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Add ncbi egapx

Open richard-burhans opened this issue 1 year ago • 2 comments

Adding NCBI Eukaryotic Genome Annotation Pipeline - External (EGAPx)

FOR CONTRIBUTOR:

  • [X] I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
  • [X] License permits unrestricted use (educational + commercial)
  • [X] This PR adds a new tool or tool collection
  • [ ] This PR updates an existing tool or tool collection
  • [ ] This PR does something else (explain below)

richard-burhans avatar Oct 14 '24 19:10 richard-burhans

I start with NCBI's docker image from dockerhub and create a new one which includes an installation of Nexflow. The augmented container is uploaded to quay.io. The strategy is to run this augmented docker container on a single large node.

I'm working on a scheduled github action that will check for new versions of EGAPx on dockerhub, build new augmented containers, and upload them to quay.io. If someone already has something like this, I can just reuse it. If not, when it's ready I can submit the github action to the IUC as well.

richard-burhans avatar Oct 14 '24 20:10 richard-burhans

You can do something like that https://github.com/galaxyproject/tools-iuc/blob/cb7f20bd60570b9115fb8a9ce793dbe9b3fd65f5/tools/pbmm2/pbmm2.xml#L131 and cite the github repo of egapx

bgruening avatar Nov 01 '24 17:11 bgruening