Most software is installed in /usr/local with the binaries in /usr/local/bin. Since /usr/local/bin is in everyones path by default, you should be able to launch any program by just typing its command name. For example, to run Mathematica:

[fisher@kimclust40]$ /usr/local/bin/mathematica
or
[fisher@kimclust40]$ mathematica

Please add your name to whatever additional libraries or programs think we should include

• CLAPACK -
• BOOST -

• ATLAS "Automatically Tuned Linear Algebra Software"
  • version 3.6.0
  • Location: /usr/local/src/ATLAS
  • http://math-atlas.sourceforge.net/
• Bioperl
  • version 1.2.2
  • location: /usr/local/lib/perl5/site_perl/5.6.1/Bio/
• LAPACK
  • version 3.0 (version 3.1 on the 64bit machines)
  • location: /usr/local/src/ATLAS/LAPACK
  • For higher performace, use the hybrid LAPACK/ATLAS library in ATLAS
    • /usr/local/src/lib/Linux/liblapack.a)
    • see: http://math-atlas.sourceforge.net/errata.html#completelp
  • http://www.netlib.org/lapack/
• LEDA "Library of Efficient Data types and Algorithms: LEDA is a versatile and easy to use C++ class library for combinatorial and geometric computing."
  • http://www.algorithmic-solutions.com/as_html/products/products.html
  • Location: /usr/local/lib/LEDA-4.3
  • For documentation see: /usr/local/lib/LEDA-4.3/Install/unix.txt
  • LEDAROOT has been set to /usr/local/lib/LEDA-4.3

• Paup
  • version 4.0b10 (command: paup)
• Maple
  • NOTE: to run Maple you need to set the following environment variable, by placing to following in your ~/.bash_profile or typing it in at the command line. If you type it at the command line, you need to do this every time you log into a new machine or start a new xterm. If you put it in your .bash_profile file, all existing xterms will still need the command entered manually.
    • "export LD_ASSUME_KERNEL=2.4.1"
  • command line version 8.0 (command: maple)
  • xwindows version 8.0 (command: xmaple)
• SAS
  • version 8.2.2 (command: sas)
• Mathematica VERSION 4 (ONLY ON KIMCLUST50)
  • command line version 4.2.1.0 (command: math)
  • xwindows version 4.2.1.0 (command: mathematica)
  • NOTE: mathematica version 4 only works on kimclust50. It will not run on other cluster computers. You must log into kimclust50 when you want to run mathematica version 4.
• Mathematica VERSION 6 (ONLY ON KIMCLUST36)
  • command line version 6.0.1.0 (command: math)
  • xwindows version 6.0.1.0 (command: mathematica)
  • NOTE: mathematica version 6 only works on kimclust36. It will not run on other cluster computers. You must log into kimclust36 when you want to run mathematica version 6.
• MatLab
  • version 7.3 (command: matlab)
  • toolboxes: curve fitting (v 1.1.6), spline (v 3.3.1), wavelet (v 3.1)
  • 64bit version running on 38 and 39
• R
  • version 2.1.1 (command: R)
  • version 1.7.1 (command: R-1.7.1)
  • version 1.6.2 (command: R-1.6.2)
  • version 1.4.1 (command: R-1.4.1)

• C/C++
  • gcc version 2.95.2 (command: gcc-2.95.2)
  • gcc version 3.2.2 (command: gcc-3.2.2)
  • gcc version 3.2.3 (command: gcc32)
  • gcc version 3.4.6 (command: gcc)
  • gcc version 4.1.0 (command: gcc4)
  • intel version 7.0-86 (command: icc)
• Java
  • JDK version 1.4.2_03 (source: /usr/local/src)
  • JRE version 1.4.2_02 (source: /usr/local/src)
  • JRE version 1.5.0_07 (source: /usr/local/src)
• Perl
  • version 5.8.5 (command: perl)
• Python
  • version 2.3.4 (command: /usr/bin/python)
  • version 2.3.3 (command: python)
  • version 2.3.4 (command: python2)
  • version 2.2.1 (command: python2.2.1)
• These programs are not necessarily available on kimclust11

• MySQL
  • Version 5.0.18-standard (command: mysql)
  • You must first contact Stephen Fisher to create a database and MySQL? user

• SWISS-PROT Our local database is updated monthly
  • Location: /usr/local/src/BLAST
  • http://us.expasy.org/

• BLAST Our local databases are updated monthly
  • Location: /usr/local/src/BLAST
  • http://www.ncbi.nlm.nih.gov/BLAST/

• MacClade
  • Version 4.0.5
  • This is installed on the lab Macintosh laptop

• Adobe Acrobat
  • Version 5 or 6
  • Every Windows desktop should have a copy of Acrobat installed.
  • If you do not have a copy of Acrobat on your computer, please see StephenFisher.