re-org docker file, upgrades - Githubissues

d3b-center / OpenPedCan-analysis

The analysis repository for the Open Pediatric Cancer Project

https://d3b-center.github.io/OpenPedCan-analysis/

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re-org docker file, upgrades #572

Closed jharenza closed 6 months ago

jharenza commented 6 months ago

Purpose/implementation Section

What scientific question is your analysis addressing?

This PR upgrades a few python packages due to newly introduced bugs in the consensus CN modules

What was your approach?

python 3.10.12-->3.11 snakemake 7.25.3-->8.1.2 pulp ? --> 2.8.0 install MM2S from GitHub

What GitHub issue does your pull request address?

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.