CSU CS Unix Software Catalogue This catalogue contains a list of all software packages and products installed on the CSU Computer Science Unix Systems. Please contact sna@cs.colostate.edu with any corrections or additional software that you would like installed. To list the software packages on a Fedora or RedHat machine that have been installed from the standard repositories use the following command: rpm -qa | grep -i packagename All additional software that has been installed is listed alphabetically below in the following format: Package -- Description OS Architecture paths Notes environment variable settings, etc Abyss -- Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler. Fedora x86_64 /usr/local/abyss Alice -- Java teaching software Fedora x86_64 /usr/local/Alice Notes: Run with /usr/local/Alice/Required/run-alice allegro -- game programming library Fedora x86_64 /s/parsons/l/sys/allegro AMDSDK -- AMD software development kit Fedora x86_64 /usr/local/amdSDK /usr/local/amdSDK/AMD-APP-SDK-v2.7-RC-lnx32 /usr/local/etc/OpenCL /usr/local/bin/clinfo /usr/local/lib/OpenCL anaconda -- Python distribution for large-scale data processing, predictive analytics and scientific computing. Fedora x86_64 Python3: /usr/local/anaconda Python2: /usr/local/anaconda2 Notes: For Python3: export PATH="/usr/local/anaconda/bin:$PATH" export PYTHONPATH="/usr/local/anaconda/lib/python3.7/site-packages:$PYTHONPATH" For Python2: export PATH="/usr/local/anaconda2/bin:$PATH" export PYTHONPATH="/usr/local/anaconda2/lib/python2.7/site-packages:$PYTHONPATH" android -- Google Android development kit Fedora x86_64 /usr/local/android ArgoUML -- UML diagramming application Fedora x86_64 /usr/local/ArgoUML armadillo -- C++ linear algebra library Fedora x86_64 /usr/local/armadillo atlas -- Automatically Tuned Linear Algebra Subroutines Fedora x86_64 /usr/local/atlas Atom -- A hackable text editor for the 21st Century Fedora x86_64 /usr/local/atom Autodia -- automatic generation of UML diagrams Fedora x86_64 /usr/local/Autodia bcl2fastq2 -- To convert base call (BCL) files from Illumina sequencing instruments into FASTQ files Fedora x86_64 /usr/local/bcl2fastq2 bibtex2html Fedora x86_64 /usr/local/localtex/bibtex2html-1.56-linux bioperl Fedora x86_64 /usr/local/bioperl bison Fedora x86_64 /usr/local/bison bitarray -- python library that returns a new array of bits. Fedora x86_64 /usr/local/bitarray Note : You need to export the pythonpath: export PYTHONPATH="$PYTHONPATH:/usr/local/bitarray/lib64/python2.7/site-packages/" bokeh -- Python interactive visualization library that targets modern web browsers for presentation Fedora x86_64 /usr/local/bokeh Note: export PYTHONPATH=/usr/local/bokeh/lib/python2.7/site-packages boost -- C++ multi-purpose library Fedora x86_64 /usr/local/boost barvinok -- library for counting the number of integer points in parametric and non-parametric polytopes Fedora x86_64 /usr/local/barvinok bowtie -- an ultrafast, memory-efficient short read aligner for short DNA sequences Fedora x86_64 /usr/local/bowtie biopython -- set of freely available tools for biological computation written in Python Notes: add this in your .bashrc export PYTHONPATH=/usr/local/biopython/lib64/python3.5/site-packages biom-format -- The Biological Observation Matrix (BIOM) format Fedora x86_64 /usr/local/biom-format blat -- Blat is a genome alignment tool Fedora x86_64 /usr/local/blat blast+ -- command-line tools to run BLAST (Basic Local Alignment Search Tool) Fedora x86_64 /usr/local/blast+ Notes: Add this in your .bashrc export PATH="$PATH:/usr/local/blast/bin" export BLASTDB="/usr/local/blastdb" bwa -- Burrows-Wheeler Aligner Fedora X86_64 /usr/local/bin/bwa cabal -- Haskell package management tool Fedora x86_64 /usr/local/cabal celera -- Celera Assembler is a de novo whole-genome shotgun (WGS) DNA sequence assembler Fedora x86_64 /usr/local/celera ch -- C/C++ interpreter Fedora x86_64 /usr/local/ch circos -- circular visualization of data and information Fedora x86_64 /usr/local/circos clafer -- language for software modeling and analysis Fedora x86_64 /usr/local/clafer clapack -- C linear algebra library Fedora x86_64 /usr/local/clapack cmake -- build system Fedora x86_64 /usr/local/cmake cpuburn -- CPU load testing tool Fedora x86_64 RedHat /usr/local/cpuburn ctypeslib -- python C interoperability Fedora x86_64 /usr/local/ctypeslib cuda -- Compute Unified Device Architecture, GPU programming tools Fedora x86_64 /usr/local/cuda Notes: See ~info/cuda-faq.html for setup instructions cutadapt -- Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads Fedora x86_64 /usr/local/cutadapt cvxopt -- convex optimization tools for python Fedora x86_64 /usr/local/cvxopt cvxpy -- convex optimization tools for python Fedora x86_64 /usr/local/cvxpy Notes: export PYTHONPATH=/usr/local/cvxpy-0.2.2/lib/python2.7/site-packages DataAnalysis -- Data analysis for 454 Sequencing System Software Fedora x86_64 /usr/local/DataAnalysis dask -- Dask provides multi-core execution on larger-than-memory datasets using blocked algorithms and task scheduling Fedora x86_64 Notes: export PYTHONPATH=/usr/local/dask/lib/python2.7/site-packages dia2code -- generage code stubs from UML diagrams Fedora x86_64 /usr/local/dia2code dpkt -- python packet creation / parsing library Fedora x86_64 /usr/local/dpkt Notes: Add the following to environment: export PYTHONPATH=/usr/local/dpkt/lib/python2.7/site-packages:${PYTHONPATH} eclipse -- integrated development environment Fedorax x86_64 /usr/local/bin/eclipse.sh Notes: /usr/bin/eclipse may hang if /usr/local/java/bin/java comes before /usr/bin/java in your PATH environment variable FDR -- Failures-Divergences Refinement, model checking Fedora x86_64 /usr/local/FDR fann -- Fast Artificial Neural Network Library Fedora x86_64 /usr/local/fann Note: When compiling make sure to specify: -I/usr/local/fann/include -L/usr/local/fann/lib -lfann When running make sure to do: export LD_LIBRARY_PATH=/usr/local/fann/lib fastx_tools -- FASTQ/A short-reads pre-processing tools Fedora x86_64 /usr/local/fastx_toolkit ffmpeg -- video/audio encoder/decoder library Fedora x86_64 /usr/local/ffmpeg Notes: Add the following to .bashrc export PATH=/usr/local/ffmpeg/bin:${PATH} export LD_LIBRARY_PATH=/usr/local/ffmpeg/lib:${LD_LIBRARY_PATH} or in .cshrc set path = ( /usr/local/ffmpeg/bin $path ) setenv LD_LIBRARY_PATH /usr/local/ffmpeg/lib:${LD_LIBRARY_PATH} firefox -- web browser Fedora x86_64 /usr/local/firefox Notes: Uses Oracle java plugin fltk -- C++ gui library Fedora x86_64 /usr/local/fltk gap -- Groups, Algorithms, Programming Fedora x86_64 /usr/local/gap gcc -- gnu c compiler collection Fedora x86_64 RedHat /usr/local/gcc gd -- php image library Fedora x86_64 /usr/local/gd GeneTorrent -- Client software for downloading sequence data from CGHub's repository. Fedora x86_64 /usr/local/GeneTorrent git -- revision control system Mac OSX i386 RedHat /usr/local/git genesis -- GEneral NEural SImulation System Fedora i386 /usr/local/genesis Notes: Copy ~info/dot.files/.simrc to home directory glade -- A user Interface Designer tool to enable quick & easy development of user interfaces for the GTK+ toolkit and the GNOME desktop environment. Fedorar x86_64 /usr/local/glade gmp -- arbitrary precision math library RedHat /usr/local/gmp go -- google go programming language Fedora x86_64 /usr/local/go gradle -- A build automation system that builds upon the concepts of Apache Ant and Apache Maven. Fedora x86_64 /usr/local/gradle