih.gov/apps/solar.html eclipse/1.4.1, eclipse/1.4.1-x86_64, eclipse/4.6.2-cpp, eclipse/4.6.2-java
eigen https://hpc.nih.gov/apps/eigensoft.html eigen/3.2.2(default), eigensoft/3.0, eigensoft/4.2, eigen/3.4.0
eigensoft https://hpc.nih.gov/apps/eigensoft.html eigensoft/3.0, eigensoft/4.2
espresso https://hpc.nih.gov/apps/express.html espresso/3.1.1, espresso/3.3.1
exonerate https://hpc.nih.gov/apps/exonerate.html exonerate/2.2.0(default)
fastqc https://hpc.nih.gov/apps/fastqc.html fastqc/0.11.5, fastqc/0.11.8, fastqc/0.11.9
fastx https://hpc.nih.gov/apps/fastxtoolkit.html fastx/0.0.13
ffmpeg https://hpc.nih.gov/apps/python.html ffmpeg/3.2.2
fftw https://hpc.nih.gov/apps/modules.html fftw/3.3.2(default), fftw/3.3.2-double, fftw/3.3.3, fftw/3.3.3-double, fftw/3.3.10
freebayes https://hpc.nih.gov/apps/freebayes.html freebayes/1.1.0
freesurfer https://hpc.nih.gov/apps/freesurfer.html freesurfer/5.3.0(default)
fsl https://hpc.nih.gov/apps/fsl.html fsl/5.0.6(default), fsl/5.0.9, fsl/6.0.5
gamess https://hpc.nih.gov/apps/GAMESS.html gamess/2013-03-01
GATK https://hpc.nih.gov/apps/GATK.html GATK/3.1-1(default), GATK/3.7, GATK/4.2.6.1
gaussian https://hpc.nih.gov/apps/Gaussian.html gaussian/g09, gaussian/g16avx, gaussian/g16avx2, gaussian/g16sse4_2
gcc https://hpc.nih.gov/development/compilers.html gcc/4.7.0, gcc/4.9.2, gcc/5.3.0, gcc/7.3.0, gcc/9.3.0, gcc/8.4.0, netcdf/4.0.0-gcc, intel-oneapi-mkl/2021.1.1-gcc-9.3.0, lhapdf5/5.9.1-gcc-4.8.5, intel-oneapi-tbb/2021.1.1-gcc-9.3.0, log4cpp/1.1.3-gcc-4.8.5, perl/5.34.0_gcc7.3.0, pythia6/6.4.28-gcc-4.8.5
gcta https://hpc.nih.gov/apps/GCTA.html gcta/1.25.2
glibc https://hpc.nih.gov/apps/csd.html glibc/2.14
glog https://hpc.nih.gov/apps/python.html glog/0.3.4, glog/0.4.0
gnu-parallel https://hpc.nih.gov/apps/parallel.html gnu-parallel/20150122
alphafold https://hpc.nih.gov/apps/alphafold2.html alphafold/2.1.1, alphafold/2.2.0
annovar https://hpc.nih.gov/apps/ANNOVAR.html annovar/202106
aria2 https://hpc.nih.gov/apps/aria2.html aria2/1.35.0
automake https://hpc.nih.gov/development/autotools.html automake/1.16.3
biobakery https://hpc.nih.gov/apps/biobakery_workflows.html biobakery/workflows
blast-plus https://hpc.nih.gov/apps/Blast.html blast-plus/2.11.0
blender https://hpc.nih.gov/apps/blender.html blender/3.4.1
cactus https://hpc.nih.gov/apps/cactus.html cactus/gpu
cellprofiler https://hpc.nih.gov/apps/cellprofiler.html cellprofiler/3.1.9, cellprofiler/4.0.6, cellprofiler/4.1.3, cellprofiler/4.2.1
cellranger-atac https://hpc.nih.gov/apps/cellranger-atac.html cellranger-atac/1.2.0
chimera https://hpc.nih.gov/apps/Chimera.html chimera64/1.6.2, chimera64-osmesa/1.4.2577, chimera/1.15
condaenv https://hpc.nih.gov/apps/python.html condaenv/bracken
ctffind https://hpc.nih.gov/apps/ctffind.html ctffind/4.1.8
