Software Currently Available

Libraries

Module Name	Description	Tags
ADIOS2	ADIOS 2 is an open-source framework that addresses scientific data management challenges.
BEAGLE	Adds the BEAGLE libraries to your environment.	`Phylogeny`, `Parallel Processing`
Bioconductor	Adds the Bioconductor libraries to your environment.
Biopython	Adds Biopython software to your environment.
Boost	Adds Boost C++ Libraries (built with GCC) to your environment.	`Linear Algebra`, `Pseudorandom`, `Multithreading`, `Image Processing`, `Regular Expressions`, `Unit Testing`
CGAL	Adds the CGAL API to your environment.
CheMPS2	Adds the CheMPS2 API to your environment.
CUDA	Adds the CUDA API to your environment.
eigen	Adds the Eigen API to your environment.
fftw	Adds the fftw API to your environment.
FLTK	Adds the FLTK API to your environment	`GUI`
GEOS	Adds the GEOS API to your environment.
gflags	Adds the gflags API to your environment.
gl2ps	Adds the gl2ps API to your environment.
glog	Adds the glog API to your environment.
GLPK	Adds the GLPK API to your environment.
GSL	Adds the GSL API to your environment.
HDF5	Adds the HDF5 API to your environment.
HTSlib	Adds the HTSlib API to your environment.
hwloc	Adds the hwloc API to your environment.
isl	Adds the isl API to your environment.
KIM	Adds the OpenKIM API to your environment.
KIM-API	Adds the OpenKIM API to your environment.
libdrm	Direct Rendering Manager	`DRM`, `DRI`
libffi	Adds the libffi API to your environment.
libgit2	libgit2 is a portable, pure C implementation of the Git core methods
libgtextutils	Adds the libgtextutils Libraries to your environment.	`Unmaintained`
libjpeg-turbo	Adds libjpeg-turbo Libraries (built with GNU gcc) to your environment.
libpng	Adds libpng Libraries (built with GNU gcc) to your environment.
libxc	Libxc is a library of exchange-correlation and kinetic energy functionals for density-functional theory.
METIS	Adds the METIS API to your environment.
MUMPS	Adds the MUMPS API to your environment.
MVAPICH2	Adds MVAPICH2 software to your environment	`MPI`
NetCDF-C	Adds the NetCDF-C API to your environment.
nlopt
OpenBLAS	Adds the OpenBLAS libraries to your environment	`Science`, `Modeling`
OpenMPI	Adds the OpenMPI libraries to your environment.
PCRE2	Adds the PCRE2 API to your environment.
perl5-libs	Adds perl5-libs libraries to your environment for some package dependencies.	`Dependencies`
PnetCDF	Adds the PnetCDF API to your environment.
PyTorch	Adds PyTorch software to your environment.	`Machine Learning`
PyTorch-GPU	Adds PyTorch software to your environment.	`GPU`, `Machine Learning`
Qhull	Adds the Qhull APIs to your environment.
Qt	Adds the Qt API to your environment.	`GUI`
ReportLab	Adds ReportLab Libraries to your environment.	`PDF Generation`
ScaFaCoS	Adds the ScaFaCoS API to your environment.
SuiteSparse	Adds the SuiteSparse API to your environment.
SUNDIALS	Adds SUNDIALS to your environment.
Szip	Adds the Szip API to your environment.
TensorFlow	Adds TensorFlow software to your environment
TensorFlow-GPU	Adds TensorFlow software to your environment	`GPU`
upcxx	Adds the UPC++ libraries to your environment.
Voro++	Adds the Voro++ API to your environment.
VTK	Adds the VTK API to your environment.
z3	Adds the z3 API to your environment.
zstd	Zstandard is a fast compression algorithm, providing high compression ratios.	`Compression`

