SimBio software on Debian (old system)

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In the SimBio account, several software packages for the standard Linux computers have been installed that can be used by the working group's members.

Adding SimBio software to your configuration

If you are using ksh, bash or sh, simply add the line 

. /home/FIAS/simbio/software/profile.simbio

to your ~/.profile or ~/.bashrc. This will set all the necessary environment variables so that the software can be used. If you can't do this (for example if you use csh</t> or tcsh), just look at the file to see which variables need to be set.

Generally, all SimBio software is installed in /home/FIAS/software/{bin,include,lib,info,man,share,opt} and all executables are accessible from /home/FIAS/software/bin.

List of installed software

The following software packages can be used:

Programs

Name Version Maintainer Description
autoconf 2.59 olenz GNU autconf is a part of the GNU Autotools. It is used to generate configure scripts for software packages. Docs: man autoconf, info autoconf
automake 1.9.6 olenz GNU automake is a part of the GNU Autotools. It is used to generate Makefile.in for software packages. Docs: man autoconf, info autoconf
Axureus 2.4.0 olenz Bittorrent client
Firefox 1.5.0.4 olenz The web browser of the Mozilla foundation.
jabref 2.0.1 olenz JabRef is an open source bibliography reference manager. The native file format used by JabRef is BibTeX, the standard LaTeX bibliography format. JabRef runs on the Java VM (version 1.4.2 or greater).
jre 1.5.0 olenz Sun Java runtime environment and plugin.
latexmk 3.07a olenz Latexmk completely automates the process of generating a LaTeX document. Docs: latexmk or man latexmk
mplayer 1.0pre7try2 olenz MPlayer is a movie player that plays a huge number of movie formats, including for example DivX and WMV. Docs: file:///home/FIAS/simbio/software/share/mplayer/doc/index.html , man mplayer or man mencoder
OpenOffice 2.0.2 olenz The Open Office Suite
povray 3.6 olenz The Persistence of Vision Raytracer is a high-quality, totally free tool for creating stunning three-dimensional graphics. Docs: file:///home/FIAS/simbio/software/share/doc/povray-3.6/html/index.html or man povray
recode 3.6 olenz GNU recode converts files between various character sets and surfaces (e.g. ibmpc to latin1). Docs: info recode
Thunderbird 1.5.0.4 olenz The mail reader of the Mozilla foundation.
Tcl/Tk 8.4 olenz The Tcl/Tk scripting language. Docs: file:///home/FIAS/simbio/software/share/tcl/doc/index.html
VMD 1.8.4 olenz VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. Docs: file:///home/FIAS/simbio/software/share/vmd/ug.pdf
xpdf 3.01 olenz xpdf is a fast reader for the PDF format. It has a "reload" key R which makes it useful for working with pdflatex. Docs: man xpdf

Libraries

Name Version Maintainer Description
FFTW 3.1.1 olenz FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data (as well as of even/odd data, i.e. the discrete cosine/sine transforms or DCT/DST). The library is compiled for maximal portability. If you want an optimised version, recompile fftw locally. Docs: info fftw3
Freetype 2.1.10 olenz Freetype is a library to raster truetype fonts for UNIX. Required by xpdf.
GSL 1.8 olenz The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting. There are over 1000 functions in total with an extensive test suite. Docs: info gsl-ref
T1Lib 5.1.0 olenz t1lib is a library for generating character- and string-glyphs from Adobe Type 1 fonts under UNIX. Required by xpdf.

Installing new software

If you want to install software, please keep to the following.

Where the files go

  • All software is archived, built and installed below /home/FIAS/simbio/software/. The environment variable SBSOFTWARE is set to this directory. You can therefore refer to this variable in all documentation.
  • Put the source or binary archives of the software into $SBSOFTWARE/tar/. If possible, heed to the GNU naming convention, i.e. add the version number of the package to the file name (like <software>-<version>.tar.gz)
  • Unpack the sources and build in $SBSOFTWARE/src/<software>. Remove the sources after appropriate time.
  • For most GNU-software, use the following commands to compile and install:
cd $SBSOFTDIR/src/<software>
configure --prefix=$SBSOFTWARE/
make
make install
  • Larger packages that have a non-standard directory stucture (e.g. eclipse, firefox, thunderbird, openoffice) should be installed completely below $SBDOFTWARE/opt/<software>. The executables can be softlinked to $SBSOFTWARE/bin.
  • Java software should go into $SBDOFTWARE/opt/java/. Jar files go into the $SBSOFTWARE/opt/java/jar subdirectory. Executable shell scripts that call the jar file go into $SBSOFTWARE/opt/java/bin and are softlinked to $SBSOFTWARE/bin.

Document the installation

  • add a short description of the package to the list above
  • if there is anything out of the ordinary, briefly document the installation procedure in a separate article (using the name <package> installation, e.g. Firefox installation)
  • add a link to the new article to the list below

Installation docs

This list contains a brief decription of how the corresponding software can be installed. For any software not on this list, the "default sequence" (see above) should be enough.

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