Personal tools
You are here: Home / Installing Biskit / Setup environment

Setup environment

Adapt Biskit to your local environment.
  • Adapt Biskit settings (binary paths etc)
    1. default settings:

      Biskit creates a ~/.biskit folder with default configuration files during the first startup. We try to make some intelligent guess about which parameters actually need to be modified (because the default path or value seems invalid) and only these are included in the .biskit/settings*.cfg files -- all others are there but commented out. However, this check is only done when the .biskit is created. If your environment has changed and you want biskit to repeat the automatic setup, simply delete the ~/.biskit folder!

      A sligthly more sophisticated script for checking and repairing the current setup is on our To-Do list.

    2. the configuration files:

      • .biskit/settings.cfg -- parameters for Biskit module
      • .biskit/settings_Mod.cfg -- parameters for Biskit/Mod homology modeling module
      • .biskit/settings_Dock.cfg -- parameters for Biskit/Dock docking module
      • .biskit/exe_*.dat -- parameters for the different external programs (replacing the default files in biskit/external/defaults)
    3. Check and adapt settings.cfg

      Have a look at .biskit/settings.cfg and check all entries that are not commented out. For each of them you should see a comment with the problem. Potential trouble makers are tempDirShared and tempDirLocal. You only need to worry about missing binaries or databases, if you have actually installed the program

  • Override settings for Biskit helper applications

    Each program used by Biskit has a configuration file in Biskit/data/defaults/. A copy placed in your local ~/.biskit/ folder will override these default settings.

    See Biskit/ for more details!

  • To use a python version other than your default one (biskit requires 2.5+)
    (This is often needed for CentOS or Redhat installations)
    • link your new python version to an alternative bin folder
    mkdir ~/bin
    ln -s /usr/local/bin/python2.7 ~/bin/python
    • edit your user environment so that this bin folder is at the beginning of your path
    example bash (edit ~/.bashrc) or zsh (edit ~/.zshenv):
    export PATH=~/bin:$PATH
(setenv PATH ~/bin:$PATH" for csh and tcsh shells)


  • Optional: include scripts in search path

    (example for zsh or similar; use setenv for csh and bash):

    export PATH=$PATH:$BPath/Biskit:$BPath/Dock:$BPath/Mod
  • Test
    ~> biskit/scripts/Biskit/

    You shouldn't get any warning or error messages any longer.