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



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

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

Autodia -- automatic generation of UML diagrams
	Fedora x86_64
		/usr/local/Autodia

bibtex2html  
	Fedora x86_64
		/usr/local/localtex/bibtex2html-1.56-linux

boost -- C++ multi-purpose library
	RedHat ia64
		/usr/local/boost

bowtie -- an ultrafast, memory-efficient short read aligner for short 
          DNA sequences
         Fedora x86_64
		/usr/local/bowtie

blat -- Blat is a genome alignment tool 
	Fedora x86_64
		/usr/local/blat

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

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 ia64
		/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

cvxopt -- convex optimization tools for python
	Fedora x86_64
		/usr/local/cvxopt

DataAnalysis -- Data analysis for 454 Sequencing System Software
	Fedora x86_64
		/usr/local/DataAnalysis

dia2code -- generage code stubs from UML diagrams
	Fedora x86_64
		/usr/local/dia2code

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

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 ia64
		/usr/local/gcc

gd -- php image library
	Fedora x86_64
		/usr/local/gd

git -- revision control system
	Mac OSX i386
	RedHat ia64
		/usr/local/git

genesis -- GEneral NEural SImulation System
	Fedora i386
		/usr/local/genesis
	Notes:
		Copy ~info/dot.files/.simrc to home directory

gmp -- arbitrary precision math library
	RedHat ia64
		/usr/local/gmp

go -- google go programming language
	Fedora x86_64
		/usr/local/go

hadoop -- Map Reduce framework
	Fedora x86_64
		/usr/local/hadoop

intel -- Intel compiler suite
	Fedora x86_64
		/s/parsons/l/sys/intel

iozone -- I/O benchmarking
	Fedora x86_64
		/usr/local/iozone

ipython -- interactive python interpreter
	Fedora x86_64
		/usr/local/ipython

JabRef -- graphical BibTeX front-end
	Fedora x86_64
		/usr/local/JabRef

java -- Oracle Java
	Fedora i386
	RedHat ia64
		/usr/local/java
	Fedora x86_64
		/usr/local/java64

JFLAP -- formal language experimentation
	Fedora x86_64
		/usr/local/JFLAP

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

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}

maple -- symbolic mathematics
	Fedora i386
		/s/parsons/l/sys/maple11
	Fedora x86_64
		/s/parsons/l/sys/maple11_64

matlab -- computational mathematics and programming language
	Fedora i686
		/s/parsons/l/sys/matlab
	Fedora x86_64
		/s/parsons/l/sys/matlab64

maven -- software project management
	Fedora x86_64
		/usr/local/maven

mercurial -- revision control system
	Fedora x86_64
		/usr/local/mercurial

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}

mpdist -- PostScript printing tools
	Fedora x86_64
		/usr/local/mpdist

mpfr -- multiple-precision math library
	RedHat ia64
		/usr/local/mpfr

mplayer -- multimedia player
	Fedora x86_64
		/usr/local/mplayer

netbeans -- integrated development environment
	Fedora x86_64
		/usr/local/netbeans

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

ocaml -- programming language
	RedHat ia64
		/usr/local/ocaml

OpenCV -- computer vision library
	Fedora x86_64
		/usr/local/OpenCV

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

passenger -- apache ruby module
	Fedora x86_64
		/usr/local/passenger

perl -- practical report and extraction language
	Fedora x86_64
		/usr/local/perl

povray -- raytracer
	Fedora x86_64
		/usr/local/povray

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}

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}

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 ia64
		/usr/local/qt

R -- programming language
	Fedora x86_64
		/usr/local/R
	RedHat ia64
		/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

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

scikits.lean -- machine learning library for python
	Fedora x86_64
		/usr/local/scikits.learn
	Notes:
		Add the following to .bashrc
			export PYTHONPATH=/usr/local/scikits.learn/lib64/python2.7/site-packages:${PYTHONPATH}
		or in .cshrc
			setenv  PYTHONPATH /usr/local/scikits.learn/lib64/python2.7/site-packages:${PYTHONPATH}

sml -- Standard ML programming language
	Fedora x86_64
		/usr/local/sml

SPAdes -- St. Petersburg genome assembler 
	Fedora x86_64
		/usr/local/SPAdes-2.4.0 

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

spim -- MIPS simulator
	Fedora x86_64
		/usr/local/spim

systemc -- C++ simulation library
	Fedora x86_64
		/usr/local/systemc

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

tophat -- A fast splice junction mapper for RNA-Seq reads
	Fedora x86_64
		/usr/local/tophat

totalview -- TotalView is a GUI-based source code defect analysis tool.
	Fedora x86_64
		/usr/local/totalview
		(/usr/local/toolworks/totalview*)

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

whizzytex -- emacs TeX plugin
	Fedora x86_64
		/usr/local/whizzytex

xforms -- xforms tools
	Fedora x86_64
		/usr/local/xforms

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

z-eves -- theorem proving tool
	Fedora x86_64
		/usr/local/z-eves