In #1421, I've added a shell script that's intended to be run as part of data release to generate analysis files included in releases. The script used for subtyping (scripts/run-for-subtyping.sh) used to run many of these steps because the subtyping modules were designed to use files in analyses/. In #1413, #1415, #1418, and #1419, I've revised the remaining subtype modules that relied on analyses to use files in the data download. I've also split out the data generation steps in #1421. So now our shell script only needs to run subtyping! However, there are still a few results from modules that are not distributed via the data download that are used in subtyping, so we need to include those in scripts/run-for-subtyping.sh and make sure that they use the base histologies file.
Splitting up the changes described in https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/1399#issuecomment-1124329628
In #1421, I've added a shell script that's intended to be run as part of data release to generate analysis files included in releases. The script used for subtyping (
scripts/run-for-subtyping.sh) used to run many of these steps because the subtyping modules were designed to use files inanalyses/. In #1413, #1415, #1418, and #1419, I've revised the remaining subtype modules that relied onanalysesto use files in the data download. I've also split out the data generation steps in #1421. So now our shell script only needs to run subtyping! However, there are still a few results from modules that are not distributed via the data download that are used in subtyping, so we need to include those inscripts/run-for-subtyping.shand make sure that they use the base histologies file.