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Installation

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Eduard Kerkhoven edited this page Jun 14, 2022 · 37 revisions

Required software

  • A functional MATLAB installation (version 2016b or later).
  • Recommended: Gurobi as alternative solver.
  • Optional: COBRA Toolbox for more simulation functions.
  • Development: if new HMMs are to be trained from a KEGG FTP-dump on a Windows PC, it is required to have Windows Subsystem for Linux installed.

Installation instructions

Obtain RAVEN Toolbox

Use one of the three following ways to obtain RAVEN Toolbox: advanced / simpler / simplest

Advanced

  • This approach is recommended, but requires git to be installed.
  • 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

Simpler

  • Download the latest release of the RAVEN Toolbox.
  • Extract the ZIP file to your favourite directory.
  • Follow the Install RAVEN in MATLAB instructions below.

Upgrade to latest RAVEN release

  • Close MATLAB.
  • First delete the complete RAVEN folder from your computer.
  • Optional: run pathtool to remove all mentions of the RAVEN folder and subfolders from the MATLAB path, and click Save. This prevents warning messages regarding non-existing paths when opening MATLAB anew.
  • Download the latest release of the RAVEN Toolbox.
  • Extract the ZIP file to your favourite directory.
  • Follow the Install RAVEN in MATLAB instructions below.

Simplest

  • Open Add-Ons Explorer in MATLAB: in the Home tab and the Environment section, click the Add-Ons icon.
  • Search for RAVEN Toolbox and click Add -> Add to MATLAB.
  • Follow the Install RAVEN in MATLAB instructions below.

Update RAVEN as MATLAB Add-On

  • In the Home tab, click on Help > Check for Updates.
  • Click on the Update button for RAVEN Toolbox.
  • If RAVEN Toolbox is not mentioned among the Updates, it might help to restart MATLAB.

Install RAVEN in MATLAB

  • If RAVEN was obtained via MATLAB Add-Ons Explorer (the "simplest" approach), directly run in MATLAB:
checkInstallation
  • If RAVEN was cloned (the "advanced" approach) or downloaded (the "simpler" approach), first open MATLAB and run the following command, where [location] is the directory where the RAVEN files can be found:
cd('[location]/RAVEN/installation'))
checkInstallation
  • checkInstallation installs and tests general functioning of RAVEN. It recognises which solvers are installed and sets the default solver (if possible gurobi, otherwise glpk).
  • The default RAVEN solver can be changed any time with: setRavenSolver('solverName'), where 'solverName' can be either 'gurobi', 'glpk' or 'cobra'.
  • checkInstallation also tests various programs that are distributed with RAVEN (BLAST+, DIAMOND, HMMER). Correct functioning of these programs generally are required for making models from homology (BLAST+, DIAMOND) or making models from KEGG (HMMER). If the tests of these programs fail, they need to be re-compiled from their corresponding source codes. See the documentation for the corresponding software for more details.
  • If you plan to train HMMs based on a KEGG FTP-dump (which is rarely done, as we already distribute these for you), you should run checkInstallation(true) to also test the CD-HIT and MAFFT binaries. If you run MATLAB on Windows, you should have Windows Subsystem for Linux installed.

Optional software

Solvers

  • The open-source GLPK solver is already distributed with RAVEN. This works well for solving LPs (e.g. "standard" flux balance analysis), but is not well-suited to solve MILP (e.g. with fillGaps or tINIT).
  • Alternatively, especially for solving MILPs, you can install Gurobi Optimizer (version 7.5 or higher), for which an academic license is available here.
  • If the user has the COBRA Toolbox installed, one can use the default COBRA solver (set be changeCobraSolver).

Gurobi

  • Download and install Gurobi to your favourite location.
  • Make sure you obtained a license following instructions for Windows, Mac or Unix.
  • To install Gurobi in MATLAB, follow the instructions for Windows, Mac or Unix.
  • Make sure that MATLAB remembers the Gurobi installation for next time, by running savepath.

COBRA Toolbox

  • To gain access to functions from the COBRA Toolbox, follow installation instructions provided here.
  • To use COBRA-specific functions on a model, you are advised to first change the model into COBRA-format, using modelCobra=ravenCobraWrapper(model).
  • 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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