2016-02-06

How to install COBRApy in Lubuntu 15.10

sudo su
aptitude install python-pip
aptitude install python-dev

Install libSBML

The next step failed for me, but one can try:

pip install python-libsbml

This method worked for me:

sh -c "echo 'deb http://download.opensuse.org/repositories/home:/fbergman:/libsbml/xUbuntu_15.10/ /' >> /etc/apt/sources.list.d/python-libsbml.list"
apt-get update
apt-get install python-libsbml

Install COBRApy dependencies

apt-get install python-glpk
apt-get install python-numpy
apt-get install python-scipy
apt-get install glpk-utils
apt-get install libglpk-dev

Install COBRApy

pip install cobra
apt-get install ipython

Test COBRApy

In python console run:

from cobra.test import test_all
test_all()

Ran 83 tests in 66.987s
OK (skipped=1)

As it is noted in the title these instructions work on Ubuntu. Unfortunately I couldn't get COBRApy to pass tests on Fedora 23 because it can't locate glpk. Any help in comments is appreciated.