Pangolin with added XDG_CACHE_HOME=/tmp

[erinyoung]

This Dockerfile is the exact same as 4.3.1-pdata-1.23.1 with one very key exception : "XDG_CACHE_HOME=/tmp" is now set in the same ENV layer as PATH. Therefore, the corresponding README is exactly the same.

This appears to resolve the issue mentioned in #802.

You can test it on your end from our repo on quay : quay.io/uphl/pangolin:tmp

I was thinking the tag for this one would be 4.3.1-pdata-1.23.1-1 - although I'm open to other suggestions.

Pull Request (PR) checklist:

• Include a description of what is in this pull request in this message.
• The dockerfile successfully builds to a test target for the user creating the PR. (i.e. docker build --tag samtools:1.15test --target test docker-builds/samtools/1.15 )
• Directory structure as name of the tool in lower case with special characters removed with a subdirectory of the version number (i.e. spades/3.12.0/Dockerfile)
  • (optional) All test files are located in same directory as the Dockerfile (i.e. shigatyper/2.0.1/test.sh)
• Create a simple container-specific README.md in the same directory as the Dockerfile (i.e. spades/3.12.0/README.md)
  • If this README is longer than 30 lines, there is an explanation as to why more detail was needed
• Dockerfile includes the recommended LABELS
• Main README.md has been updated to include the tool and/or version of the dockerfile(s) in this PR
• Program_Licenses.md contains the tool(s) used in this PR and has been updated for any missing

[kapsakcj]

Since it's now available (and recommended by pangolin developers), I've upgraded the usher version to 0.6.3.

Also fixed an odd link in the readme for orthofinder. Something odd going on with dockerhub API (badge shows error 500) so maybe changing the capitalization in the link didn't really do anything? Either way all the dockerhub urls for orthofinder are now uniform.

[kapsakcj]

I tested the docker image quay.io/uphl/pangolin:tmp in a few different ways to confirm the added environmental variable will not negatively impact other users:

• local docker run as root user ✅
• local docker run as non-root user ✅
• cloud usage via WDL workflow run on Terra.bio (where cromwell workflow management software runs the container as root) ✅

Everything ran as expected. Thanks for making this image available for testing.

I'll use the docker image tag as you suggested 4.3.1-pdata-1.23.1-1

[kapsakcj]

please delete your dev branch when you are finished with it

deploy workflow here: https://github.com/StaPH-B/docker-builds/actions/runs/7106482940

Thank you for the bug report and fix for this docker image!

[erinyoung]

Thank you!