hadoop -- Map Reduce framework Fedora x86_64 /usr/local/hadoop hisat2 -- graph-based alignment of next generation sequencing reads to a population of genomes Fedora x86_64 /usr/local/hisat2 humann2 -- The HMP Unified Metabolic Analysis Network 2 Fedora x86_64 /usr/local/humann2 Notes: Add the following to environment: export PYTHONPATH="/usr/local/humann2/lib/python2.7/site-packages:$PYTHONPATH" hyda -- Hybrid De Novo Assembler Fedora x86_64 /usr/local/hyda hyperopt -- Distributed Asynchronous Hyperparameter Optimization Fedora x86_64 /usr/local/hyperopt Notes: Add the following to environment: export PYTHONPATH="$PYTHONPATH:/usr/local/hyperopt/lib/python2.7/site-packages/" idba -- De Bruijn Graph De Novo Assembler Fedora x86_64 /usr/local/idba idea -- IntelliJ IDEA Fedora x86_64 /usr/local/idea intel -- Intel compiler suite (icc, etc) Fedora x86_64 /s/parsons/l/sys/intel intervaltree -- A mutable, self-balancing interval tree for Python 2 and 3 FEdora x86_64 /usr/local/intervaltree Notes: Add the following to the environment: export PYTHONPATH="$PYTHONPATH:/usr/local/intervaltree/lib/python2.7/site-packages/" iozone -- I/O benchmarking Fedora x86_64 /usr/local/iozone ipython -- interactive python interpreter Fedora x86_64 /usr/local/ipython Notes: Add the following to environment: export PYTHONPATH=${PYTHONPATH}:/usr/local/ipython/lib/python JabRef -- graphical BibTeX front-end Fedora x86_64 /usr/local/JabRef java -- Oracle Java Fedora i386 RedHat /usr/local/java Fedora x86_64 /usr/local/java64 jellyfish - Fast, Parallel k-mer Counting for DNA Fedora x86_64 /usr/local/jellyfish JFLAP -- formal language experimentation Fedora x86_64 /usr/local/JFLAP keras -- Python library for neural networks computing. Fedora x86_64 Python3: /usr/local/anaconda Python2: /usr/local/anaconda2 Notes: For Python3: export PATH="/usr/local/anaconda/bin:$PATH" export PYTHONPATH="/usr/local/anaconda/lib/python3.7/site-packages:$PYTHONPATH" kraken -- Kraken is a system for assigning taxonomic labels to short DNA sequences, Fedora x86_64 /usr/local/kraken kmergenie -- KmerGenie estimates the best k-mer length for genome de novo assembly. Fedora x86_64 /usr/local/kmergenie lapack -- linear algebra library Fedora x86_64 /usr/local/lapack LC3 -- little computer, assembly language interpreter Fedora x86_64 /usr/local/LC3 Notes: Insert the following aliases in your .cshrc or .bashrc file: alias simulator '/usr/local/java/bin/java -classpath /usr/local/LC3/lc3.jar simulator.Main' alias assembler '/usr/local/java/bin/java -classpath /usr/local/LC3/lc3.jar assembler.Assembler' alias convert '/usr/local/java/bin/java -classpath /usr/local/LC3/lc3.jar assembler.ASCIIToBin' alias archsim '/usr/local/java/bin/java -classpath /usr/local/LC3/lc3arch.jar LC3ArchitecturalSimulatorGUI' libmpq -- library for manipulating MPQ archives Fedora x86_64 /usr/local/libmpq mahotas -- Python Computer Vision Library Fedora x86_64 /usr/local/mahotas Notes: Add the following to environment: export PYTHONPATH=$PYTHONPATH:/usr/local/mahotas/lib64/python2.7/site-packages matplotlib -- python plotting library Fedora x86_64 /usr/local/matplotlib Notes: Add the following to environment: export PYTHONPATH=/usr/local/matplotlib/lib64/python2.7/site-packages:${PYTHONPATH} matlab -- computational mathematics and programming language Fedora x86_64 /s/parsons/l/sys/matlab/bin maven -- software project management Fedora x86_64 /usr/local/maven mercurial -- revision control system Fedora x86_64 /usr/local/mercurial metaphlan -- Metagenomic Phylogenetic Analysis Fedora x86_64 /usr/local/metaphlan2 mlabwrap -- Library to execute matlab functions in python Fedora x86_64 /usr/local/mlabwrap Notes: Add the following to environment: export