Short instruction

1 Installation from source

Installation from source should work on any platform.

• I) download or git/checkout (see below) the biskit source package:

  Select the latest biskit tar.gz from the github releases area.

  Or type in your terminal:

  wget https://github.com/graik/biskit/archive/v2.4.2.tar.gz
  tar xvf v*.tar.gz
  

  or check out the latest development snapshot:

  git clone https://github.com/graik/biskit.git biskit
  

• II) Install dependencies

  pip install numpy scipy biopython
  

• III) Install Biskit

  cd biskit
  python setup.py install
  

  This will install biskit into the "site-packages" folder of the python version that you used for calling setup.py. If you use a virtual environment (virtualenv), this will be venv/lib/python2.7/site-packages.

  Running setup.py is not really needed. You can also simply add the biskit folder to your PYTHONPATH environment variable. This has the advantage that you can easily update biskit using git.

• IV) Install Biggles

  Many Biskit modules use Biggles for generating publication-quality plots. Earlier or later, Biskit will likely raise import errors or Warnings if biggles is not installed. It is currently not available with pip. On Ubuntu, install biggles into Python 2.x with:

  sudo apt-get install python-pybiggles
  

  Otherwise, use the PyPi package:

  You need development files for Python, X11 and plotutils (a.k.a libplot). (http://www.gnu.org/software/plotutils/). On some distros, this requires a separate x11-devel package. On Ubuntu / Debian:

  sudo apt-get install plotutils libplot-dev python-dev
  

  On Mac OSX:

  • you will first have to install XQuartz -- see: https://www.xquartz.org/

  • Then install plotutils:

    brew install plotutils --with-X11
    

  Check that x11 and libplot include+library files are installed:

  ~> ll /usr/lib/libXaw.so
     lrwxrwxrwx 1 root root 10 2007-05-16 14:36 /usr/lib/libXaw.so -> libXaw8.so
  

  Download and install biggles from PyPi:

  pip install biggles
  

  Test Biggles:

  python
  >>> import biggles
  >>>
  

  Then paste the following code snippet into your python interpreter:

  import biggles, numpy
  x = numpy.arange(0,10,0.3)
  p = biggles.FramedPlot()
  p.add( biggles.Curve(x, numpy.cos(x)) )
  p.show()
  

  Consult our biggles troubleshooting guide if you experience any problems!

  Other plotting and visualization-related tools that are useful:

  sudo apt-get install gnuplot pymol
  

  Or on Mac OS-X:

  brew install gnuplot --with-x11
  brew install pymol
  

• V) Test your installation

  python Biskit/test.py -e exe old pvm
  

  This will run all Biskit tests which are not marked as requiring third-party programs (exe) or as old (old) and which do not require pvm parallelization (pvm). They should all pass.

  Update 06/2016:

  • On MacOSX, I encountered one test failure from PDBCleaner.test_capping_extra. This seems to be a mere numeric difference meaning the chain break detection is slightly more tolerant on MacOSX systems.
  • While Biskit can be used without Biggles, several tests strictly depend on it and fail if biggles is not installed.

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!