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gge-ucd / Discussion

Class discussion for R-DAVIS course
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Using FARM with private github repo #46

Closed JepsonNomad closed 5 years ago

JepsonNomad commented 5 years ago

Hey folks - do you know if there's a way to use code and data from a private github repo on the UC Davis FARM? Historically I've used a shell script (which was uploaded onto my FARM account) to call an R script (also on my FARM account) that works with data that was already uploaded onto the FARM.

MCMaurer commented 5 years ago

I'm not sure if this is possible, I haven't seen any documentation on it. I just use rsync to send files back and forth, so I have a little rsync script to send files to the FARM, and one to take them from the FARM. Then for every script I want to run, I actually have two scripts: my R script, which has all the code, plus makes sure to save the output files, and then a shell script that contains all the proper SLURM headers and then calls the R script and runs it. I have my local folder set up as a repo, so after I pull results from the FARM, I can push those results and stuff to GitHub. I don't know if there's a more direct way to interface between GitHub and the FARM though

JepsonNomad commented 5 years ago

Ok, that's the approach I've used up to this point as well. Thanks Michael.