Programming

Module Name	Description	Tags
Anaconda2	Adds the Anaconda2 software to your environment	`Python2`
Anaconda3	Adds the Anaconda3 software to your environment	`Python3`
Argbash	adds Argbash to your environment
Autoconf	Autoconf is an extensible package of M4 macros that produce shell scripts to automatically configure software source code packages.
Bazel	adds the Bazel cross-platform build tools to your environment
Boost.Build	Adds the Boost.Build software to your environment
CMake	adds the CMake cross-platform build tools to your environment
DDD	adds DDD debugger to your environment
Eclipse	Adds the Eclipse IDE to your environment	`Editor`, `GUI`
Gaussian	Adds Gaussian to your environment	`Science`, `Modeling`
gcc	adds gcc compilers to your environment
Go	Adds Go programming language to your environment
Intel	None
Julia	Adds the Julia programming language to your environment
Libtool	Adds newer libtool scripts to your environment
LLVM	Adds LLVM compilers to your environment
Make	Adds the Make cross-platform build tools to your environment
Maple	Adds Maple to your environment.
Mathematica	Adds Mathematica to your environment
MATLAB	Adds MATLAB to your environment
Miniforge3	Adds the Miniforge3 software to your environment	`Python3`
Ninja	Adds Ninja to your environment
oneAPI-advisor	Intel(R) Advisor 2021.1 (build 607872)	`oneAPI`, `Code Analysis`
oneAPI-ccl	Intel(R) oneAPI Collective Communications Library	`oneAPI`
oneAPI-clck	Sets up the Intel(R) Cluster Checker environment.	`oneAPI`, `Cluster Checker`
oneAPI-compiler	Configure for use with Intel 64-bit compiler(s).	`oneAPI`, `Compilers`, `C`, `C++`, `FORTRAN`
oneAPI-compiler-rt	Configure runtime libraries for use with Intel 64-bit compiler(s).	`oneAPI`, `Runtime Libraries`, `C`, `C++`, `FORTRAN`
oneAPI-compiler-rt32	Configure runtime libraries for use with Intel 32-bit compiler(s).	`oneAPI`, `Runtime Libraries`, `C`, `C++`, `FORTRAN`
oneAPI-compiler32	Configure for use with Intel 32-bit compiler(s).	`oneAPI`, `Compilers`, `C`, `C++`, `FORTRAN`
oneAPI-dal	Configure for use with Intel Data Analytics Library for intel64	`DAL`, `DAAL`
oneAPI-debugger	The gdb-oneapi debugger (an extension of standard gdb).	`oneAPI`, `Debugger`, `gdb`
oneAPI-dev-utilities	Add the oneAPI dev-utilities/bin and ../include to PATH and CPATH.	`oneAPI`
oneAPI-dnnl	Intel® oneAPI Deep Neural Network Library for the cpu_dpcpp_gpu_dpcpp configuration.	`oneAPI`, `dnnl`
oneAPI-dnnl-cpu-gomp	Intel® oneAPI Deep Neural Network Library for the cpu_gomp configuration.	`oneAPI`, `dnnl`
