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
- download and execute the windows installer (biskit*w32.exe) from the Biskit download area.
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)
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"
- 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) )