dssp https://hpc.nih.gov/apps/DSSP.html dssp/3.1.4
emacs https://hpc.nih.gov/apps/Editors.html emacs/26.3, emacs/27.1_ccgpu, emacs/X26.3
eman2 https://hpc.nih.gov/apps/EMAN2.html eman2/2.91
fastjar https://hpc.nih.gov/apps/R.html fastjar/0.98
fasttree https://hpc.nih.gov/apps/FastTree.html fasttree/2.1.10
Fiji https://hpc.nih.gov/apps/Fiji.html Fiji/1.53t, Fiji/ImageJ
flash https://hpc.nih.gov/systems/hardware.html flash/1.2.11
fontconfig https://hpc.nih.gov/apps/python.html fontconfig/2.13.94
freetype https://hpc.nih.gov/apps/python.html freetype/2.11.0
hail https://hpc.nih.gov/apps/Hail.html hail/202106
gstreamer https://hpc.nih.gov/apps/python.html gstreamer/0.10
imagej https://hpc.nih.gov/apps/Fiji.html imagej/1.52a, imagej/1.5.2
hdf5 https://hpc.nih.gov/apps/ont-fast5-api.html hdf5/1.10.4, hdf5/1.12.1
hmmer https://hpc.nih.gov/apps/hmmer.html hmmer/3.3, hmmer/3.1b2
htslib https://hpc.nih.gov/apps/samtools.html htslib/1.9, htslib/1.2.1
libuuid https://hpc.nih.gov/apps/python.html libuuid/1.0.3
gem https://hpc.nih.gov/apps/gem.html gem/1.4.3, imagemagick/7.1.0
harfbuzz https://hpc.nih.gov/apps/python.html harfbuzz/2.9.1, harfbuzz/5.1.0
intel https://hpc.nih.gov/systems/hardware.html intel/mpi_2021.5.0, intel/compilers_2022.0.1, intel-oneapi-mkl/2021.1.1-gcc-9.3.0, intel-oneapi-tbb/2021.1.1-gcc-9.3.0, intel/2013_sp1, intel/tbb433
lftp https://hpc.nih.gov/docs/transfer.html lftp/4.8.1
fribidi https://hpc.nih.gov/apps/python.html fribidi/1.0.5
lastz https://hpc.nih.gov/apps/LASTZ.html lastz/1.03
netcdf https://hpc.nih.gov/apps/python.html netcdf/4.0.0-gcc, netcdf/4.0.0-pgi, netcdf/4.0.0, netcdf/c-4.8.1, netcdf/fortran-4.5.2, netcdf/fortran-4.5.3, netcdf/4.7.4
java https://hpc.nih.gov/development/java.html eclipse/4.6.2-java, java/11.0.2, java/15.0.2, java/1.5.0_64bit, java/1.6.0_64bit, java/1.5.0, java/1.4.2, java/1.6.0, java/1.6.0_25, java/1.6.0_25_64bit, java/1.8.0_60, java/1.7.0_51, structure-java/2.3.4
lapack https://hpc.nih.gov/development/LAPACK.html lapack/3.9.0, lapack/3.4.0, lapack/3.2.1, lapack/3.5.0, scalapack/1.8.0
gromacs https://hpc.nih.gov/apps/Gromacs.html gromacs/4.6.5, gromacs/4.6.5d, gromacs/5.0.1, gromacs/4.5.5(default), gromacs/4.6.1, gromacs/4.6.5-gls, gromacs/4.6.1-slurm, gromacs/4.6.7, gromacs/4.6.7-gpu, gromacs/5.1.0, gromacs/5.1.4-gpu, gromacs-plumed-libmatheval/2014-06-17(default), gromacs/4.6.5+plumed, gromacs/5.1.4
matlab https://hpc.nih.gov/apps/Matlab.html matlab/2020a, matlab/2019a, matlab/2019b, matlab/2020b, matlab/2021a, matlab/2022a, matlab/2016a, matlab/2016b, matlab/2017b, matlab/2018a, matlab/2017a(default)
mpfr https://hpc.nih.gov/apps/python.html mpfr/2.4.2(default), mpfr/3.1.2
julia https://hpc.nih.gov/apps/julia.html julia/1.6.0, julia/1.5.3, julia/0.3
