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
$ gurobi/py38/9.5
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
$ matlab
Finally, run the following command to test CobraToolbox using the following Matlab command
>> initCobraToolbox
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