Installation and upgrade

Required software

• MATLAB version 2019b or later, no additional MathWorks toolboxes are required
• RAVEN Toolbox 2.9.2 or later, see installation instructions
• Optional: Gurobi Optimizer solver to be used by RAVEN, see installation instructions. SCIP is an open-source alternative. The RAVEN default glpk solver is not recommended
• Docker for running DLKcat, see installation instructions

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Installation

Choose one of the three alternatives: easy / medium / advanced, followed by activation in MATLAB.

Easy

• Open Add-Ons Explorer in MATLAB: in the Home tab and the Environment section, click the Add-Ons icon
• Search for GECKO Toolbox and click Add -> Add to MATLAB
• Run activation in MATLAB

Upgrade GECKO after Easy installation

• Run GECKOInstaller.uninstall to remove all mentions of the GECKO folder and subfolders from the MATLAB path. This prevents potential warning messages regarding non-existing paths when opening MATLAB anew
• In the Home tab, click on Help > Check for Updates
• Click on the Update button for GECKO Toolbox
• If GECKO Toolbox is not mentioned among the Updates, it might help to restart MATLAB
• Run activation in MATLAB

Medium

• Download the latest release of the GECKO Toolbox
• Extract the ZIP file to your favourite directory
• Run activation in MATLAB

Upgrade GECKO after Medium installation

• Run GECKOInstaller.uninstall to remove all mentions of the GECKO folder and subfolders from the MATLAB path. This prevents potential warning messages regarding non-existing paths when opening MATLAB anew
• Close MATLAB
• First delete the complete GECKO folder from your computer
• Download the latest release of the GECKO Toolbox
• Extract the ZIP file to your favourite directory
• Run activation in MATLAB

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/GECKO .git

• Run activation in MATLAB

Upgrade GECKO after Advanced installation

• Run GECKOInstaller.uninstall to remove all mentions of the GECKO folder and subfolders from the MATLAB path. This prevents potential warning messages regarding non-existing paths when opening MATLAB anew
• Close MATLAB
• Through your usual git routines, pull and checkout the latest commit on the main branch
• Run activation in MATLAB

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Activation in MATLAB

• Skip step 1 if GECKO was installed as MATLAB Add-On (easy):

1. In MATLAB, navigate to the directory where GECKO was installed: cd('C:\path\to\GECKO') % Modify to match GECKO folder and operating system
2. In the MATLAB Command Window, run GECKOInstaller.install

All set! 🚀