gcam https://hpc.nih.gov/apps/gautomatch.html gcam/5.3, gcam/5.4
giflib https://hpc.nih.gov/apps/python.html giflib/5.1.4
gobject-introspection https://hpc.nih.gov/apps/python.html gobject-introspection/1.56.1
interproscan https://hpc.nih.gov/apps/interproscan.html interproscan/5.20
glib https://hpc.nih.gov/apps/python.html glibc/2.14, glib/2.56.1, glib/2.66.7
lammps https://hpc.nih.gov/apps/lammps.html lammps/20210310, lammps/27Aug13(default), lammps/10Aug15, lammps/16Mar18
libgmp https://hpc.nih.gov/apps/R.html libgmp/4.1.4
libicu https://hpc.nih.gov/apps/python.html libicu/4.2.1
imod https://hpc.nih.gov/apps/IMOD.html imod/4.11.18, imod/4.9.9, imod/4.9.12
ld_lib https://hpc.nih.gov/apps/modules.html ld_lib/2.2.21
libiconv https://hpc.nih.gov/apps/python.html libiconv/1.16
libtiff https://hpc.nih.gov/apps/python.html libtiff/4.2.0
gurobi https://hpc.nih.gov/apps/gurobi.html gurobi/9.5.0, gurobi/6.5.1, gurobi/7.5.1, gurobi/8.1.0
metal https://hpc.nih.gov/apps/metal.html metal/2010-02-08, metal/2011-03-25(default), metal/2010-08-01, metal/2009-10-10
mirdeep2 https://hpc.nih.gov/apps/mirdeep.html mirdeep2/2.0.0.5(default)
openmpi https://hpc.nih.gov/development/MPI.html openmpi/1.8.6, openmpi/1.8.2(default), openmpi/2.1.2, openmpi/4.0.4, openmpi/4.0.5, openmpi/1.10.1, openmpi/1.10.2, openmpi/1.6.3-gnu, openmpi/4.1.2, openmpi/3.1.2, openmpi/4.1.1, openmpi/3.1.6, openmpi/3.1.6_slurm, openmpi/4.1.2_slurm, openmpi/4.1.4
hisat https://hpc.nih.gov/apps/hisat.html hisat/2.0.5, hisat/2.1.0
namd https://hpc.nih.gov/apps/NAMD.html namd/2014-07-10, namd/2.12-mpi, namd/2.8(default)
openmm https://hpc.nih.gov/apps/charmm/older_charmm.html openmm/4.1.1(default), openmm/5.1
PEET https://hpc.nih.gov/apps/PEET.html PEET/1_13.0, PEET/1_12.0
NCAR https://hpc.nih.gov/docs/deep_learning.html NCAR/5.2.1
opencv https://hpc.nih.gov/apps/python.html opencv/3.1.0, opencv/4.5.1
IGV https://hpc.nih.gov/apps/IGV.html IGV/1.5.30
MCR https://hpc.nih.gov/apps/dynamo.html MCR/R2012b, MCR/R2012a
MDAnalysis https://hpc.nih.gov/apps/mdtraj.html MDAnalysis/0.8.1
multinest https://hpc.nih.gov/policies/multinode.html multinest/201911
icc https://hpc.nih.gov/apps/R.html icc/10.1.017
jupyter https://hpc.nih.gov/apps/jupyter.html jupyter/3.0, jupyter/1.0(default)
kallisto https://hpc.nih.gov/apps/kallisto.html kallisto/0.45.0
mothur https://hpc.nih.gov/apps/mothur.html mothur/1.25.1, mothur/1.29.1, mothur/1.36.1(default), mothur/1.48, mothur/1.44, mothur/1.47
graphviz https://hpc.nih.gov/apps/modules.html graphviz/2.40.1
HTSeq https://hpc.nih.gov/apps/htseq.html HTSeq/0.5.4p5(default), HTSeq/0.6.1p1
misopy https://hpc.nih.gov/apps/misopy.html misopy/0.5.2(default)
mrbayes https://hpc.nih.gov/apps/mrbayes.html mrbayes/3.1.2
