{"type":"doc","content":[{"type":"heading","attrs":{"level":4},"content":[{"text":"Legacy software stack","type":"text"}]},{"type":"paragraph","content":[{"text":"The environment modules for these packages are somewhat old at this point. However, there are packages in this stack that are not yet in the newer stacks. Work is ongoing to get packages updated and migrated to newer stacks. Please begin using newer versions whenever possible.","type":"text"}]},{"type":"expand","attrs":{"title":"View legacy software stack"},"content":[{"type":"paragraph","content":[{"type":"hardBreak"}]},{"type":"extension","attrs":{"extensionType":"com.atlassian.confluence.migration","extensionKey":"__confluenceADFMigrationUnsupportedContentInternalExtension__","text":"","parameters":{"cxhtml":"ProgramtrueS,FF,SINLINE

Program	Version	Link to main page
bamtools	2.5.1	pezmaster31/bamtools: C++ API & command-line toolkit for working with BAM data
augustus	3.3.2	Augustus: gene prediction
cmake	3.7.2 3.13.2	CMake - Cross Platform Make
RHash	1.3.7	rhash/RHash: Great utility for computing hash sums
FFTW	3.3.6 3.3.7	FFTW Home Page
GCC	5.4.0 6.3.0 7.3.0 8.3.0	GCC, the GNU Compiler Collection - GNU Project - Free Software Foundation (FSF)
GMP	6.1.2	The GNU MP Bignum Library
grib_api	1.19.0	Home - GRIB-API - ECMWF Confluence Wiki
GSL	2.2.3	GSL - GNU Scientific Library - GNU Project - Free Software Foundation (FSF)
Gurobi Optimizer	5.6.3 7.0.2 8.1.0 9.0.0	Gurobi Optimizer
HDF5	1.8.18	HDF Group - HDF5
Intel Parallel Studio Intel compilers MKL DAAL IPP TBB	2017.1 2017.4	Intel® Composer XE Suites
Intel-MKL	2019.3.199	Intel® Math Kernel Library (Intel® MKL) \| Intel® Software
matlab	R2016b 2018a	MATLAB - The Language of Technical Computing
MPC	1.0.3	MPC
MPFR	3.1.5	The GNU MPFR Library
NCO	4.6.4	NCO Homepage
netcdf	4.4.1.1	Unidata \| NetCDF
netcdf-cxx	4.3.0	Unidata \| NetCDF
netcdf-fortran	4.4.4	Unidata \| NetCDF
openmpi	2.0.1 2.1.2	Open MPI: Open Source High Performance Computing
		Welcome to Python.org
		The R Project for Statistical Computing
valgrind	3.12.0	Valgrind Home
ocaml	4.04.0	OCaml
Ansys	17.2	ANSYS - Simulation Driven Product Development
CFITSIO	3.410	FITSIO Home Page
Pythia	8.223	PYTHIA
Platypus	0.8.1	Platypus Variant Caller
Ruby	2.4.0	Ruby Programming Language
	0.5.0 0.5.1	The Julia Language
MOSEK	8.0.0.53 8.0.0.80	MOSEK ApS
JDK	8u121 8u172	Java SE \| Oracle Technology Network \| Oracle
RSL	1.49	RSL (Radar Software Library)
Perl	5.24.1	The Perl Programming Language
Postgresql	11.2	PostgreSQL: The world's most advanced open source database
Graphviz	2.40.1	Graphviz - Graph Visualization Software
htslib	1.3.2	Releases · samtools/htslib
samtools	1.3.1	Releases · samtools/samtools
bcftools	1.3.1	Releases · samtools/bcftools
bedtools	2.26.0	bedtools: a powerful toolset for genome arithmetic
lzo	2.09	LZO real-time data compression library
CUDA	8.0.44 8.0.61 9.0.176.1 9.1.85.1 9.1.85.2	Parallel Programming and Computing Platform \| CUDA \| NVIDIA
Beagle-lib	2.1.2 3.1.2	general purpose library for evaluating the likelihood of sequence evolution on trees
Tecplot360	2016R2	Tecplot 360 CFD post processing tools to analyze data
CDO	1.8.0	Overview - CDO
I/O API	3.2	CMAS: Community Modeling and Analysis System I/O API
Plink	1.07	PLINK: Whole genome data analysis toolset
CMAQ	5.1	Community Multi-scale Air Quality (CMAQ) Modeling System for Air Quality Management \| Air Research \| US EPA
NCL	6.4.0	NCL Overview
HDF-EOS2	2.19	HDF-EOS Tools and Information Center
HDF-EOS5	1.15	HDF-EOS Tools and Information Center
g2clib	1.60	GRIB2
Gaussian 09	D.01	Gaussian.com \| Expanding the limits of computational chemistry
NBO	6.0	NATURAL BOND ORBITAL 6.0 HOME
HDF	4.2.1	HDF Group - HDF4
AutoDock Vina	1.1.2	AutoDock Vina - molecular docking and virtual screening program
BEAST	1.8.4	BEAST Software - Bayesian Evolutionary Analysis Sampling Trees
XCrySDen	1.5.60	XCrySDen - (X-Window) Crystalline Structures and Densities
Mesa	17.0.1	The Mesa 3D Graphics Library
LLVM	4.0.0	The LLVM Compiler Infrastructure Project
Open Babel	2.4.1	Open Babel
Eigen	3.3.3	Eigen
Protobuf (C++)	3.2.0	Protocol Buffers \| Google Developers
Snappy	1.1.4	Snappy by google
LevelDB	1.20	GitHub - google/leveldb: LevelDB is a fast key-value storage library written at Google that provides an ordered mapping from string keys to string values.
