Commit 15b5e8ed authored by Mohammed Tanash's avatar Mohammed Tanash
Browse files

Merge branch 'cobraToolbox' into 'master'

Add the guide for Matlab CobraToolbox in the Application Specific Guides page

See merge request !310
parents 6b1d12c6 99cd97e0
+++
title = "Install and Running Matlab CobraToolbox"
description = "How to install and run Matlab CobraToolbox"
+++
## This document provides the steps to install and run MATLAB CobraToolbox in the cluster.
### INSTALLATION GUIDE
After logging into the cluster, load the requierd GIT module.
{{< highlight bash >}}
$ module load git/2.22
{{< /highlight >}}
Download Cobra toolbox in your local $WORK directory by using the following command
{{< highlight bash >}}
$ git clone --depth=1 https://github.com/opencobra/cobratoolbox.git cobratoolbox
{{< /highlight >}}
After the download been finished, a directory named "cobratoolbox" should be created in your WORK directory.
Enter the directory "cobratoolbox" using the following command
{{< highlight bash >}}
$ cd cobratoolbox
{{< /highlight >}}
Then run the following command for uploading the required modules for cobratoolbox
{{< highlight bash >}}
$ git submodule update --init
{{< /highlight >}}
Then run Matlab using the following command
{{< highlight bash >}}
$ matlab
{{< /highlight >}}
Finally run the following command to test CobraToolbox using the following Matlab command
```Matlab
>> initCobraToolbox
```
NOTE: you need to install CobraToolbox under your WORK directory NOT HOME directory. Because HOME directories are read-only from the compute nodes.
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