nccl https://hpc.nih.gov/docs/deeplearning/multinode_DL.html nccl/2.7.8-1
impute https://hpc.nih.gov/apps/IMPUTE.html impute/2.0.3
mach https://hpc.nih.gov/apps/mash.html mach/1.0.16
MACS https://hpc.nih.gov/apps/macs.html MACS/1.4.2-1
merlin https://hpc.nih.gov/apps/merlin.html merlin/1.1.2
mvapich2 https://hpc.nih.gov/development/MPI.html mvapich2/1.6-1
ont-guppy https://hpc.nih.gov/apps/guppy.html ont-guppy/3.3.0-gpu, ont-guppy/3.3.0-cpu, ont-guppy/4.5.2-cpu, ont-guppy/4.5.2-gpu, ont-guppy/5.0.11-gpu, ont-guppy/5.0.11-cpu
gpaw-mpi https://hpc.nih.gov/development/MPI.html gpaw-mpi/0.4.2627
idl https://hpc.nih.gov/apps/idl.html idl/8.4
libffi https://hpc.nih.gov/apps/python.html libffi/3.2.1
maq https://hpc.nih.gov/docs/helixdrive.html maq/0.7.1
mathematica https://hpc.nih.gov/apps/mathematica.html mathematica/13.1, mathematica/13.2.1, mathematica/10.4.0, mathematica/10.4.1, mathematica/11.0.0, mathematica/11.3.0, mathematica/12.0, mathematica/13.0, mathematica/12.1(default), mathematica/12.2, mathematica/12.3
muscle https://hpc.nih.gov/apps/muscle.html muscle/3.8.31
gromacs-plumed-libmatheval https://hpc.nih.gov/apps/Gromacs.html gromacs-plumed-libmatheval/2014-06-17(default)
MAnorm https://hpc.nih.gov/apps/manorm.html MAnorm/2014-04-03
multiqc https://hpc.nih.gov/apps/multiqc.html multiqc/1.7.0
paraview https://hpc.nih.gov/apps/paraview.html paraview/3.8.1, paraview/4.4
povray https://hpc.nih.gov/apps/POVRay/index.html povray/3.6.1
haploview https://hpc.nih.gov/apps/plink.html haploview/4.1
pcre https://hpc.nih.gov/apps/python.html pcre/8.38
mafft https://hpc.nih.gov/apps/mafft.html mafft/7.481
metaphlan https://hpc.nih.gov/apps/metaphlan.html metaphlan/2.6.0
nextflow https://hpc.nih.gov/apps/nextflow.html nextflow/21.10.1, nextflow/21.10.6
ORFfinder https://hpc.nih.gov/apps/ORFfinder.html ORFfinder/0.4.3
orthofinder https://hpc.nih.gov/apps/orthofinder.html orthofinder/2.5.4
libxml2 https://hpc.nih.gov/apps/python.html libxml2/2.9.10, libxml2/2.9.12
libxpm https://hpc.nih.gov/apps/python.html libxpm/3.5.12
mamba https://hpc.nih.gov/apps/python.html mamba/22.9.0-2
minimap2 https://hpc.nih.gov/apps/minimap2.html minimap2/2.15
orca https://hpc.nih.gov/apps/python.html orca/5.0.3, orca/5.0.4
structure-java https://hpc.nih.gov/development/java.html structure-java/2.3.4
salmon https://hpc.nih.gov/apps/salmon.html salmon/1.6.0, salmon/0.13.1
openssl https://hpc.nih.gov/apps/python.html openssl/1.1.1
ninja https://hpc.nih.gov/apps/python.html ninja/1.10.1
tcltk https://hpc.nih.gov/apps/R.html tcltk/08.5.11-rhel6, tcltk/8.5.11
rstudio https://hpc.nih.gov/apps/RStudio.html rstudio/0.96.331, rstudio/1.1.447, rstudio/1.1.383, rstudio/0.99.903
tophat https://hpc.nih.gov/apps/tophat.html tophat/1.0.14, tophat/2.0.10, tophat/2.0.9(default), tophat/2.0.13
