federatedcloud / cobracontainers Goto Github PK

This is to keep a version a pointer to dependency versions.

Use UUIDs for mounting.

• /opt
• /data ?

Essentially need to write a MATLAB script to do at least the following:

• Host matlab priles private - can we fetch via sftp?
• Repackage MATLAB as something living in the /nix/store (need to resize disk to test this)
• Set up and test gurobi, including savepath
• Set up and test COBRA with gurobi, including initCobraToolBox

Unfortunately, will likely need to upgrade MATLAB to support jdk8 as well - we're just one version off currently (2017a - would need at least 2017b; 2019a clients are purportedly on RedCloud so we can copy that over and try the jdk option).

See here: https://www.mathworks.com/matlabcentral/answers/103056-how-do-i-change-the-java-virtual-machine-jvm-that-matlab-is-using-on-macos

In particular, this is the part that isn't working for Java:

https://github.com/federatedcloud/COBRAContainers/blob/master/nix/shells/MATLAB/patchMATLAB.sh#L16

Gurobi

GUROBI_HOME=getenv('GUROBI_HOME')
cd(strcat(GUROBI_HOME, '/matlab'))
gurobi_setup
# could do savepath at this point