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Windows installation

At least the Biskit core library should also work on Windows. We just haven't really tested it on this platform. The interface to external programs may or may not work. Please report your experience!

1. Install core prerequisites

All of the required packages have windows installers. Python 3.0 is currently not supported by Biskit. Please install:

2. Install Biskit

or... create your own windows installer (also works on unix):

cd biskit
python setup.py bdist_winst

The binary windows installer is then found in biskit/dist

3. Install useful optional libraries

The above minimal installation lacks some functionality. Install also:

  • gnuplot -- for quick and dirty plotting (plot() and scatter()). The gnuplot binary must be in the search $PATH (see Notes below)
  • Biopython -- enables the remote fetching of PDBs from the NCBI web site. It is also required for homology modeling (though this pipeline depends on many more programs and probably won't be operational on windows).
  • Plotutils + Biggles 1.6.5 -- for the advanced plotting functions that are built, for example, into PDBModel and Trajectory. This is a very useful extension but Biggles doesn't come with a windows installer and needs to be built from source using the conventional 'python setup.py install' command (after plotutils has been installed). Please report your experience!
  • SciPy -- allows for more accurate statistics in the Roc-curve module (ROCalyzer)

4. Notes

Putting gnuplot into PATH:

Click your way to:

  • My Computer (right click) / Properties (click) / Advanced (tab) / Environment Variables (Button)
  • Edit entry $PATH and add ";C:pathtognuplotprogram"
Test:
open a "DOS" command line window. Type: gnuplot

This should give you the gnuplot Info screen:

G N U P L O T
Version 4.0 patchlevel 0
last modified Thu Apr 15 14:44:22 CEST 2004
...

Then open python and try again:

python
>>> from Biskit.gnuplot import*
>>> plot( range(10) )