picard https://hpc.nih.gov/apps/picard.html picard/1.139, picard/2.8.0
protobuf https://hpc.nih.gov/apps/python.html protobuf/3.18, protobuf/2.6
R https://hpc.nih.gov/apps/R.html abaqus/V6R2017, abaqus/V6R2018, NCAR/5.2.1, MCR/R2012b, mirPRo/1.1.4, MCR/R2012a, ORFfinder/0.4.3, sf/R_4.0.0, R/3.2.2, R/3.4.1, R/4.0.0, R/3.2.5, PyRosetta/r55194, R/3.6.3, RepeatMasker/4.0.7, STAR/2.7.0a, R/3.3.3, R/3.4, R/4.2.2, tecplot/2013R1, R/3.4_dulla, R/3.0.3, R/3.5.0, RetroSeq/20130716(default), STAR/2.6.1d, R/3.0.2, R/3.1.0, ViennaRNA/2.1.6(default), PyRosetta/r55193, R/3.0.1, R/3.3.2, R/3.4.3(default), R/4.1.1, STAR/2.3.0e, R/2.15.3, STAR/2.5.2b(default), RAxML/8.2.12, R/4.2.0
rosetta https://hpc.nih.gov/apps/rosetta.html rosetta/3.4, rosetta/3.13_mpi, rosetta/3.7, rosetta/3.13
usearch https://hpc.nih.gov/apps/usearch.html usearch/8.1.1861, usearch/10.0.240, usearch/7.0.1001(default)
ncbi-magicblast https://hpc.nih.gov/apps/magicblast.html ncbi-magicblast/1.5.0
QIIME https://hpc.nih.gov/apps/QIIME.html QIIME/1.9.0(default), QIIME/1.7.0, QIIME/1.8.0, QIIME/1.5.0, QIIME/1.6.0
samtools https://hpc.nih.gov/apps/samtools.html samtools/0.1.18(default), samtools/0.1.19, samtools/1.9, samtools/1.2
plink https://hpc.nih.gov/apps/plink.html plink/1.90b5, plink2/2.0, plink/1.06, plinkseq/0.10
sra https://hpc.nih.gov/apps/sratoolkit.html sra/2.5.0, sra/2.10.8, sra/2.9.2
root https://hpc.nih.gov/apps/singularity.html root/6.22.08_pythia6, root/6.24.06, root/5.34.18, proot/5.1.0, root/6.22.08
python https://hpc.nih.gov/apps/python.html boost/1.63.0-python3, python/2.7.4, python/3.8.8, python/3.6.0, tensorflow/11-python3.5, python/2.7.6, python/3.5.0, tensorflow/11-python2.7, python/2.6.5, python/2.7.3(default)
rsem https://hpc.nih.gov/apps/rsem.html rsem/1.3, rsem/1.3.3, rsem/1.2.14(default), rsem/1.3.1
singularity https://hpc.nih.gov/apps/singularity.html singularity/3.6.1, singularity/2.6.1(default), singularity/3.1.0, singularity/3.5.3, singularity/3.8.4
subread https://hpc.nih.gov/apps/subread.html subread/1.6.3, subread/1.5.1
vmd https://hpc.nih.gov/apps/VMD.html vmd/1.9.4, vmd/1.9
pytorchgpu https://hpc.nih.gov/docs/deep_learning.html pytorchgpu/1
perl https://hpc.nih.gov/apps/modules.html bioperl/1.7.6, perl/5.34.0, perl/5.34.0_gcc7.3.0, superlu/4.0, perl/5.32.1
PyRosetta https://hpc.nih.gov/apps/PyRosetta.html PyRosetta/r55194, PyRosetta/r55193
trinity https://hpc.nih.gov/apps/trinity.html trinity/10.15.15, trinity/7.17.14
plink2 https://hpc.nih.gov/apps/plink.html plink2/2.0
RepeatMasker https://hpc.nih.gov/apps/repeatmasker.html RepeatMasker/4.0.7
STAR https://hpc.nih.gov/apps/STAR.html STAR/2.7.0a, STAR/2.6.1d, STAR/2.3.0e, STAR/2.5.2b(default)
rclone https://hpc.nih.gov/apps/rclone.html rclone/1.51.0, rclone/1.59.0
