The Libra Cluster
List of Available Software
| Software | Version | Description | Node | Path/Command |
|---|---|---|---|---|
| AIR | 5.2.5 | Automated Image Registration | All | /miscapps/AIR |
| AIX | 5.3 | IBM Unix | All | |
| Amber | 8 | Assisted Model Building with Energy Refinement | All | . /sciapps/Amber/amber8.ksh or source /sciapps/Amber/amber8.csh |
| ARPACK | F77 eigenvalue routines | All | /libapps/ARPACK/lib/libarpack_AIX.a | |
| Blastz | 2003-02-28 | Bioinformatics Genome Alignment Program | All | /miscapps/blastz/bin/blastz |
| CVS | 1.11.17 | Concurrent Versions System | All | /opt/freeware/bin/cvs |
| DB2 Enterprise Edition | 8.2 | IBM database server and client | libra00 until 1/1/08 then Libra45 | . /home/db2inst2/sqllib/db2profile;db2 or source /home/db2inst2/sqllib/db2cshrc;db2 |
| dosutils | 2002 | DOS file utilities | All | /miscapps/dosutils/dos2unix,unix2dos |
| EMBOSS | 5.0 | Molecular Biology Analysis | All | http://rtinfo.uits.iu.edu/bioinformatics/EMBOSSwEMBOSS.shtml |
| ESSL | 4.2 | Engineering & Scientific Subroutine Library | All | -l essl |
| Gauss | 6.0 | Statistical package | All | /statapps/gauss/tgauss |
| Gaussian | 98 | Electronic structure calculations | All | setenv g98root /sciapps source $g98root/bsd/g98.login |
| Gaussian | 03 | Electronic structure calculations | All | setenv g03root /sciapps source $g03root/bsd/g03.login |
| ghostview | 3.5.8 | Viewer for postscript files | All | /opt/freeware/bin/gv |
| GMT | 3.4.4 | Generic Mapping Tools | All | /miscapps/GMT/bin/* |
| gnuplot | 3.7.1 | Interactive plotter | All | /opt/freeware/bin/gnuplot |
| GNU autoconf | 2.59 | m4 macros for autoconfiguration | All | /software/gnu/bin/autoconf |
| GNU automake | 1.8.5 | Makefile.in generator | All | /opt/freeware/bin/automake |
| GNU bash | 2.05a | GNU Bourne-Again shell | All | /opt/freeware/bin/bash |
| GNU bison | 1.875 | Parser generator | All | /opt/freeware/bin/bison |
| GNU binutils | 2.15 | Binary tools | All | /opt/freeware/bin/gld,as,ar,strings,nm,etc. |
| GNU C,C++ | 4.0.0 | GNU C and C++ compilers | All | /usr/local/bin/gcc,g++,etc. |
| GNU diffutils | 2.8.1 | File comparison utilities | All | /opt/freeware/bin/diff,sdiff,zdiff,etc. |
| GNU Emacs | 21.3.1 | Fullscreen editor | All | /opt/freeware/bin/emacs |
| GNU fileutils | 4.1 | File utilities | All | /opt/freeware/bin/cp,ls,rm,etc. |
| GNU findutils | 4.1 | Find utilities | All | /opt/freeware/bin/find,xargs,locate,etc. |
| GNU flex | 2.5.4 | Lexical analyzer generator | All | /opt/freeware/bin/flex |
| GNU gawk | 3.1.3 | GNU awk interpreter | All | /opt/freeware/bin/gawk |
| GNU gdb | 6.0 | GNU debugger | All | /opt/freeware/bin/gdb |
| GNU grep | 2.5.1 | GNU grep | All | /opt/freeware/bin/grep,egrep,fgrep,zgrep,etc. |
| GNU less | 374 | File viewing utility | All | /opt/freeware/bin/less |
| GNU libtool | 1.5.8 | Generic Library Support Script | All | /opt/freeware/bin/libtool |
| GNU m4 | 1.4.1 | Macro processor | All | /opt/freeware/bin/m4 |
| GNU nano | 1.3.0 | Text editor (Pico clone) | All | /opt/freeware/bin/nano |
| GNU make | 3.80 | Program maintenance utility | All | /opt/freeware/bin/gmake |
| GNU RCS | 5.7 | Revision control system | All | /opt/freeware/bin/rcs |
| GNU rsync | 2.6.2 | Remote file synchronization | All | /opt/freeware/bin/rsync |
| GNU sed | 4.0.7 | Stream Editor | All | /opt/freeware/bin/sed |
| GNU Scientific Library | 1.4 | Numerical computing routines | All | -L/libapps/gsl-1.4/lib -l gsl |
| GNU screen | 3.09.10 | Screen terminal utility | All | /opt/freeware/bin/screen |
| GNU sharutils | 4.2 | Archive utilities | All | /opt/freeware/bin/shar,unshar,etc. |
| GNU tar | 1.13 | Tape/disk archive | All | /opt/freeware/bin/gtar |
| GNU textutils | 5.0 | Text manipulation utilities | All | /opt/freeware/bin/cat,cut,sort,etc. |
| GNU wget | 1.9 | File retrieving utility | All | /opt/freeware/bin/wget |
| GNU zip | 1.2.4 | File compression utility | All | /opt/freeware/bin/gzip,gunzip,etc. |
| Grace | 5.1.9 | Plotting package | All | GRACE_HOME=/miscapps/grace;xmgrace |
| HDF4 | 4.2r1 | general purpose library and file format | All | /libapps/hdf4 |
