Difference between revisions of "SimBio software on Debian (old system)"

From ICPWiki
Jump to: navigation, search
(Programs)
 
(55 intermediate revisions by 2 users not shown)
Line 1: Line 1:
 +
'''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.
 
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 ==
 
== Adding SimBio software to your configuration ==
 
If you are using <tt>ksh</tt>, <tt>bash</tt> or <tt>sh</tt>, simply add the line
 
If you are using <tt>ksh</tt>, <tt>bash</tt> or <tt>sh</tt>, simply add the line
  . /home/users/simbio/software/profile.simbio
+
  . /home/simbio/software/profile.simbio
to your <tt>~/.profile</tt> or <tt>~/.bashrc</tt>. 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 <tt>csh</t> or <tt>tcsh</tt>), just look at the file to see which variables need to be set.
+
to your <tt>~/.profile</tt> or <tt>~/.bashrc</tt>. 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 <tt>csh</tt> or <tt>tcsh</tt>), just look at the file to see which variables need to be set.
  
Generally, all SimBio software is installed in <tt>/home/users/software/{bin,include,lib,info,man,share,opt}</tt>
+
Generally, all SimBio software is installed in <tt>/home/simbio/software/{bin,include,lib,info,man,share,opt}</tt>
and all executables are accessible from <tt>/home/users/software/bin</tt>.
+
and all executables are accessible from <tt>/home/simbio/software/bin</tt>.
  
 
== List of installed software ==
 
== List of installed software ==
Line 15: Line 17:
 
=== Programs ===
 
=== Programs ===
  
{| style="border: thin solid black;" rules="all" cellpadding="7px"
+
{| class="prettytable"
 
|-
 
|-
 
!Name !! Version !! Maintainer  
 
!Name !! Version !! Maintainer  
Line 21: Line 23:
 
|-
 
|-
  
|| [http://www.gnu.org/software/autoconf/autoconf.html autoconf] || 2.59 || olenz
+
|| [http://www.gnu.org/software/autoconf/ autoconf] || 2.61 || olenz
| GNU autconf is a part of the GNU Autotools. It is used to generate <tt>configure</tt> scripts for software packages. Docs: <tt>man autoconf</tt>, <tt>info autoconf</tt>
+
| GNU autoconfe is a part of the GNU Autotools. It is used to generate <tt>Makefile</tt>s for software packages. Docs: <tt>man autoconf</tt>, <tt>info autoconf</tt>
 
 
 
|-
 
|-
  
|| [http://sources.redhat.com/automake/ automake] || 1.9.6 || olenz
+
|| [http://sources.redhat.com/automake/ automake] || 1.10 || olenz
| GNU automake is a part of the GNU Autotools. It is used to generate <tt>Makefile.in</tt> for software packages. Docs: <tt>man autoconf</tt>, <tt>info autoconf</tt>
+
| GNU automake is a part of the GNU Autotools. It is used to generate <tt>Makefile.in</tt> for software packages. Docs: <tt>man automake</tt>, <tt>info automake</tt>
|-
 
  
|| [http://azureus.sourceforge.net Azureus] || 2.4.0 || olenz
 
| Bittorrent client
 
 
|-
 
|-
 
+
|| bibclean || 2.11.4 || olenz
|| [http://www.mozilla.com/firefox Firefox] || 1.5.0.4 || olenz
+
| Tool to prettyprint and normalise a bibtex file. Docs: <tt>man bibclean</tt>
| The web browser of the Mozilla foundation.
 
 
|-
 
|-
  
|| [http://jabref.sourceforge.net/ jabref] || 2.0.1 || olenz
+
|| bibsort || 0.17 || 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).
+
| Tool to sort the entries in a bibtex file. Docs: <tt>man bibsort</tt>
 
|-
 
|-
  
|| jre || 1.5.0 || olenz
+
|| [http://en-us.www.mozilla.com/en-US/firefox/ Firefox] || 2.0.0.7 || olenz
| Sun Java runtime environment and plugin.
+
| Version 2 of the web browser of the Mozilla foundation. To start it, call <tt>firefox-2.0</tt>.
 
|-
 
|-
  
|| latexmk || 3.07a || olenz
+
|| [http://www.gnuplot.info/ Gnuplot] || 4.0 || kgrass
| Latexmk completely automates the process of generating a LaTeX document. Docs: [[latexmk]] or <tt>man latexmk</tt>
+
| Gnuplot  is a portable command-line driven interactive data and function plotting utility for UNIX and many other platforms.
 