rsync https://hpc.nih.gov/docs/transfer.html rsync/3.2.2
pythia https://hpc.nih.gov/apps/python.html root/6.22.08_pythia6, pythia/8235, pythia/8219, pythia6/6.4.28-gcc-4.8.5, pythia6/6.4.28
trinotate https://hpc.nih.gov/apps/trinotate.html trinotate/2.0.2
stacks https://hpc.nih.gov/apps/R.html stacks/2.53, stacks/1.12(default)
plinkseq https://hpc.nih.gov/apps/plinkseq.html plinkseq/0.10
spades https://hpc.nih.gov/apps/spades.html spades/3.12.0, spades/3.15.4
zlib https://hpc.nih.gov/apps/R.html zlib/1.2.8, zlib/1.2.11
phred https://hpc.nih.gov/apps/modphred.html phred/0.0
rnaseqmut https://hpc.nih.gov/apps/VIRTUS.html rnaseqmut/1.0
pandoc https://hpc.nih.gov/apps/python.html pandoc/2.14
valgrind https://hpc.nih.gov/development/debugging.html valgrind/3.16.1
pilon https://hpc.nih.gov/apps/pilon.html pilon/1.22
qiime2 https://hpc.nih.gov/apps/QIIME.html qiime2/2017.7, qiime2/2021.11, qiime2/2018.8
SAS https://hpc.nih.gov/apps/SAS.html SAS/9.3, SAS/9.4(default)
solar https://hpc.nih.gov/apps/solar.html solar/4.2.7
squid https://hpc.nih.gov/docs/transfer.html squid/1.9g(default)
relion https://hpc.nih.gov/apps/RELION/index.html relion/4.0
tabix https://hpc.nih.gov/apps/samtools.html tabix/20131216
proj4 https://hpc.nih.gov/apps/R.html proj4/4.4
sniffles https://hpc.nih.gov/apps/sniffles.html sniffles/1.0.10
SuiteSparse https://hpc.nih.gov/apps/python.html SuiteSparse/3.6.1
tensorflow https://hpc.nih.gov/docs/deep_learning.html tensorflow/11-python3.5, tensorflow/11-python2.7
vcftools https://hpc.nih.gov/apps/vcftools.html vcftools/0.1.13(default), vcftools/0.1.12b
phenix https://hpc.nih.gov/apps/Phenix.html phenix/1.13
Qt https://hpc.nih.gov/apps/RStudio.html Qt/4.8.4
RetroSeq https://hpc.nih.gov/apps/VIRTUS.html RetroSeq/20130716(default)
tinker https://hpc.nih.gov/apps/mdtraj.html tinker/7.1
trimmomatic https://hpc.nih.gov/apps/trimmomatic.html trimmomatic/0.38
tmhmm https://hpc.nih.gov/apps/trinotate.html tmhmm/2.0c
vim https://hpc.nih.gov/apps/Editors.html vim/8.1
randfold https://hpc.nih.gov/apps/randfold.html randfold/2.0(default)
spark https://hpc.nih.gov/apps/spark.html spark/2.0.1, spark/2.3.0(default)
ViennaRNA https://hpc.nih.gov/apps/viennarna.html ViennaRNA/2.1.6(default)
readline https://hpc.nih.gov/apps/python.html readline/8.1
proot https://hpc.nih.gov/docs/biowulf_tools.html proot/5.1.0
Schrodinger https://hpc.nih.gov/apps/schrodinger/index.html Schrodinger/2015-4, Schrodinger/2012
sqlite3 https://hpc.nih.gov/apps/sqlite.html sqlite3/3.33.0
trim-galore https://hpc.nih.gov/apps/trimgalore.html trim-galore/0.6.4_dev
zmq https://hpc.nih.gov/apps/python.html zmq/4.8.1
RAxML https://hpc.nih.gov/apps/raxml.html RAxML/8.2.12
transdecoder https://hpc.nih.gov/apps/TransDecoder.html transdecoder/2.0