Short instruction

1(a) Installation from source

Installation from source should work on any platform. The last release of Biskit comes with a Python-typical setup script.

• I) Install dependencies

  Before you run this script, you have to install some other python libraries. Biskit depends on: numpy, ScientificPython, and [optionally] on biopython, scipy, and biggles. The Debian names of these packages are python-numpy, python-scientific, python-biopython, python-scipy, python-pybiggles (or python-biggles). A table of all dependencies is at the end of this page. Once, at least, numpy and ScientificPython are installed, proceed with...

• II) download or svn-checkout (see below) the biskit source package:

  Select the latest biskit tar.gz from the biskit download area.

  Or type in your terminal:

  wget http://downloads.sourceforge.net/biskit/biskit-2.4.0.tar.gz
  tar xvf biskit-2.4.0.tar.gz
  

  or check out the latest development snapshot:

  svn co https://biskit.svn.sourceforge.net/svnroot/biskit/trunk biskit
  

  Note:

  If you are a biskit developer (contact us to become one!), use the following checkout command:

  svn co https://developername@biskit.svn.sourceforge.net/svnroot/biskit/trunk biskit
  

  (replace 'developername' with your sourceforge login)

  Trouble-shooting:

  If you are sitting on a non-English system, subversion may insert special characters into the $Date: $ string of Biskit python files and you will get something like "SyntaxError: Non-ASCII character in ...". Define an environment variable LC_ALL=C to circumvent this problem.

• III) Install Biskit:

  cd biskit
  sudo python setup.py install
  

  or consider an alternative target location:

  sudo python setup.py install --prefix /usr/local
  

  This will install biskit into the local "site-packages" folder of the python version that you used for calling setup.py. There are some additional utility programs that are not strictly required but really useful for Biskit hackers. On Ubuntu/Debian, type:

  sudo apt-get install  gnuplot pymol gawk
  

1(b) Installation from Ubuntu / Debian package

Fetch the debian package (.deb) from the biskit download area on sourceforge: http://downloads.sourceforge.net/biskit/python-biskit_2.4.0-1_all.deb

On Ubuntu, a click on the .deb file will automatically open the Ubuntu package manager. Just press "Install". Otherwise type:

gdebi python-biskit_2.3.1-1_all.deb

This gives you a biskit installation that is lacking parallelization because there are no up-to-date debian packages for pypvm (see below).

1(c) Installation on Mac OS X

Marc-Michael Blum has compiled a Fink package for easy installation: http://biskit.pasteur.fr/install/osx_install

1(d) Installation from rpm package

Source and platform-independent "binary" rpms are provided in the biskit download area. These files have not yet been tested. Please, report success or failure and the steps needed.

1(e) Installation on Windows

This is rather experimental. The core functions seem to work though. See Windows installation

2) setup PVM for parallelization (optional)

PVM is really useful and many Biskit scripts use it to distribute calculations. Most Unix distributions have a precompiled pvm package and you should use it. The python bindings for PVM (pypvm) are available from the biskit web site. See the PVM section in install dependencies for detailed instructions.

3) install helper applications

This depends on what you actually need. A list of all helper applications is given here: Helper applications. See also Install helper applications for more detailed installation instructions and troubleshooting. The Biskit library itself doesn't need any external programs but most people find the following programs useful: gnuplot, surfaceracer, and DSSP.

4) test Biskit

run:

~> python
Python 2.4.1 (#1, May 16 2005, 15:15:14)
[GCC 4.0.0 20050512 (Red Hat 4.0.0-5)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import Biskit

You should get several warnings about missing configuration files. That's OK. But make sure you don't get any exception.ImportError because the latter would indicate missing or broken libraries or an incorrect $PYTHONPATH.

Next, see Testing Howto for instructions on how to test all Biskit modules! In short:

cd /usr/lib/python2.5/site-packages/Biskit
python test.py -e old pvm exe

...will run all tests, except those that are depending on PVM and external helper applications (the intervor test is not tagged as 'exe' test case in release 2.3.1 and will report an error, please ignore this one).

5) Customize biskit

If at all necessary, adapt ~/.biskit/settings.cfg to your environment.

See Setup environment for details!

6) Removing Biskit

• After installation from Debian packages:

  sudo apt-get remove python-biskit
  

• After installation from source:

  cd /usr/local/lib/python2.5/site-packages
  sudo rm -r biskit* Biskit
  

  Biskit may also have ended up in /usr/lib/python2.5/site-packages or /usr/lib/python2.6/site-packages

7) List of all Biskit dependencies

See Install dependencies for detailed (cut-and-paste) instructions!