After logging into the cluster, load the requierd GIT module.
$ module load git/2.22
Download Cobra toolbox in your local $WORK directory by using the following command
$ git clone --depth=1 https://github.com/opencobra/cobratoolbox.git cobratoolbox
After the download been finished, a directory named “cobratoolbox” should be created in your WORK directory.
Enter the directory “cobratoolbox” using the following command
$ cd cobratoolbox
Then run the following command for uploading the required modules for cobratoolbox
$ git submodule update --init
If you need to use Gurobi then you need to load its module using the following command
More versions of Gurobi are installed on the HCC resources and can be discovered used the following command
$ module spider gurobi
If you need to use IBM ILOG CPLEX then you need to load its module using the following command
$ module load ibm-ilog-cplex
Then run Matlab using the following command
Finally, run the following command to test CobraToolbox using the following Matlab command
NOTE: you need to install CobraToolbox under your WORK directory NOT HOME directory. Because HOME directories are read-only from the compute nodes.
NOTE: if you load Gurobi and IBM ILOG CPLEX modules before starting matlab and running initCobraToolbox, CobraToolbox will automatically find them and configure them for use