metatoolkit

Metatoolkit master project repository, includes sub-modules cbmpy, metadraft and studio


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MetaToolKit

MetaToolKit (C) 2010-2016 Brett G. Olivier, VU University Amsterdam, Amsterdam, The Netherlands

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/

Author: Brett G. Olivier Contact email: bgoli@users.sourceforge.net Last edit: $Author: bgoli $ ($Id: CBConfig.py 144 2014-01-16 22:27:55Z bgoli $)

Installation

MetaToolKit depends on CBMPy for its core functionality

New cross-platform conda support

CBMPy is now available as a crosss platform Anaconda package available for Win32/64, Linux32/64 and OSX from the Anaconda cloud (https://anaconda.org/bgoli/repo). This is the first major release using the conda platform and all feedback is welcomed. If you have Anaconda installed (tested with 4.2.0) simply try the following::

conda install -c bgoli -c SBMLTeam cbmpy

which should install CBMPy, libSBML and all the required (non-solver) dependencies. If you do not use Anaconda or would like to try install things in a semi-automated way carry on reading.

The following installation instructions are for Ubuntu 16.04 but should be adaptable to any Linux package managment system, OSX, Debian, etc. Except for GLPK (4.47) and SymPy (0.7.4 or newer) no specific library version is required. For more detailed installation instructions and Windows please see the online documentation http://cbmpy.sourceforge.net/reference/install_doc.html

Auto-dependency configuration

I am in the process of creating automated dependency checking and building tools for CBMPy.

Ubuntu build support is complete with cross platform conda support is now available from the build repository (https://github.com/bgoli/cbmpy-build.git)::

Or simply download the install script that will run the system tests::

curl –remote-name https://raw.githubusercontent.com/bgoli/cbmpy-build/master/ubuntu/1_install_cbmpy_dependencies.py

This script will analyse your Python distribution for missing dependencies and generate a shell script that will auto-install them.

For an installation using the native Python supplied with Ubuntu run::

python 1_install_cbmpy_dependencies.py UBUNTU

For a local user installation of Anaconda try the following. This is not strictly necessary if only CBMPy is going to be installed (see above)::

python 1_install_cbmpy_dependencies.py CONDA

in both cases a shell script metatoolkit_install_dependencies.sh is generated and printed to the screen. Run this script or install the relevant packages by hand.

Installing or upgrading CBMPy

Installing or upgrading CBMPy can easily be done with pip::

sudo pip install cbmpy sudo pip install –upgrade cbmpy

or try the new CONDA support::

conda install -c bgoli -c SBMLTeam cbmpy conda update cbmpy

or download the relevant source from SourceForge:

https://sourceforge.net/projects/cbmpy/files/release/0.7/

and run::

python setup.py build sdist sudo python setup.py install

Installing glpk/python-glpk

CBMPy requires a linear solver for numerical analysis, the open source (glpk) solver can be automatically built and installed as follows (requires git to be installed and accessible):

Download the install script that will install GLPK/PyGLPK for CBMPy on Ubuntu 14.04 or newer::

curl –remote-name https://raw.githubusercontent.com/bgoli/cbmpy-glpk/master/install_glpk.sh

Make executable::

chmod 744 install_glpk.sh

and run::

./install_glpk.sh

Note this script is designed to be used for building containers and will remove any installed version of GLPK and build and install the correct version needed for PyGLPK.

No warranty of any kind assumed or otherwise, use at own risk!

(c) Brett G. Olivier, Amsterdam, 2014-2016