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V16 subset files for CircleCI testing #670
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add folder for notebooks
add gitignore
update output file path handle in get-tcga-capture_kit.py
add boxplot.R
skip the manifest header
add ci for tcga-capture-kit-investigation
Merge branch 'analyses/tcga-capture-kit-investigation' of https://github.com/yuankunzhu/OpenPBTA-analysis into Teja_tmbQC
…vestigation.sh script
Co-Authored-By: jashapiro <josh.shapiro@ccdatalab.org>
…_ewings_foi.tsv for v16
cansavvy
commented
Apr 3, 2020
| @@ -68,9 +68,6 @@ cp $FULL_DIRECTORY/independent-specimens*.tsv $SUBSET_DIRECTORY | |||
| # all bed files | |||
| cp $FULL_DIRECTORY/*.bed $SUBSET_DIRECTORY | |||
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| # the release notes | |||
| cp $FULL_DIRECTORY/release-notes.md $SUBSET_DIRECTORY | |||
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Ah, this is why I was missing files. Because the script failed at this step before and the other files after it did not get copied. I ran everything again just in case.
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Purpose/implementation Section
What scientific question is your analysis addressing?
Setting up the subset files for v16 release so we can test the changes on CircleCI.
What was your approach?
analyses/create-subset-files/create_subset_files.shupdate to v16bash analyses/create-subset-files/create_subset_files.shv16-cibranch.data/testing/release-v16-20200320/totesting_v16.zipWhat GitHub issue does your pull request address?
#657
Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.
create_subset_files.shscript noted that there is no release-notes.md file in the v16 data?? Is that forth coming?Are there any steps that I should have taken that are not mentioned here?
If all looks as expected, I will upload the subsetted v16 files so we can begin working on breaking changes, but probably would be good to track down the
release-notes.mdfile first.