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AlexsLemonade / OpenPBTA-analysis

The analysis repository for the Open Pediatric Brain Tumor Atlas Project
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Add shell script to generate analysis files that are included in data releases #1421

Closed jaclyn-taroni closed 2 years ago

jaclyn-taroni commented 2 years ago

⚠️ Review #1419 and #1420 first ⚠️ this can not be stacked because these are from my branch.

Continuing to break up the changes described in https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/1399#issuecomment-1124329628

Here I'm adding scripts/generate-analysis-files-for-release.sh, a shell script for generating analysis files that are included in the data download. As a reminder, an analysis file is defined as:

Any file created by a script in analyses/*.

It is intended to be used as part of a series of steps during the data release process, which will be as follows:

  1. We start a release that has all of the PBTA data files (i.e., upstream files) included
  2. We run scripts/generate-analysis-files-for-release.sh, which should generate all the analysis files for a release and put them in scratch/analysis_files_for_release, and commit any changes to files that are included in the repository.
  3. We add all the analysis files to the release.
  4. We run scripts/run-for-subtyping.sh and commit any changes to files that are included in the repository. (PR coming soon!)
  5. We add pbta-histologies.tsv to the release