|-
 
|-
  
|| [http://www.mplayerhq.hu mplayer] || 1.0pre7try2 || olenz
+
|| [http://jabref.sourceforge.net/ jabref] || 2.3 || 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 , <tt>man mplayer</tt> or <tt>man mencoder</tt>
+
| 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).
|-
 
 
 
|| [http://www.openoffice.org OpenOffice] || 2.0.2 || olenz
 
|The Open Office Suite
 
 
|-
 
|-
  
|| [http://www.povray.org/ povray] || 3.6 || olenz
+
|| [http://www.phys.psu.edu/~collins/software/latexmk-jcc/versions.html latexmk] || 3.20 || 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 <tt>man povray</tt>
+
| Latexmk completely automates the process of generating a LaTeX document. Docs: See '''[[latexmk]]''' or <tt>man latexmk</tt>
 
|-
 
|-
  
|| recode || 3.6 || olenz
+
|| texinfo || 4.8 || olenz
| GNU recode converts files between various character sets and surfaces (e.g. ibmpc to latin1). Docs: <tt>info recode</tt>
+
| TeXinfo is a documentation system that can produce both online information and a printed manual from a single source. Docs: <tt>man info</tt>
 
|-
 
|-
  
|| [http://www.mozilla.com/thunderbird Thunderbird] || 1.5.0.4 ||olenz
+
|| [http://en-us.www.mozilla.com/en-US/thunderbird Thunderbird] || 2.0.0.6 || olenz
| The mail reader of the Mozilla foundation.
+
| Version 2 of the mail user agent of the Mozilla foundation. To start it, call <tt>thunderbird-2.0</tt>.
 
|-
 
|-
  
|| [http://www.activestate.com/Products/ActiveTcl/ Tcl/Tk] || 8.4 || olenz
+
|| [http://www.cis.upenn.edu/~bcpierce/unison/ unison] || 2.13.16 || olenz
|The Tcl/Tk scripting language. Docs: file:///home/FIAS/simbio/software/share/tcl/doc/index.html
+
| 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: [http://www.cis.upenn.edu/~bcpierce/unison/download/releases/stable/unison-manual.html unison-manual.html]
 
|-
 
|-
  
|| [http://www.ks.uiuc.edu/Research/vmd/ VMD] || 1.8.4 || olenz
+
|| [http://www.ks.uiuc.edu/Research/vmd/ 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/share/vmd/ug.pdf
+
|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
 
|-
 
|-
  
|| [http://www.foolabs.com/xpdf/ xpdf] || 3.01 || olenz
+
|| [http://www.foolabs.com/xpdf/ 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: <tt>man xpdf</tt>
 
| xpdf is a fast reader for the PDF format. It has a "reload" key R which makes it useful for working with pdflatex. Docs: <tt>man xpdf</tt>
 
|-
 
|-
Line 86: Line 79:
 
=== Libraries ===
 
=== Libraries ===
  
{| style="border: thin solid black;" rules="all" cellpadding="7px"
+
{| class="prettytable"
 
|-
 
|-
 
!Name !! Version !! Maintainer  
 
!Name !! Version !! Maintainer  
Line 92: Line 85:
 
|-
 
|-
  
|| [http://www.fftw.org/fftw FFTW] || 3.1.1 || olenz
+
|| [http://www.adobe.com/products/flashplayer/ Macromedia flash player] || 9 || 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: <tt>info fftw3</tt>
+
| Version 9 of the flash player. The plugin is integrated into the firefox version in the simbio account (<tt>firefox-2.0</tt>).
 
|-
 
|-
  
|| [http://www.foolabs.com/xpdf/freetype Freetype] || 2.1.10 || olenz
+
|| [http://www.foolabs.com/xpdf/freetype Freetype] || 2.3.1 || olenz
 
|  Freetype is a library to raster truetype fonts for UNIX. Required by xpdf.
 
|  Freetype is a library to raster truetype fonts for UNIX. Required by xpdf.
 
