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SysBioChalmers / ecModels

A container for all enzyme constrained models created by GECKO.
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Workflow failing on the eciYali step #61

Closed IVANDOMENZAIN closed 3 years ago

IVANDOMENZAIN commented 3 years ago

In the latest long runs of the automated pipeline (run1, run2, run3) it has been observed an error in the MATLAB command for the iYali case. All of these errors point out to the same line (429) in the corresponding manualModifications script, however this script is much shorter for this case, which makes conclude that the pipeline is not substituting the iYali-specific scripts into GECKO, therefore an error pops-up in MATLAB and our pipeline is crashing.

Any ideas on how to solve this? I also think that we've seen happening before but don't remember so well.

IVANDOMENZAIN commented 3 years ago

@mihai-sysbio

mihai-sysbio commented 3 years ago

It seems that the Matlab code moving the files has no effect. I suspect what it has to do with the git command being slow, so the Matlab command is invoked before the git clone step finished. If so, then this is fixed by changing how the commands are invoked.

mihai-sysbio commented 3 years ago

It was a good idea to change check_call to check_output, but to solve the problem the base branch of the pipeline has to be different than the pull_request_target in config.ini. Things look promissing in line 5

INFO:main:Pipeline started on branch fix/issues-with-scripts-folder

mihai-sysbio commented 3 years ago

Alright, this has been resolved.