PYTHONPATH=/usr/local/mlabwrap/lib64/python2.7/site-packages:${PYTHONPATH} export PATH=/s/parsons/l/sys/matlab64/bin:${PATH} mmh3 -- Python wrapper for MurmurHash (MurmurHash3), a set of fast and robust hash functions. Fedora x86_64 /usr/local/mmh3 Note: You need to export the python path: export PYTHONPATH="$PYTHONPATH:/usr/local/mmh3/lib64/python2.7/site-packages/" mpd -- Music Player Daemon Fedora x86_64 /usr/local/mpd mpdist -- PostScript printing tools Fedora x86_64 /usr/local/mpdist mpfr -- multiple-precision math library RedHat /usr/local/mpfr mplayer -- multimedia player Fedora x86_64 /usr/local/mplayer Notes: Add the following to environment: export LD_LIBRARY_PATH='$LD_LIBRARY_PATH:/usr/local/mplayer/lib' mrjob -- package that helps you write and run Hadoop Streaming jobs. Fedora x86_64 /usr/local/mrjob Notes: Add the following to environment: export PYTHONPATH=/usr/local/mrjob/lib/python2.7/site-packages:${PYTHONPATH} multichain -- software to build and deploy blockchain applications Fedora x86_64 /usr/local/multichain Notes: Add the following to environment: export PATH=$PATH:/usr/local/multichain netbeans -- integrated development environment Fedora x86_64 /usr/local/netbeans networkx -- python graph analysis tool Fedora x86_64 /usr/local/networkx Notes: Add the following to environment: export PYTHONPATH=/usr/local/networkx/lib/python2.7/site-packages:${PYTHONPATH} newbler -- Sofware package designed specifically for assembling DNA sequence data Fedora x86_64 /usr/local/newbler ns -- network simulator Fedora x86_64 /usr/local/ns numpy -- python numerical library Fedora x86_64 /usr/local/numpy numpy-mkl -- python numerical library linked against Intel Math Kernel Library Fedora x86_64 /usr/local/numpy-mkl nvtop -- a (h)top like task monitor for NVIDIA GPUs Fedora x86_64 /usr/local/nvtop Notes: Add the following to the environment: export PATH=$PATH:/usr/local/nvtop/bin obs-studio -- video and audio recording studio Fedora x86_64 /usr/local/obs-studio/bin/64bit/obs Notes: Add the following to the environment: export PATH=$PATH:/usr/local/ffmpeg/bin export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/ffmpeg/lib ocaml -- programming language RedHat /usr/local/ocaml openarena -- is a community-produced deathmatch FPS like Quake 3 Fedora x86_64 /usr/local/openarena OpenCV -- computer vision library Fedora x86_64 /usr/local/OpenCV Note : The following environment variables need to be exported: export PYTHONPATH="$PYTHONPATH:/usr/local/OpenCV/lib/python3.7/site-packages" ODE -- ODE is an open source, high performance library for simulating rigid body dynamics. Fedora x86_64 /usr/local/ODE Notes: The following environmental variables need to be exported: export LD_LIBRARY_PATH=/usr/local/ODE/lib:${LD_LIBRARY_PATH} opera -- opera_v1.2 is a software designed for Reconstructing Optimal Genomic Scaffolds with High-Throughput Paired-End Sequences Fedora x86_64 /usr/local/opera panda3d -- a framework for 3D rendering and game development for Python and C++ programs. Fedora x86_64 /usr/local/panda3d Note: The following environmental variables need to be exported: export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/local/panda3d/lib64/panda3d" passenger -- apache ruby module Fedora x86_64 /usr/local/passenger perl -- practical report and extraction language Fedora x86_64 /usr/local/perl PDT -- Program Database Toolkit (PDT) is a framework for analyzing source code written in several programming languages. Fedora x86_64 /usr/local/PDT pluto -- automatic source-to-source transformer that can optimize nested loop sequences for coarse-grained parallelism and cache locality simultaneously Fedora x86_64 /usr/local/pluto povray -- raytracer Fedora x86_64 /usr/local/povray propy -- A package to compute protein