SimBio software on Debian (old system)

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Important: Note, that this page refers to the old Linux installation! When your Linux Desktop already runs on Ubuntu, this page is not for you. Refer to SimBio software instead.

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/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 or tcsh), just look at the file to see which variables need to be set.

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

List of installed software

The following software packages can be used:

Programs

Name Version Maintainer Description
autoconf 2.61 olenz GNU autoconfe is a part of the GNU Autotools. It is used to generate Makefiles for software packages. Docs: man autoconf, info autoconf
automake 1.10 olenz GNU automake is a part of the GNU Autotools. It is used to generate Makefile.in for software packages. Docs: man automake, info automake
bibclean 2.11.4 olenz Tool to prettyprint and normalise a bibtex file. Docs: man bibclean
bibsort 0.17 olenz Tool to sort the entries in a bibtex file. Docs: man bibsort
Firefox 2.0.0.7 olenz Version 2 of the web browser of the Mozilla foundation. To start it, call firefox-2.0.
Gnuplot 4.0 kgrass Gnuplot is a portable command-line driven interactive data and function plotting utility for UNIX and many other platforms.
jabref 2.3 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).
latexmk 3.20 olenz Latexmk completely automates the process of generating a LaTeX document. Docs: See latexmk or man latexmk
texinfo 4.8 olenz TeXinfo is a documentation system that can produce both online information and a printed manual from a single source. Docs: man info
Thunderbird 2.0.0.6 olenz Version 2 of the mail user agent of the Mozilla foundation. To start it, call thunderbird-2.0.
unison 2.13.16 olenz Unison is a file-synchronization tool for Unix and Windows. It allows two replicas of a collection of files and directories to be stored on different hosts (or different disks on the same host), modified separately, and then brought up to date by propagating the changes in each replica to the other. Docs: unison-manual.html
VMD 1.8.6 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/lib/vmd/doc/ug.pdf
xpdf 3.02 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
Macromedia flash player 9 olenz Version 9 of the flash player. The plugin is integrated into the firefox version in the simbio account (firefox-2.0).
Freetype 2.3.1 olenz Freetype is a library to raster truetype fonts for UNIX. Required by xpdf.
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.
Readline 5.1.0 kgrass The GNU Readline library provides a set of functions for use by applications that allow users to edit command lines as they are typed in. Required by Gnuplot to make tab completion & history available.

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/users/simbio/software/. The environment variable SBSOFTDIR 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 $SBSOFTDIR/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 $SBSOFTDIR/src/<software>. Remove the sources after appropriate time.
  • For most GNU-software, use the following commands to compile and install:
cd $SBSOFTDIR/src/<software>
configure --prefix=$SBSOFTDIR/
make
make install
  • Larger packages that have a non-standard directory stucture (e.g. eclipse, firefox, thunderbird, openoffice) should be installed completely below $SBDOFTDIR/opt/<software>. The executables can be softlinked to $SBSOFTDIR/bin.
  • Java software should go into $SBDOFTDIR/opt/java/. Jar files go into the $SBSOFTDIR/opt/java/jar subdirectory. Executable shell scripts that call the jar file go into $SBSOFTDIR/opt/java/bin and are softlinked to $SBSOFTDIR/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.

Installed software

Software that was installed once

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