oneAPI-dnnl-cpu-iomp	Intel® oneAPI Deep Neural Network Library for the cpu_iomp configuration.	`oneAPI`, `dnnl`
oneAPI-dpct	Configure for Intel(R) DPC++ Compatibility Tool.	`oneAPI`
oneAPI-dpl	Configure for Intel(R) DPC++ Library.	`oneAPI`
oneAPI-init_opencl	Submodule for Intel(R) oneAPI DPCPP compiler FPGA environment	`oneAPI`
oneAPI-inspector	Intel(R) Inspector 2021.1 (build 604894)	`oneAPI`
oneAPI-intel_ipp_ia32	Intel(R) Integrated Performance Primitives IA-32 architecture. For a full Intel(R) IPP functionality, you should load Intel(R) oneAPI Compiler and Intel(R) oneAPI Threading Building Blocks modules.	`oneAPI`, `IPP`
oneAPI-intel_ipp_intel64	Intel(R) Integrated Performance Primitives Intel(R) 64 architecture. For a full Intel(R) IPP functionality, you should load Intel(R) oneAPI Compiler and Intel(R) oneAPI Threading Building Blocks modules.	`oneAPI`, `IPP`
oneAPI-intel_ippcp_ia32	Intel(R) Integrated Performance Primitives Cryptography IA-32 architecture. For a full Intel(R) IPP functionality, you should load Intel(R) oneAPI Compiler and Intel(R) oneAPI Threading Building Blocks modules.	`oneAPI`, `IPPCP`, `Cryptogaraphy`
oneAPI-intel_ippcp_intel64	Intel(R) Integrated Performance Primitives Cryptography Intel(R) 64 architecture. For a full Intel(R) IPP functionality, you should load Intel(R) oneAPI Compiler and Intel(R) oneAPI Threading Building Blocks modules.	`oneAPI`, `IPPCP`, `Cryptography`
oneAPI-itac	Intel(R) Trace Analyzer and Collector	`oneAPI`, `IPPCP`, `Cryptography`
oneAPI-mkl	Sets up environment for oneMKL IA-64 architecture	`oneAPI`, `MKL`, `BLAS`, `LAPACK`, `ScaLAPACK`, `FFT`
oneAPI-mkl32	Sets up environment for oneMKL IA-32 architecture	`oneAPI`, `MKL`, `BLAS`, `LAPACK`, `ScaLAPACK`, `FFT`
oneAPI-mpi	Intel(R) MPI Library	`oneAPI`, `MPI`
oneAPI-oclfpga	Intel(R) oneAPI DPCPP compiler FPGA environment	`oneAPI`, `MPI`
oneAPI-tbb	Intel(R) oneAPI Threading Building Blocks for intel64.	`oneAPI`, `TBB`
oneAPI-tbb32	Intel(R) oneAPI Threading Building Blocks for ia32.	`oneAPI`, `TBB`
oneAPI-vpl	Intel(R) oneAPI Video Processing Library.	`oneAPI`, `VPL`
oneAPI-vtune	Intel(R) oneAPI VTune(TM) Profiler 2021.1.1 (build 613804)	`oneAPI`, `VPL`
OpenJDK	Adds the OpenJDK software to your environment	`JAVA`, `JDK`, `JRE`
protobuf	Adds Google's protocol buffers support to your environment.	`compiler`
R	Adds R software to your environment
re2c	Adds re2c to your environment
ROOT	Adds the ROOT cross-platform build tools to your environment
rust	Adds the Rust programming language to your environment.
SWIG	Adds the SWIG cross-platform build tools to your environment