YASM	1.3.0	The Yasm Modular Assembler Project
FFMPEG	3.2.4	About FFmpeg
OpenCV	3.2.0	OpenCV library
JAGS	4.2.0	JAGS - Just Another Gibbs Sampler
STAR-CCM+	12.02.010 13.04.010	STAR-CCM+® \| CFD Simulation Software
Cufflinks	2.2.1	Cufflinks
PETSc hpre metis parmetis mpi4py mumps petsc4py ptscotch suitesparse superlu_dist	3.7.5 3.10.3	PETSc: Home Page
Wannier90	2.1.0	wannier.org
Atompaw	4.0.0.14	Atompaw Web Page
Libxc	2.2.3 3.0.0	Libxc - OctopusWiki
ABINIT	8.2.2	ABINIT
c-blosc	1.11.2	Blosc, an extremely fast, multi-threaded, meta-compressor library \| Blosc Main Page
MDTraj	1.8.0	MDTraj
lmfit	6.1	lmfit [MLZ Scientific Computing Group]
Gromacs	2016.3	Gromacs
ELPA	2016.05.004 2018.11.001	About ELPA — Eigenvalue SoLvers for Petaflop-Applications (ELPA)
Quantum Espresso	6.1	Quantum ESPRESSO
BWA	0.7.15	Burrows-Wheeler Aligner
libcerf	1.5	libcerf [MLZ Scientific Computing Group]
Gnuplot	5.0.6	gnuplot homepage
GEOS	3.6.1	GEOS
Ncview	2.1.7	Ncview
git	2.13.0	Git
BLAST databases: nt, nt, swissprot	2.6.0+	BLAST: Basic Local Alignment Search Tool
	5.4.0	ParaView Home
cuDNN	5.1 6.0 7.0.5	NVIDIA cuDNN \| NVIDIA Developer
Leptonica	1.74.4	Leptonica
Tesseract	3.05.01	Tesseract Open Source OCR Engine
WebP	0.6.0	A new image format for the Web \| WebP \| Google Developers
giflib	5.1.4	The GIFLIB project
Subread	1.5.2	Subread
GLPK	4.62	GLPK - GNU Project - Free Software Foundation (FSF)
Symphony	5.6.16	SYMPHONY
gavl	1.4.0	Gmerlin homepage - gavl
frei0r-plugins	1.6.1	Frei0r :: Free Video Effects collection
MPFI	1.5.1	InriaForge: MPFI: Project Home
ESBTL	1.0-beta01	ESBTL (Easy Structural Biology Template Library)
gf2x	1.2	InriaForge: gf2x: Project Home
NTL	10.4.0	NTL: A Library for doing Number Theory
CGAL	4.10 4.13	The Computational Geometry Algorithms Library
SQLite	3.16.2 3.30.0	SQLite Home Page
scotch	6.0.4	SCOTCH: Static Mapping, Graph, Mesh and Hypergraph Partitioning, and Parallel and Sequential Sparse Matrix Ordering Package
metis	5.1.0	METIS - Serial Graph Partitioning and Fill-reducing Matrix Ordering \| Karypis Lab
parmetis	4.0.3	ParMETIS - Parallel Graph Partitioning and Fill-reducing Matrix Ordering \| Karypis Lab
OpenFOAM	4.1 5.0	OpenFOAM \| Free CFD Software \| The OpenFOAM Foundation
STAR	2.5.3a	STAR \| Spliced Transcripts Alignment to a Reference
libunwind	1.2.1	The libunwind project
glog	0.3.5	google/glog: C++ implementation of the Google logging module
gflags	2.2.1	How To Use Gflags (formerly Google Commandline Flags)
LMDB	0.9.21	LMDB/lmdb: Read-only mirror of official repo on openldap.org.
