Snakemake modifications for big models

[Timon-R]

I used the workflow on a big model with 300 runs and had to make adjustments to the snakemake workflow. I note them here for convenience.

• Change shell commands to script commands when there are multiple arguments. Command line commands have limited arguments and if lists are given, this can cause the workflow to break.
• Use priority: 100 for the function that solves the lp file as well as for all functions that process it
• and use priority 0 for the function that creates it; also give the function that creates the lp file 4 threats. Reason for this is that the lp file is large and can take up a lot of space on your hard drive.

[robertodawid]

Hi @Timon-R , I am running the snakemake workflow in Windows. It seems there are issues with the (shell sections in the workflow) since most of these sections were developed for *nix. I am NOT super literate on this, but you mentioned changing the shell commands to scrips. Would that work on Windows? If so, do you have an example I can look at? or in any case. Would you happen to have a suggestion so I can run the workflow in Windows.?

[Timon-R]

Hi @robertodawid, try using my modified workflow for Windows: https://github.com/Timon-R/OSEMBN

[robertodawid]

Hi @Timon-R , I am running the snakemake workflow in Windows. It seems there are issues with the (shell sections in the workflow) since most of these sections were developed for *nix. I am NOT super literate on this, but you mentioned changing the shell commands to scrips. Would that work on Windows? If so, do you have an example I can look at? or in any case. Would you happen to have a suggestion so I can run the workflow in Windows.?

Dear @Timon-R , Thanks! I took a couple of the *.py from your workflow, and now mine seems to be working.