Add shell script to generate analysis files that are included in data releases #1421
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…-analysis-generation
| # Run hotspot detection | ||
| echo "Run hotspots detection" | ||
| bash ${analyses_dir}/hotspots-detection/run_overlaps_hotspots.sh |
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Noting that this module (and output file pbta-snv-scavenged-hotspots.maf.tsv.gz) appears to be missing from here but it should be there, right?
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Yes they should, but maybe that should get fixed on #1424 and not here?
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I'll open an issue. Edit: #1428
| # Set the working directory to the directory of this file | ||
| cd "$(dirname "${BASH_SOURCE[0]}")" | ||
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| # If RUN_LOCAL is used, the time-intensive steps are skipped because they cannot |
| # Compile all the files that need to be included in the release in one place | ||
| # in the scratch directory | ||
| compiled_dir=${scratch_dir}/analysis_files_for_release | ||
| mkdir -p ${compiled_dir} |
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I would move these lines up before you start running modules, right after other directories are defined in lines 19-21
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| # Run GISTIC step -- only the part that generates ZIP file | ||
| echo "Run GISTIC" | ||
| # Run a step that subs ploidy for NA to allow GISTIC to run |
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Just a question about the whether the CI if lines might be needed here.
OpenPBTA-analysis/analyses/run-gistic/run-gistic-module.sh
Lines 9 to 32 in e31b58c
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I don't follow. I don't necessarily expect this script (scripts/generate-analysis-files-for-release.sh) to get run in CI.
We don't use analyses/run-gistic/run-gistic-module.sh at all here.
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I don't necessarily expect this script (scripts/generate-analysis-files-for-release.sh) to get run in CI.
Just looking for a confirmation of this, and whether it might ever change! 👍
…9-analysis-generation
Continuing to break up the changes described in #1399 (comment)
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:It is intended to be used as part of a series of steps during the data release process, which will be as follows:
scripts/generate-analysis-files-for-release.sh, which should generate all the analysis files for a release and put them inscratch/analysis_files_for_release, and commit any changes to files that are included in the repository.scripts/run-for-subtyping.shand commit any changes to files that are included in the repository. (PR coming soon!)pbta-histologies.tsvto the release