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INSTALL.md

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For installation help, please use the [Google Group] (http://groups.google.com/group/cobra-pie).

For usage instructions, please see the documentation

All releases require Python 2.7 to be installed before proceeding. Mac OS X (10.7+) and Ubuntu ship with Python. Windows users without python can download and install python from the python website.

Python 3 support is still considered experimental.

#Installation of cobrapy

Stable version installation

Mac OS X

  1. [install pip] (http://pip.readthedocs.org/en/latest/installing.html).
  2. In a terminal, run sudo pip install cobra --pre

GNU/Linux

  1. [install pip] (http://pip.readthedocs.org/en/latest/installing.html).
  2. Install the glpk and gmp libraries. On debian-based systems (including Ubuntu and Mint), this can be done with sudo apt-get install libglpk-dev libgmp-dev
  3. In a terminal, run sudo pip install cobra --pre

Microsoft Windows

Download and install the appropriate 32 bit or 64 bit installer, both of which can be downloaded from the python package index.

Hacking version installation

Use pip to install Cython. Install libglpk and libgmp using your package manger. This would be brew install glpk gmp on a Mac and sudo apt-get install libglpk-dev libgmp-dev on debian-based systems (including Ubuntu and Mint). They can obviously also be compiled from the released source.

Clone the git repository using your preferred mothod. Cloning from your own github fork is recommended! Afterwards, open a terminal, enter the cobrapy repository and run the following command:

python setup.py develop --user

Installation of optional dependencies

Optional Dependencies

On windows, these can downloaded from [this site] (http://www.lfd.uci.edu/~gohlke/pythonlibs/). On Mac/Linux, they can be installed using pip, from binary installers, or from package managers.

  1. libsbml >= 5.10 to read/write SBML files
  1. numpy >= 1.6.1 for double_deletion_analysis
  1. scipy >= 0.11 for ArrayBasedModel and saving to *.mat files.

Other solvers

cobrapy comes with bindings to the GNU Linear Programming Kit ([glpk] (http://www.gnu.org/software/glpk/)) using its own bindings called "cglpk" in cobrapy. In addition, cobrapy currently supports these linear programming solvers:

ILOG/CPLEX and Gurobi are commercial software packages that, currently, provide free licenses for academics and support both linear and quadratic programming. GLPK is an opensource linear programming solver; however, it does not support quadratic programming and is not as robust as the commercial solvers when it comes to mixed-integer linear programming. QSopt_ex esolver is also open source, and can solve linear programs using rational operations, giving exact solutions.

Testing your installation

  1. Start python
  2. Type the following into the Python shell
from cobra.test import test_all
test_all()