Complete step-by-step instructions for a manual installation of Biskit and it's dependencies from source is described here: Install dependencies. Refer to this page if you get stuck with any of the steps below.
You can either install Biskit from source or use one of the installation packages that we provide for different platforms. The latter is easier because your package manager should be able to resolve dependencies automatically.
- 1(a) Installation from source
- 1(b) Installation from Ubuntu / Debian package
- 1(c) Installation on Mac OS X
- 1(d) Installation from rpm package
- 1(e) Installation on Windows
- 2) setup PVM for parallelization (optional)
- 3) install helper applications
- 4) test Biskit
- 5) Customize biskit
- 6) Removing Biskit
- 7) List of all Biskit dependencies
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
If you are a biskit developer (contact us to become one!), use the following checkout command:
svn co https://email@example.com/svnroot/biskit/trunk biskit
(replace 'developername' with your sourceforge login)
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:
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
~> 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!
|program/library||comment or link|
|core functions||--------- absolutely necessary ---------|
|python||http://www.python.org/ (2.4, 2.5, or 2.6)|
|python-dev||python development files|
the new incarnation of Numeric (for Biskit 2.1+)
required by Scientific Python
Scientific Python (not to be confused with SciPy)
|plotting||--------- recommended ---------|
required for building biggles
|ROC areas||--------- recommended ---------|
If scipy is missing, ROCalyzer falls back to an
internal statistics module that has some numeric
|homology modeling||--------- recommended ---------|
required by BioPython
required for homology modeling (Biskit.Mod)
also required for fetching PDBs remotely from NCBI
|parallelization||--------- required by Biskit.PVM ---------|
|openssh-server||usually already pre-installed|
|pvm-dev||PVM development files|
|pypvm||PVM python bindings -- use our repackaged pypvm!|