Software

Module Name	Description	Tags
ABCluster	Adds ABCluster software to your environment	`ABC Algorithm`, `Chemistry`
ABINIT	Adds ABINIT software to your environment.
AlphaFold	AlphaFold can accurately predict 3D models of protein structures and has the potential to accelerate research in every field of biology.
ANNOVAR	Adds ANNOVAR software to your environment
aria2	High-speed download utility with resuming and segmented downloading.	`Utility`
asciinema	Adds asciinema software to your environment
AtomEye	Adds AtomEye software to your environment	`Atomistic Configuration Viewer`
AUGUSTUS	Adds AUGUSTUS software to your environment
Avogadro	Adds Avogadro software to your environment	`Visualization`, `Molecular Editor`
BamTools	Adds BamTools software to your environment.
bat	Adds bat software to your environment.	`Utility`
BayeScan	Adds BayeScan software to your environment
BCFtools
BEDOPS	Adds BEDOPS software to your environment
bedtools	Adds bedtools software to your environment.	`Genome Arithmetic`
bowtie	Adds bowtie software to your environment.	`Sequence Alignment`
bowtie2	Adds bowtie2 software to your environment.	`Sequence Alignment`
BUSCO	Adds BUSCO software to your environment
BWA	Adds BWA software to your environment
Canu	Adds Canu software to your environment.
Clustal-Omega	Adds Clustal-Omega software to your environment	`Multiple Sequence Alignment`
clustalw	Adds clustalw software to your environment	`Multiple Alignment`
CompHEP	Adds CompHEP software to your environment
COMSOL	Adds COMSOL software to your environment	`Finite Element Analysis`
Consed	Adds Consed software to your environment
Cufflinks	Adds Cufflinks software to your environment.
DaliLite	Adds DaliLite software to your environment.
deltaSHAPE	Adds the deltaSHAPE script to your environment	`Biology`, `BioChem`, `Weeks-UNC`
dftbplus	Adds the DFTB+ software to your environment.
Dialign	Adds Dialign software to your environment
Doxygen	Adds Doxygen software to your environment
eems	An implementation of the EEMS method for analyzing and visualizing spatial population structure from geo-referenced genetic samples.
ELPH	Adds ELPH software to your environment
EMBOSS	Adds EMBOSS software to your environment.
FAST	Adds FAST software to your environment	`Structure Alignment`
FASTA	Adds FASTA software to your environment
FastJet	Adds FastJet Software to your environment
FASTX-Toolkit	Adds FASTX-Toolkit software to your environment
FDist2	Adds FDist2 software to your environment
FFmpeg	Adds FFmpeg software to your environment	`Multimedia Framework`
FLASH	Adds FLASH software to your environment	`Structure Alignment`
FLOW3D-HYDRO	FLOW-3D HYDRO is the complete CFD modeling solution for the civil and environmental engineering industry.	`CFD`
FORM	Adds FORM software to your environment	`Particle Physics`
FUSTr	Adds FUSTr software to your environment	`Phylogeny`, `Maximum Likelihood`
GAMESS	Adds GAMESS software to your environment
Gblocks	Adds Gblocks software to your environment
GDAL	Adds GDAL Utilities and Libraries to your environment
Genepop	Adds Genepop software to your environment
git	Adds GIT software to your environment.	`SCM`, `Version Control`
Glimmer	Adds Glimmer software to your environment	`DNA`, `Alignment`, `Gene`
GMAP	Adds GMAP software to your environment.	`Genome Mapping`, `Sequence Alignment`
gnuplot	Adds gnuplot software to your environment	`Scientific Plotting`
Grace	Adds Grace software to your environment
GROMACS	Adds GROMACS software to your environment
Gurobi	Adds Gurobi Optimizer to your environment
HEASoft	Adds HEASoft software to your environment	`FITS`, `fv`, `XANADU`, `XSTAR`
HH-SUITE	Adds HH-SUITE software to your environment	`HHAlign`, `HHBlits`, `HHFilter`, `HHMake`, `HHSearch`
HMMER	Adds HMMER software to your environment	`Biosequence Analysis`
I-TASSER	Adds I-TASSER software to your environment	`Alignment`, `Protein`, `Structure Prediction`
ImageMagick	Adds ImageMagick software to your environment
ipyrad	Adds ipyrad software to your environment.
Jellyfish	Adds JellyFish software to your environment.
LAMMPS	Adds LAMMPS software to your environment	`Molecular Dynamics`
lp_solve	Adds lp_solve software to your environment.
LS-DYNA	Adds LS-DYNA software to your environment.
LS-PrePost	Adds LS-PrePost software to your environment.
luscus	Adds luscus software to your environment.	`Sequence Alignment`
MAFFT	Adds MAFFT software to your environment.	`Multiple Sequence Alignment`, `Global Pairwise`, `Local Pairwise`
MCNP	Adds MCNP software to your environment.
MG5_aMC	Adds MG5_aMC Software to your environment.
Modeller	Adds Modeller software to your environment	`Protein`, `3D Structure`, `Alignment`
Molcas@UU	Adds Molcas software from the Molcas@UU distribution to your environment.	`Sequence Alignment`
Molden	Adds Molden software to your environment.	`Molecular Structure`