| HDF5 | 1.6.4 | general purpose library and file format | All | /libapps/hdf5 |
| IBM XL C/C++ | 7.0 | C,C++ compilers and libraries | All | cc,xlc,CC,XLC |
| IBM XL Fortran | 9.1 | Compiler and libraries | All | xlf |
| IMSL | 5.0 | Fortran, C libraries | All | /usr/loca/bin/imsl.sh or /usr/local/bin/imsl.csh |
| JDK | 1.4 | Java Developer Kit 32-bit | All | /usr/java14/bin/java |
| JDK 64-bit | 1.4 | Java Developer Kit 64-bit | All | /usr/java14_64/bin/java |
| JDK 5 64bit | 1.5 | Java Developer Kit 64-bit | All | /usr/java5_64/bin/java |
| LAPACK | 3.0 | Fortran numerical library | All | -L /libapps/lapack3.0 -l lapack |
| libjpeg | v6b | JPEG reference library | All | -L/opt/freeware/lib -ljpeg |
| libpng | 1.2.8 | official PNG reference library | All | -L/opt/freeware/lib -lpng |
| LISREL | 8.54 | Statistical package | libra01 | /statapps/lisrel/lisrel |
| LoadLeveler | 3.3 | Load balancing batch queueing system | All | llq |
| Lynx | 2.8.4.1 | Text-based Web browser | All | /opt/freeware/bin/lynx |
| Maple | 7 | Algebra system | All | /mathapp/maple/bin/maple,xmaple |
| MASS | 4.1 | Mathematical Acceleration Subsystem library | All | -l mass |
| Mathematica | 5.0 | Symbolic math system (Command-line version) | All | /mathapps/math/bin/math |
| Mathematica | 5.0 | Symbolic math system (Xwindows version) | All | /mathapps/math/bin/mathematica Requires Mathematica fonts installation on local workstation |
| MATLAB | 6.5.0 | Numerical math system | All | /mathapps/matlab/bin/matlab -nojvm |
| Maui Scheduler | 3.2.6 | Batch scheduler and reservation system | All | showq,showfairshare,checkjob,checknode,etc. |
| MIT Kerberos | 1.2.8 | MIT Kerberos 5 implementation | All | /miscapps/krb5/bin/kinit,etc. |
| Mktemp | 1.5 | safe temporary file creation | All | /opt/freeware/bin/mktemp |
| MUMmer | 2.13 | Genome alignment program | All | /miscapps/mummer/bin/mummer1,mummer2,etc. |
| Mx | 1.55 | Matrix algebra interpreter and numerical optimizer | All | /miscapps/mx/bin/mxt |
| NAGlib | Mark18 | Numerical Fortran libraries | all | -l nag, -l nagfl90 |
| NCBI Toolkit | 2.2.12 | Stand-alone blast and utilities for searching DNA/protein databases | all | /miscapps/ncbi/bin/blast,blastall,getseq,etc |
| Octave | 2.1.57 | Open-source matlab alternative | All | /mathapps/octave/bin/octave |
| OpenSSH | 3 | secure shell server/clients | All | ssh |
| Ox | 3.4.0 | object-oriented statistical system - Gauss alternative | All | /statapps/ox/bin/oxl |
| PAML | 3.13d | Phylogenetic Analysis by Maximum Likelihood | All | /miscapps/PAML/* |
| paup | 4.0b10 | Phylogenetic Analysis Using Parsimony | All | /miscapps/paup/paup |
| Perl | 5.8.2 | Script programming language | All | /bin/perl |
| Perl | 5.8.0 | Script programming language: Installed Modules | All | /miscapps/perl/bin/perl |
| PHYLIP | 3.63 | Phylogeny Inference Package | All | /miscapps/phylip/bin/* |
| Pico | 4.2 | Text editor | All | /usr/local/bin/pico |
| PRELIS | 2.54 | Statistical system | libra01 | /statapps/lisrel/prelis |
| Python | 2.2 | Interpreted programming language | All | /opt/freeware/bin/python |
| R | 2.0.1 | Statistical package | All | /statapps/R/bin/R |
| RATS | 5.01 | Regression and Time Series | All | /statapps/rats/bin/rats |
| SAS | 6.1.2 | Statistical Analysis System | All | /statapps/sas6.1.2/bin/sas |
| SAS | 9.1.3 | Statistical Analysis System | All | /statapps/sas9.1.3/sas |
| SPRNG | 2.0 | Parallel Random Number Generator | All | -L /libapps/SPRNG/lib |
| SPSS | 6.1.4 | Statistical Program for the Social Sciences | All | /statapps/spss/bin/spss |
| Stat Transfer | 9.03.07.0621 | Statistics Data Conversion | All | /statapps/st/bin/st |
| Stata/SE | 10.0 | Statistics/Data Analysis | All | /statapps/stata/stata-se |
| SVDLIBC | 1.31 | Singular Value Decomposition of sparse matrices | All | /libapps/svdlibc/bin/svd |
| tcsh | 6.11.0 | Extended C shell | All | /opt/freeware/bin/tcsh | TSP | 4.5 | Time Series Processor | All | /statapps/tsp/tsp |
| Vienna RNA | 1.4 | RNA structures prediction | All | /miscapps/viennarna/bin/RNAfold,etc. |
| VI Enhanced | 6.3 | Enhanced version of vi with GUI | All | /miscapps/vim/bin/gvim,vim |