descriptors using python. Fedora x86_64 /usr/local/propy pybedtools -- Python wrapper -- and more -- for Aaron Quinlan's BEDTools Fedora x86_64 /usr/local/pybedtools Notes: Add the following to the environment: export PYTHONPATH="$PYTHONPATH:/usr/local/pybedtools/lib64/python2.7/site-packages/" PyCharm Community -- A Python IDE Fedora x86_64 /usr/local/pycharm PyCharm Professional -- A Python IDE Fedora x86_64 /usr/local/pycharm-pro Notes: This edition of PyCharm requires a licence pydoop -- Python interface to Hadoop Fedora x86_64 /usr/local/pydoop Notes: export PYTHONPATH="$PYTHONPATH:/usr/local/pydoop/lib/python2.7/site-packages/" PyML -- python machine learning library Fedora x86_64 /usr/local/PyML Notes: Add the following to .bashrc export PYTHONPATH=/usr/local/PyML/lib64/python2.7/site-packages/ or in .cshrc setenv PYTHONPATH /usr/local/PyML/lib64/python2.7/site-packages/ pypar -- openmpi python bindings Fedora x86_64 /usr/local/pypar Notes: Add the following to .bashrc export PYTHONPATH=/usr/local/pypar/lib64/python2.7/site-packages/:${PYTHONPATH} or in .cshrc setenv PYTHONPATH /usr/local/pypar/lib64/python2.7/site-packages/:${PYTHONPATH} Pyrex -- a Language for Writing Python Extension Modules Fedora x86_64 /usr/local/Pyrex Notes: Add the following to .bashrc to help python to locate the Pyrex modules: export PYTHONPATH=/usr/local/Pyrex/lib/python2.7/site-packages/:${PYTHONPATH} pysam -- a python module for reading, manipulating and writing genomic data sets. Fedora x86_64 /usr/local/pysam Notes : Add the following to .bashrc to help python to locate the module: export PYTHONPATH="$PYTHONPATH:/usr/local/pysam/lib64/python2.7/site-packages/" PyQt -- python Qt bindings Fedora x86_64 /usr/local/PyQt python -- programming language Fedora x86_64 /usr/local/python PyODE -- Python bindings for The Open Dynamics Engine, an open-source physics engine. Fedora x86_64 /usr/local/PyODE Notes: Add the following to .bashrc to help python to locate the PyODE modules: export PYTHONPATH=/usr/local/Pyrex/lib/python2.7/site-packages:/usr/local/PyODE/lib64/python2.7/site-packages/:${PYTHONPATH} export LD_LIBRARY_PATH=/usr/local/ODE/lib/:/usr/local/PyODE/lib64/:${LD_LIBRARY_PATH} pyrameter -- library for designing hierarchical parameter searches with continuous and discrete domains, and then search those spaces. Fedora x86_64 /usr/local/pyrameter Notes: export PYTHONPATH=/usr/local/pyrameter/lib/python3.7/site-packages/:${PYTHONPATH} QIIME -- Package for comparison and analysis of microbial communities Fedora x86_64 /usr/local/qiime Quast -- QUAST stands for QUality ASsesment Tool. QUAST evaluates genome assemblies by computing various metrics. Fedora x86_64 /usr/local/quast qt -- graphics library RedHat /usr/local/qt R -- programming language Fedora x86_64 /usr/local/R RedHat /usr/local/R Ray -- Ray is a parallel de novo genome assembler that utilises the message-passing interface everywhere and is implemented using peer-to-peer communication. Fedora X86_64 /usr/local/Ray racket -- scheme programming language Fedora x86_64 /usr/local/racket RealPlayer -- multimedia player Fedora x86_64 /usr/local/RealPlayer Rar -- WinRAR is a powerful archive manage Fedora x86_64 /usr/local/rar Readability -- A collection of functions that measure the readability of a given body of text using surface characteristics. Fedora x86_64 /usr/local/readability Notes: Add the following to .bashrc export PYTHONPATH=/usr/local/readability/lib/python2.7/site-packages:${PYTHONPATH} Readability-lxml -- A fast html to text parser. Fedora x86_64 /usr/local/readability-lxml Notes: Add the following to .bashrc export PYTHONPATH=/usr/local/readability-lxml/lib/python2.7/site-packages:${PYTHONPATH} REAPR -- Recognising Errors in Assemblies using