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Installation

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Simonas Marcišauskas edited this page Sep 19, 2019 · 37 revisions

Installation

Required Software

  • A functional MATLAB installation (version 2013b or later)

Dependencies

  • libSBML MATLAB API (version 5.16 is recommended), which is utilised for importing and exporting GEMs in SBML format. Note: not needed if the COBRA Toolbox is installed
  • At least one solver for linear programming:
    • Preferred: Gurobi Optimizer (version 7.5 or higher), academic license is available here
    • Alternative/legacy: MOSEK (version 7 only), academic license is available here
    • If the user has the COBRA Toolbox installed, it is possible to use the default COBRA solver (the one which is set by changeCobraSolver)

Installation Instructions

The RAVEN Toolbox

Obtain the RAVEN Toolbox in one of the following ways:

  • In Terminal/Command Prompt, navigate to the desired installation directory and run the following Git command:
git clone --depth=1 https://github.com/SysBioChalmers/RAVEN.git
  • Alternatively, download the latest release of the RAVEN Toolbox and extract to your favourite directory.

Once extracted, ensure that all other software dependencies (e.g. libSBML, Gurobi) are installed (see above for list, below for instructions. Then, open MATLAB and run the following command:

cd('[location]/RAVEN/installation'))
checkInstallation

where [location] is the directory where you installed RAVEN.

This function checks the functionality for libSBML MATLAB API and solver software. It automatically recognises which solvers are installed and sets the first functional solver as the default RAVEN solver. The default RAVEN solver be changed any time by typing in Matlab:

setRavenSolver('solverName')

Available solver names are gurobi, mosek and cobra.

In Unix-based systems checkInstallation also checks the consistency of external binary programs. If these binaries are broken, they need to be re-compiled from their corresponding source codes. See the documentation for the corresponding software for more details.

libSBML

  1. Download libSBML from the link above and install to your favourite directory.
  2. In MATLAB, run the following command:
addpath('[location]/libSBML-5.x.0-matlab')
savepath

where [location] is where you installed libSBML and 5.x.0 is your libSBML version.

Gurobi

  1. Download from the link above and install Gurobi to your favourite location.
  2. Make sure you obtained a license following instructions for Windows, Mac or Unix.
  3. To install Gurobi in MATLAB, follow the instructions for Windows, Mac or Unix.
  4. Make sure that MATLAB remembers the Gurobi installation for next time, by running the following command:
savepath

Mosek

  1. Download from the link above and install Mosek to your favourite location.
  2. Make sure you obtained a license following [instructions] (https://docs.mosek.com/8.0/install/installation.html#setting-up-the-license).
  3. To install Mosek in MATLAB, follow instructions. Note: the documentation mentions version 8, but RAVEN only works with version 7 of Mosek.
  4. Make sure that MATLAB remembers the Mosek installation for next time, by running the following command:
savepath

The COBRA Toolbox

  1. To gain access to functions from the COBRA Toolbox, follow installation instructions provided here.
  2. To use COBRA-specified solvers (e.g. open-source GLPK solver), configure COBRA and RAVEN with the following commands:
changeCobraSolver('glpk')
setRavenSolver('cobra')

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