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rivas-lab / hla-assoc

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Move notebook and scripts output directories into repo #5

Closed cdeboever3 closed 5 years ago

cdeboever3 commented 5 years ago

The output directories for Julia's notebooks are at /oak/stanford/groups/mrivas/users/jolivier/repos/hla-assoc/notebooks/output. The output directories for her scripts are at /oak/stanford/groups/mrivas/users/jolivier/repos/hla-assoc/scripts/output. These should be moved to output which will be tracked with git lfs or private_output if too big or sensitive which will no be tracked.

cdeboever3 commented 5 years ago

I copied everything from /oak/stanford/groups/mrivas/users/jolivier/repos/hla-assoc/notebooks/output into output. These are tracked with lfs and pushed. I could have linked to her directory, but I want to preserve her copies of the files in case we start changing them.

cdeboever3 commented 5 years ago

I've copied some things from /oak/stanford/groups/mrivas/users/jolivier/repos/hla-assoc/scripts/output to output and some to private_output. If we were to re-run Julia's notebooks or scripts, we'd have to route the output to the correct directories. I've also gzipped some files to try to cut down the sizes a bit.

I left the original files in Julia's directory unchanged.

cdeboever3 commented 5 years ago

Script output files are also committed and pushed. I've updated the path variables for a few of Julia's notebooks. In particular, the paths should look something like

path = os.path.realpath('..')
outpath = os.path.join(path, 'output/compare_cutoff_pvals')

where the outpath has the correct name that matches the notebook name.

cdeboever3 commented 5 years ago

Closing for now as I think that everything relevant has been added. We can update the paths in the notebooks (and scripts) as needed. I expect we won't need to run the scripts again.

cdeboever3 commented 5 years ago

I also copied /oak/stanford/groups/mrivas/users/jolivier/repos/hla-assoc/data/PLINK_results/ into private_output and /oak/stanford/groups/mrivas/users/jolivier/repos/hla-assoc/data/ukbb_files/ into private_data.