Paired Reads (A tool that evaluates the accuracy of a genome assembly using mapped paired end reads.) Fedora x86_64 /usr/local/Reapr RoboCup Soccer Simulator -- The RoboCup Soccer Simulator is a research and educational tool for multi-agent systems and artificial intelligence. It enables for two teams of 11 simulated autonomous robotic players to play soccer (football). Fedora x86_64 /usr/local/robocupsimulator reportlab: Solution to generate rich, attractive and fully bespoke PDF with Python Notes: Add the following to .bashrc export PYTHONPATH=/usr/local/reportlab-2016-10-17/lib64/python3.5/site-packages/ Rstudio -- IDE for R programming language Fedora x86_64 /usr/local/rstudio SageMath -- SageMath is a computer algebra system with features covering many aspects of mathematics, including algebra, combinatorics, graph theory, numerical analysis, number theory, calculus and statistics. Fedora x86_64 /usr/local/sage scikit-learn -- machine learning library for python Fedora x86_64 /usr/local/scikit-learn Notes: Add the following to .bashrc export PYTHONPATH=/usr/local/scikit-learn/lib64/python2.7/site-packages:${PYTHONPATH} or in .cshrc setenv PYTHONPATH /usr/local/scikit-learn/lib64/python2.7/site-packages:${PYTHONPATH} scala : Scala is a programming language for general software applications. Fedora x86_64 /usr/local/scala Notess : Add the following to .bashrc export SCALA_HOME=/usr/local/scala export PATH=$SCALA_HOME/bin:/$PATH scenebuilder : A visual layout tool that lets users quickly design JavaFX application user interfaces Fedora x86_64 /usr/local/scenebuilder SciPy -- Python-based ecosystem of open-source software for mathematics, science, and engineering. Fedora x86_64 /usr/local/scipy shadho -- a framework for distributed hyperparameter optimization developed for machine/deep learning applications Fedora x86_64 /usr/local/shadho Notes: Add the following to .bashrc export PATH=/usr/local/cctools/bin:$PATH export PYTHONPATH=/usr/local/pyrameter/lib/python3.7/site-packages/:/usr/local/numpy/lib64/python3.7/site-packages:/usr/local/cctools/lib/python3.7/site-packages:/usr/local/shadho/lib/python3.7/site-packages/ sml -- Standard ML programming language Fedora x86_64 /usr/local/sml SPAdes -- St. Petersburg genome assembler Fedora x86_64 /usr/local/SPAdes Spark : Apache Spark is a fast and general engine for big data processing, with built-in modules for streaming, SQL, machine learning and graph processing. Fedora x86_64 /usr/local/spark spark-sklearn : Integration tools for running scikit-learn on Spark Fedora x86_64 /usr/local/spark-sklearn Note : You need to export the following python path: export PYTHONPATH="$PYTHONPATH:/usr/local/spark-sklearn-0.2.0/lib/python2.7/site-packages/" sphinx_rtd_theme : Read the Docs Sphinx Theme Fedora x86_64 /usr/local/sphinx_rtd_theme spim -- MIPS simulator Fedora x86_64 /usr/local/spim SOAPdenovo2 -- SOAPdenovo, a short read de novo assembly tool, is a package for assembling short oligonucleotide into contigs and scaffolds. Fedora X86_64 /usr/local/SOAPdenovo2 sratoolkit -- The Sequence Read Archive (SRA) stores raw sequence data from "next-generation" sequencing technologies. SRA is NIH’s primary archive of high-throughput sequencing data. Fedora x86_64 /usr/local/sratoolkit systemc -- C++ simulation library Fedora x86_64 /usr/local/systemc TAU -- Portable profiling and tracing toolkit for performance analysis of parallel programs written in Fortran, C, C++, UPC, Java, Python. Fedora x86_64 /usr/local/TAU tensorflow -- Python library for machine learning computing. Fedora x86_64 Python3: /usr/local/anaconda Python2: /usr/local/anaconda2 Notes: For Python3: export PATH="/usr/local/anaconda/bin:$PATH" export PYTHONPATH="/usr/local/anaconda/lib/python3.7/site-packages:$PYTHONPATH" theona -- A CPU and GPU Math Expression Compiler Fedora x86_64 /usr/local/theona Notes: Add the following to .bashrc export PYTHONPATH=/usr/local/theano-0.7.0/lib/python2.7/site-packages/:${PYTHONPATH} thrust -- C++ template library for CUDA. Thrust is a parallel algorithms library which resembles the C++ Standard Template Library (STL) Fedora x86_64 /usr/local/thrust tig -- An ncurses-based text-mode interface for git /usr/local/tig tophat -- A fast splice junction mapper for RNA-Seq reads Fedora x86_64 /usr/local/tophat transabyss -- De novo assembly of RNA-Seq data using ABySS Fedora x86_64 /usr/local/transabyss truffle -- Truffle is a development environment, testing framework and asset pipeline for Ethereum, aiming to make life as an Ethereum developer easier Fedora x86_64 /usr/local/truffle Notes: Add the following to .bashrc export PATH=/usr/local/truffle/bin:$PATH torch -- Torch is a scientific computing framework with wide support for machine learning algorithms. It uses LuaJIT, and an underlying C/CUDA implementation. Fedora x86_64 /usr/local/torch/ Notes: Add the following to .bashrc export PATH=/usr/local/torch/install/bin:$PATH totalview -- TotalView is a GUI-based source code defect analysis tool. Fedora x86_64 /usr/local/totalview (/usr/local/toolworks/totalview*) twin -- Efficient Indexed Alignment of Contigs to Optical Maps. Fedora x86_64 /usr/local/twin umbrello -- UML modeler Fedora x86_64 /usr/local/umbrello unison -- File Synchronizer Fedora x86_64 /usr/local/bin/unison USE -- USE is a system for the specification of information systems based on the Unified Modeling Language (UML) Fedora x86_64 /usr/local/use velvet -- Sequence Assembler for Very Short Reads. Fedora x86_64 /usr/local/velvet virtualenv --A tool for creating isolated 'virtual' python environments. Note: Add the following to .bashrc export PATH=$PATH:/usr/local/virtualenv/bin/ For Python2: export PYTHONPATH=/usr/local/virtualenv/lib/python2.7/site-packages/:$PYTHONPATH For Python3: export PYTHONPATH=/usr/local/virtualenv/lib/python3.7/site-packages/:$PYTHONPATH visual studio code -- An IDE from Microsoft Fedora x86_64 /usr/local/visual-studio-code/ vtune -- Intel Performance Profiler Fedora x86_64 /usr/local/vtune webstorm -- JavaScript IDE Fedora x86_64 /usr/local/webstorm weka -- Collection of machine learning algorithms for data mining tasks. Fedora x86_64 /usr/local/weka whizzytex -- emacs TeX plugin Fedora x86_64 /usr/local/whizzytex xforms -- xforms tools Fedora x86_64 /usr/local/xforms xgboost -- An optimized distributed gradient boosting library Fedora x86_64 /usr/local/xgboost Python library : /usr/local/xgboost_fc27 Note : Add the following to .bashrc export PYTHONPATH=/usr/local/xgboost_fc27/lib/python2.7/site-packages/:${PYTHONPATH} xgobi -- data visualization Fedora x86_64 /usr/local/xgobi xilinx -- FPGA tools Fedora x86_64 /usr/local/xilinx xine -- multimedia player Fedora x86_64 /usr/local/xine xmms -- multimedia player Fedora x86_64 /usr/local/xmms xmpi -- run/debug GUI for mpi Fedora x86_64 /usr/local/xmpi yalmip -- a toolbox for modeling and optimization in MATLAB Fedora x86_64 /usr/local/yalmip Notes: Add the following directories to your MATLAB path /usr/local/yalmip /usr/local/yalmip/extras /usr/local/yalmip/demos /usr/local/yalmip/solvers /usr/local/yalmip/modules /usr/local/yalmip/modules/parametric /usr/local/yalmip/modules/moment /usr/local/yalmip/modules/global /usr/local/yalmip/modules/sos /usr/local/yalmip/operators yed -- yED Graphical Editor Fedora X86_64 /usr/local/yed z-eves -- theorem proving tool Fedora x86_64 /usr/local/z-eves z3 -- Z3 is an SMT solver that combines several theory solvers into a combined framework. Fedora x86_64 /usr/local/z3