|-
 
|-
  
 
+
|| [http://www.foolabs.com/xpdf/t1lib T1Lib] || 5.1.0 || olenz
|| [http://sources.redhat.com/gsl/gsl GSL] || 1.8 || olenz
+
| t1lib is a library for generating character- and string-glyphs from Adobe Type 1 fonts under UNIX. Required by xpdf.
| 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: <tt>info gsl-ref</tt>
 
 
|-
 
|-
  
 
+
|| [http://tiswww.tis.case.edu/~chet/readline/rltop.html Readline] || 5.1.0 || kgrass
|| [http://www.foolabs.com/xpdf/t1lib T1Lib] || 5.1.0 || olenz
+
| 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.
| t1lib is a library for generating character- and string-glyphs from Adobe Type 1 fonts under UNIX. Required by xpdf.
 
 
|-
 
|-
  
Line 118: Line 109:
 
=== Where the files go ===
 
=== Where the files go ===
  
* All software is archived, built and installed below <tt>/home/FIAS/simbio/software/</tt>. The environment variable <tt>SBSOFTWARE</tt> is set to this directory. You can therefore refer to this variable in all documentation.
+
* All software is archived, built and installed below <tt>/home/users/simbio/software/</tt>. The environment variable <tt>SBSOFTDIR</tt> 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 <tt>$SBSOFTWARE/tar/</tt>. If possible, heed to the GNU naming convention, i.e. add the version number of the package to the file name (like <tt><software>-<version>.tar.gz</tt>)
+
* Put the source or binary archives of the software into <tt>$SBSOFTDIR/tar/</tt>. If possible, heed to the GNU naming convention, i.e. add the version number of the package to the file name (like <tt><software>-<version>.tar.gz</tt>)
  
* Unpack the sources and build in <tt>$SBSOFTWARE/src/<software></tt>. Remove the sources after appropriate time.
+
* Unpack the sources and build in <tt>$SBSOFTDIR/src/<software></tt>. Remove the sources after appropriate time.
  
 
* For most [http://www.fsf.org GNU-software], use the following commands to compile and install:
 
* For most [http://www.fsf.org GNU-software], use the following commands to compile and install:
 
  cd $SBSOFTDIR/src/<software>
 
  cd $SBSOFTDIR/src/<software>
  configure --prefix=$SBSOFTWARE/
+
  configure --prefix=$SBSOFTDIR/
 
  make
 
  make
 
  make install
 
  make install
  
* Larger packages that have a non-standard directory stucture (e.g. eclipse, firefox, thunderbird, openoffice) should be installed completely below <tt>$SBDOFTWARE/opt/<software></tt>. The executables can be softlinked to <tt>$SBSOFTWARE/bin</tt>.
+
* Larger packages that have a non-standard directory stucture (e.g. eclipse, firefox, thunderbird, openoffice) should be installed completely below <tt>$SBDOFTDIR/opt/<software></tt>. The executables can be softlinked to <tt>$SBSOFTDIR/bin</tt>.
  
* Java software should go into <tt>$SBDOFTWARE/opt/java/</tt>. Jar files go into the <tt>$SBSOFTWARE/opt/java/jar</tt> subdirectory. Executable shell scripts that call the jar file go into <tt>$SBSOFTWARE/opt/java/bin</tt> and are softlinked to <tt>$SBSOFTWARE/bin</tt>.
+
* Java software should go into <tt>$SBDOFTDIR/opt/java/</tt>. Jar files go into the <tt>$SBSOFTDIR/opt/java/jar</tt> subdirectory. Executable shell scripts that call the jar file go into <tt>$SBSOFTDIR/opt/java/bin</tt> and are softlinked to <tt>$SBSOFTDIR/bin</tt>.
  
 
=== Document the installation ===
 
=== Document the installation ===
Line 143: Line 134:
 
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.
 
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 ====
 
* [[Automake installation]]
 
* [[Automake installation]]
* [[Azureus installation]]
 
 
* [[Firefox installation]]
 
* [[Firefox installation]]
 +
* [[Gnuplot installation]]
 
* [[JabRef installation]]
 
* [[JabRef installation]]
* [[JRE installation]]
 
 
* [[latexmk installation]]
 
* [[latexmk installation]]
* [[MPlayer installation]]
 
* [[OpenOffice installation]]
 
* [[Povray installation]]
 
 
* [[Thunderbird installation]]
 
* [[Thunderbird installation]]
 
* [[VMD installation]]
 
* [[VMD installation]]
 
* [[XPDF installation]]
 
* [[XPDF installation]]
 +
 +
==== Software that was installed once ====
 +
* [[Azureus installation]]

Latest revision as of 16:03, 18 January 2008

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