Welcome to COBRApy Help - Install

2013-03-13
2013-05-30
  • Daniel Hyduke
    Daniel Hyduke
    2013-03-13

    Welcome to COBRApy Help - Install

     
  • Kai Zhuang
    Kai Zhuang
    2013-03-20

    Hi.  Here are some instructions for installing COBRApy and related packages using OSX native python (tested on Mountain Lion):

    1. Python
         use Mac native python
    2. LibSBML
         1/ use the pre made package
         2/ add following to .bash_profile
              export PYTHONPATH="/usr/local/lib/python2.7/site-packages/libsbml"     3/ ln .bash_profile .bash_rc

    3. COBRAPy
         sudo easy_install cobra
    4. Gurobi
         1/ setup Gurobi using installer
              default directory is: /Library/gurobi510/mac64     2/ install Python interface: sudo python setup.py install
    5. GCC and FORTRAN
         1/ install GCC
              - install XCODE
              - install "Command Line Tools" under Preference>Downloads
                   Command Line Tools contain gcc     2/ install GFORTRAN
              - download the tar package from http://hpc.sourceforge.net
              - sudo tar -xvf gfortran-mlion.tar -C /.

    6. Install Scipy and NumPy
         1/ sudo easy_install numpy
         2/ sudo easy_install scipy
    7. Install Matplotlib
         1/ dependencies are provided by XQuartz, so use Xterm from XQuartz instead of Terminal to install
         2/ sudo easy_install matplotlib

    8. Install PIP package manager
         sudo easy_install pip
    9. Install Nose
         sudo easy_install nose
    10. IDEs
         a/ PyCharm
              install from .DMG
              set Preference>Project Interpreter>Python Interpreters
         b/ IPython
              1/ sudo easy_install readline
              2/ sudo easy_install ipython

         c/ Spyder IDE
              1/ dependencies
                   a/ sudo pip install sphinx
                   b/ QT 4.8 and PySide 1.1.1: http://qt-project.org/wiki/PySide_Binaries_MacOSX
              2/ add to .bash_profile:
                   export LANG=en_US.UTF-8
                   export LC_ALL=en_US.UTF-8
             
              3/ sudo easy_install spyder
                   do not use the binary because it contains it's own version of python and it's hard to get libsbml hooked up to it.