Colonyzer: installation under OSX

I don't have regular access to OSX machines, but Katja Luck and Adriana San Miguel have kindly provided the notes below which outline the steps to successful installation on various flavours of OSX.

General installation notes

  1. Install python 2.7 from and make sure it's the python version used by the system
  2. Install the most recent version of Xcode for your operating system (needed by homebrew)
    • Updating current installation is not possible
    • Delete current Xcode installation from applications folder by simply trashing the Xcode app
    • Install new Xcode
    • With the newer versions of Xcode, install Xcode command line tools via preferences/download. With older versions of Xcode, this is given as an option during Xcode installation
  3. Install homebrew
    • type into terminal:
      ruby -e "$(curl -fsSL"
    • different procedure for Mac OS X 10.5, see webpage
    • type in terminal:
      brew doctor
    • WARNING: brew may complain about order of paths
  4. Change path in .bash_profile for homebrew
    • Look in your home directory ('cd ~' to get there, 'ls -a' to look) for a .bash_profile or .bashrc file.
    • If you find one of them, open it up and you should see a line like this:
      export PATH=/usr/bin:/usr/local/bin:/opt/local/sbin:$PATH
    • Cut the "/usr/bin:" and paste it after the "/usr/local/bin:"
    • If you don't find either of those files, create one called .bash_profile and put this line inside:
      export PATH=/usr/local/bin:$
  5. installation of gfortran compiler with homebrew (needed for scipy):
    • type into terminal:
      brew install gfortran
  6. installation of libjpeg library with homebrew (needed for PIL):
    • type into terminal:
      brew install libjpeg
  7. installation of pip package manager and the dependency:
  8. installation of numpy, scipy, PIL, pandas, matplotlib with pip:
    • type in terminal:
      pip install package_name
  9. for installation of pygame:
  10. install colonyzer with pip
    • type into terminal:
      pip install Colonyzer2
    • this brought some warnings about a file that it couldn't locate but still said that installation was successful
    • for running colonyzer we had to do the following trick:
      • first, run parametryzer as follows in terminal in folder that contains the image:
        python2.7-32 path_to_parametryzer/parametryzer
      • run independent as usual:

Tips for installing colonyzer on Mac OS X 10.5.8