Caffe	1.0	Caffe \| Deep Learning Framework
NCCL	1.3.4 2.1.4	NVIDIA/nccl: Optimized primitives for collective multi-GPU communication
WIEN2K license required	17.1	WIEN 2k
Turbomole	7.2.0 7.2.1	Turbomole: Program Package for ab initio Electronic Structure Calculations
Parallel NetCDF	1.8.1	parallel-netcdf
Amber	2017 (Amber16 + AmberTools17)	The Amber Molecular Dynamics Package
TransPS	1.1.0	TransPS
cusplibrary	0.4.0 0.5.1	CUSP: Main Page
Mesquite	2.3.0	Mesquite – The Trilinos Project
foam-extend	4.0	foam-extend download \| SourceForge.net
HPL	2.2	HPL - A Portable Implementation of the High-Performance Linpack Benchmark for Distributed-Memory Computers
PortAudio	19.6.0	PortAudio - an Open-Source Cross-Platform Audio API
openSMILE	2.3.0	audEERING \| Intelligent Audio Engineering – openSMILE
log4j	2.10.0	Log4j – Apache Log4j 2 - Apache Log4j 2
flex	2.6.4	GitHub - westes/flex: The Fast Lexical Analyzer - scanner generator for lexing in C and C++
WRF WRF-chem WPS (WRF Preprocessing System)	3.9.1.1	Weather Research and Forecasting Model \| MMM: Mesoscale & Microscale Meteorology Laboratory
Darshan	3.5.1	Darshan
RngStreams	1.0.1	RngStreams - multiple independent streams of pseudo-random numbers
UNU.RAN	1.8.1	UNU.RAN - Universal Non-Uniform RANdom number generators
LZ4	1.8.1.2	LZ4 - Extremely fast compression
GL2PS	1.4.0	GL2PS: an OpenGL to PostScript printing library
XRootD	4.8.1	Home Page \| XRootD
Z3	4.6.0	GitHub - Z3Prover/z3: The Z3 Theorem Prover
Davix	0.6.7	GitHub - cern-it-sdc-id/davix: High-performance file management over WebDAV / HTTP
xxHash	0.6.4	GitHub - Cyan4973/xxHash
Oracle instantclient	12.2.0.1.0	Oracle Instant Client - Free tools and libraries for connecting to Oracle Database
ROOT	6.12.06	ROOT a Data analysis Framework
Praat	6.0.37	Praat: doing Phonetics by Computer
MKL-DNN	0.12	GitHub - intel/mkl-dnn: Intel(R) Math Kernel Library for Deep Neural Networks (Intel(R) MKL-DNN)
NASM	2.13.03	NASM
Yeppp	1.0.0	MDukhan / Yeppp — Bitbucket
CNVnator	0.3.3	GitHub - abyzovlab/CNVnator: a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
CPLEX	12.8.0	ILOG CPLEX Optimization Studio \| IBM
SAS License required SAS \| Information Technology Services	9.4_TS1M2	Foundation Tools \| SAS
Gentle	0.10.1	lowerquality/gentle: gentle forced aligner
Bazel	0.12.0	Bazel - a fast, scalable, multi-language and extensible build system - Bazel
TensorBoard	1.7.0	tensorflow/tensorboard: TensorFlow's Visualization Toolkit
TensorFlow	1.7.0	TensorFlow
libedit	3.1-20170329	Editline Library (libedit) - Port of NetBSD Command Line Editor Library
GEANT4	10.4.1	Overview \| geant4.web.cern.ch
Google Test	1.8.0	google/googletest: Google Test
InsightToolkit	4.13.0 4.13.2	ITK - Segmentation & Registration Toolkit
RTK	1.4.0	RTK - Reconstruction Toolkit
Gate	8.1	Forewords \| GATE
SimplElastix	0.10.0	SimpleElastix
Elastix	4.9.0	elastix
PGI Community Edition	18.4	PGI \| Products \| Community Edition
Nettle	3.4	Nettle - a low-level crypto library
libarchive	3.3.2	libarchive - C library and command-line tools for reading and writing tar, cpio, zip, ISO, and other archive formats
SRA-tools	2.9.0	ncbi/sra-tools: SRA Tools
NGS	2.9.0	ncbi/ngs: NGS Language Bindings
NCBI-VDB	2.9.0-1	ncbi/ncbi-vdb: ncbi-vdb
LASzip	2.2.0 3.2.2	LASzip - free and lossless LiDAR compression
libLAS	1.8.1	libLAS - LAS 1.0/1.1/1.2 ASPRS LiDAR data translation toolset — liblas.org
libgeotiff	1.4.2	GeoTIFF
libgpuarray	0.7.6	Welcome to libgpuarray’s documentation!
