Pull survival module from OpenPBTA

jharenza commented 8 months ago

Purpose/implementation Section

What scientific question is your analysis addressing?

No analysis, but pulled the latest code from OpenPBTA to OPC for survival. Module is still not actively used. Simply a copy over.

What was your approach?

What GitHub issue does your pull request address?

Closes #392

Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.

Which areas should receive a particularly close look?

Is there anything that you want to discuss further?

Is the analysis in a mature enough form that the resulting figure(s) and/or table(s) are ready for review?

Results

What types of results are included (e.g., table, figure)?

What is your summary of the results?

Reproducibility Checklist

[ ] The dependencies required to run the code in this pull request have been added to the project Dockerfile.
[ ] This analysis has been added to continuous integration.

Documentation Checklist

[ ] This analysis module has a README and it is up to date.
[ ] This analysis is recorded in the table in analyses/README.md and the entry is up to date.
[ ] The analytical code is documented and contains comments.

naqvia commented 8 months ago

Keep get the error below. Seems to be missing a file. Also the readme there is a typo it should be: bash run_survival.sh (without dash).

root@863e34fd0db9:/home/rstudio/OpenPedCan-analysis/analyses/survival-analysis# bash run_survival.sh

processing file: survival-analysis_subtypes.Rmd
  |....................                        |  44% (Read in metadata)       Quitting from lines 82-102 (survival-analysis_subtypes.Rmd)
Error: '../../data/pbta-histologies.tsv' does not exist in current working directory ('/home/rstudio/OpenPedCan-analysis/analyses/survival-analysis').

jharenza commented 8 months ago

No analysis, but pulled the latest code from OpenPBTA to OPC for survival. Module is still not actively used. Simply a copy over.

Sorry for the confusion- this was not intended to be run, just copied the docs from OpenPBTA

jharenza commented 7 months ago

This is not currently implemented in OPC or CI, just moving folders over from OpenPBTA

d3b-center / OpenPedCan-analysis