Using Cobra Toolbox in a cluster environment

[Maximilian Lularevic]

Hi all,

Since updating the cobra toolbox I have not been able to use/initialize it on our university cluster (Matlab2016b).

The problem seems to be that the automated update it does in initCobraToolbox.m does not work on the cluster. 

unable to access 'https://github.com/opencobra/COBRA.binary.git/': error setting certificate verify locations:

  CAfile: /etc/ssl/certs/ca-certificates.crt

Has anyone else experienced this issue or is there an easy way to adapt the function in a way so it does not try to connect to github?

(just changing solvers doesn't work either as it seems to go back into initCobraToolbox.m (changeCobraSolber.m - line 197))

Any help is greatly appreciated!

Best,

Max

[Laurent Heirendt]

Hi Max,

A connection to Github is required to install all submodules, especially COBRA.binary. There is no automatic update.

Are you allowed to have an outgoing internet connection from your cluster? Can Github be reached from your cluster?

Best,

Laurent

[Maximilian Lularevic]

Hi Laurent,

Thanks for the swift reply.

I am currently in contact with our research computing support team to find that out. 

However, from the looks I think that might be the problem.

I tried simply cloning the toolbox earlier from the Terminal to see if any kind of connection works (outside of MATLAB) which it did not (telling me it was unable to access github)

I assume that there is no way of running COBRA offline then?

Thanks!

Max 

[Laurent Heirendt]

Hi Max,

It is possible to use the COBRA Toolbox offline, but all submodules must be present first. Do you have the option to prepare a full clone of the COBRA Toolbox, and then move that folder to the cluster?

I would suggest the following steps on your local machine:

1) git clone g...@github.com:opencobra/cobratoolbox.git

2) start Matlab, then run >> initCobraToolbox (this will download all submodules)

3) copy the entire folder cobratoolbox to the cluster using either FTP or scp.

Don't you have the option to mount a common drive on your local machine and on your cluster?

Please let me know if this works.

Best,

Laurent

[Maximilian Lularevic]

Hi Laurent,

Thank you for your tip!

The toolbox works after following your steps on the cluster!

Best,

Max

[Laurent Heirendt]

Hi Max,

Great to hear that it works!

Enjoy,

Laurent