Molpro	Adds Molpro software to your environment.
mothur	Adds mothur software to your environment.	`bioinformatics`, `dotur`, `sons`, `treeclimber`, `unifrac`, `s-libshuff`
Mplus	Adds Mplus Basic Program plus Combination Add-On to your environment.
MrBayes	Adds MrBayes software to your environment.	`Phylogeny`, `Evolutionary Models`, `Bayesian Inference`
MT-Toolbox	Adds MT-Toolbox software to your environment.	`Molecular Tagging`
MToolBox	Adds MToolBox software to your environment.	`Sequence Alignment`
MUSCLE	Adds MUSCLE software to your environment.	`Multiple Sequence Alignment`, `Tree-Building`, `Profile Alignment`
NBO	Adds NBO software to your environment.
NCBI-Blast	Adds NCBI-Blast software to your environment.	`Sequence Alignment`
Netpbm	Adds Netpbm software to your environment.
OpenBabel	Adds Open Babel software to your environment.
OpenFOAM	Adds OpenFOAM software to your environment.	`Computational Fluid Dynamics`, `CFD`
OpenMolcas	Adds OpenMolcas to your environment.	`Sequence Alignment`
OpenSees	Adds OpenSees software to your environment.
OpenSSL	Updated OpenSSL Crypto Software and Libraries
PAML	Adds PAML software to your environment.	`Phylogeny`
ParaView	Adds ParaView software to your environment.	`GUI`
phd2fasta	Adds phd2fasta software to your environment.
Phrap	Adds Phrap software to your environment.
Phred	Adds Phred software to your environment.
PHYLIP	Adds PHYLIP software to your environment.	`Phylogeny`
PhyML	Adds PhyML software to your environment.	`Phylogeny`, `Maximum Likelihood`
primer3	Adds primer3 software to your environment.	`Designing PCR Primers`
PROBCONS	Adds PROBCONS software to your environment.	`Multiple Sequence Alignment`
PROJ	Adds PROJ Software to your environment.
PROMALS	Adds PROMALS software to your environment.	`Multiple Sequence Alignment`, `3D Structure`
ProtTest	Adds ProtTest software to your environment.
PyMol	Adds PyMol software to your environment.
qhost	Adds QHost software to your environment.	`Local Mod`
qtop	Adds qtop software to your environment.
RAxML	Adds Guassian to your environment.	`Science`, `Modeling`, `Phylogenetic Trees`
rclone	Adds the rclone software to your environment.	`Utility`, `Cloud Storage`
RingMapper	Adds RingMapper and PairMapper to your environment
ripgrep	Adds the ripgrep software to your environment.	`Utility`
RNAstructure	Adds RNAstructure to your environment	`Biology`, `Biochem`, `Structure Prediction`
RNATools	Adds the RNATools and foldPK scripts to your environment	`Biology`, `BioChem`, `Weeks-UNC`
Salmon	Adds Salmon Optimizer to your environment.
SAMtools	Adds SAMtools and BCFtools software to your environment.	`Data Manipulation`, `Sequencing`
SCOTCH	Adds SCOTCH software to your environment.
SeaView	Adds SeaView software to your environment.	`GUI`
SediFoam	Adds SediFoam software to your environment.
Serpent	Adds SERPENT software to your environment.
ShapeJumper	Adds ShapeJumper.sh script to your environment	`Biology`, `BioChem`, `Weeks-UNC`
ShapeMapper	Adds ShapeMapper to your environment.	`Biology`, `BioChem`, `Weeks-UNC`, `RNA`, `Parallel Sequencing`
SiLiX	Adds SiLIX software to your environment.
Simcoal2	Adds Simcoal2 software to your environment.
Singularity	Adds Singularity to your environment.
SQLite	Adds SQLite software to your environment.
SRAToolkit	Adds SRAToolkit software to your environment.
stacks	Adds the stacks software pipeline to your environment.	`Genetic Mapping`, `Population Genomics`, `Phylogenetics`
Stata	Adds Stata software to your environment	`statistics`
StructureAnalysis	Adds the StructureAnalysis python scripts to your environment	`Biology`, `BioChem`, `Weeks-UNC`
SuperFold	Adds SuperFold to your environment	`Biology`, `BioChem`, `Weeks-UNC`
texinfo	Adds texinfo software to your environment.
TeXLive	Adds TeXLive software to your environment.
Tinker	Adds Tinker software to your environment.
tmux	Adds tmux software to your environment.	`Terminal Multiplexer`
TopHat	Adds TopHat software to your environment.
Trinity	Adds Trinity software to your environment.	`RNA`, `Inchwork`, `Chrysalis`, `Butterfly`, `De Novo Reconstruction`, `Transcription`
VCFtools	Adds VCFtools software to your environment.	`VCF Files`
Velvet	Adds Velvet software to your environment.
Vim	Adds Vim software to your environment
VMD	Adds VMD software to your environment.
Wannier90	Wannier90 is an open-source code (released under GPLv2) for generating maximally-localized Wannier functions and using them to compute advanced electronic properties of materials with high efficiency and accuracy.
Wise2	Adds Wise2 software to your environment.
Xmakemol	Adds Xmakemol software to your environment.	`GUI`, `OpenGL`, `Molecular Structure`

SysAdmin

Module Name	Description	Tags
fping	multiple host ping command	`Network`
[xCAT](modules/SysAdmin/xCAT	Helper Aliases for xCAT Maintenance	`xCAT`

Last Modified: Sun Jun 26 03:04:28 EDT 2022