GATK	4.0.5.2	GATK \| Home
SNAP	0.15	SNAP Sequence Aligner
zstd	1.3.5	Zstandard - Real-time data compression algorithm
magma	2.4.0	Magma
ZeroMQ	4.2.5	Distributed Messaging
CUB	1.8.0	CUB: Main Page
pybind11	2.2.3	pybind/pybind11: Seamless operability between C++11 and Python
pytorch/caffe2	0.4.0	PyTorch
torchvision	0.2.1	pytorch/vision: Datasets, Transforms and Models specific to Computer Vision
bowtie	1.2.2	Bowtie: An ultrafast, memory-efficient short read aligner
bowtie2	2.3.4.2	Bowtie 2: fast and sensitive read alignment
WRF-Hydro	5.0.0	Overview \| NCAR Research Applications Laboratory \| RAL
libuuid	1.0.3	libuuid download \| SourceForge.net
CZMQ	4.1.1	CZMQ - High-level C Binding for ZeroMQ - libzapi
cppzmq	4.3.0	zeromq/cppzmq: Header-only C++ binding for libzmq
libtool	2.4.6	GNU Libtool - GNU Project - Free Software Foundation
libunistring	0.9.10	libunistring - GNU Project - Free Software Foundation (FSF)
libatomic_ops	7.6.4	ivmai/libatomic_ops: The atomic_ops project (Atomic memory update operations portable implementation)
GC	7.6.4	A garbage collector for C and C++
Guile	2.2.4	GNU's programming and extension language — GNU Guile
libctl	4.1.3	Overview - libctl Documentation
OpenBUGS	3.2.3	FrontPage - OpenBUGS
TopHat	2.1.1 2.1.2	TopHat
VCFtools	0.1.16	VCFtools
Jellyfish	2.2.10	gmarcais/Jellyfish: A fast multi-threaded k-mer counter
BLAT	35	Human BLAT Search
Mapsembler2	2.2.4	mapsembler2
cortex_con	0.04c (beta)	CORTEX website (cortex_con)
cortex_var	1.0.5.21	CORTEX website (cortex_var)
CoNIFER	0.2.2	Conifer - COpy Number Inference From Exome Reads - Home
libgtextutils	0.7	agordon/libgtextutils: Gordon's Text utils Library
fastx_toolkit	0.0.14	agordon/fastx_toolkit: FASTA/FASTQ pre-processing programs
Abaqus license required	2018	Abaqus Unified FEA - SIMULIA™ by Dassault Systèmes®
GMT	5.4.4	GenericMappingTools/gmt: The Generic Mapping Tools
RocksDB	5.17.2	RocksDB \| A persistent key-value store \| RocksDB
TeXLive	20180414	TeX Live - TeX Users Group
ARPACK-NG	3.7.0	opencollab/arpack-ng: Collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.
SuperLU	5.2.1	SuperLU: Home Page
Armadillo	9.200.7	Armadillo: C++ library for linear algebra & scientific computing
PEST	13.6	PESThomePage.org - HOME PAGE
FEniCS	2018.1.0	FEniCS Project
mpiP	3.4.1	mpiP: Lightweight, Scalable MPI Profiling
PAPI	5.7.0	PAPI
SimpleITK	1.2.0	SimpleITK
OpenJDK	11.0.2	OpenJDK
libogg	1.3.3	Xiph.org
flac	1.3.2	FLAC - Free Lossless Audio Codec
mpg123	1.25.10	mpg123, Fast MP3 Player for Linux and UNIX systems
libvorbis	1.3.6	Xiph.org
libsndfile	1.0.28	Libsndfile
lame	3.100	LAME MP3 Encoder
libmad	0.15.1b	Underbit: MAD (MPEG Audio Decoder)
libid3tag	0.15.1b	Underbit: MAD (MPEG Audio Decoder)
opus	1.3.1	Opus Codec
wavpack	5.1.0	WavPack Audio Compression
TwoLAME	0.3.13	TwoLAME - MPEG Audio Layer 2 Encoder
libao	1.2.0	Xiph.org: libao: a cross platform audio library
opencore-amr	0.1.5	opencore-amr download \| SourceForge.net
opusfile	0.11	Opus Codec
SoX	14.4.2	http://sox.sourceforge.net/
SCons	3.0.5	SCons: A software construction tool - SCons
ISCE2	2.3.1	isce-framework/isce2: InSAR Scientific Computing Environment version 2
Mono	5.18.0.240	Home \| Mono
VASP	5.4.4	VASP - Vienna Ab initio Simulation Package
zip	3.0	Info-ZIP Home Page

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