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AlexsLemonade / alsf-scpca

Management and analysis tools for ALSF Single-cell Pediatric Cancer Atlas data.
BSD 3-Clause "New" or "Revised" License
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Update alevin-fry docker to 0.3.0 #94

Closed allyhawkins closed 3 years ago

allyhawkins commented 3 years ago

In starting to run samples with the splici index and narrow in on testing alevin-fry, it was necessary to update the current docker image to alevin-fry 0.3.0. The new image has now been built and pushed to the git hub repository and can be pulled using docker pull ghcr.io/alexslemonade/scpca-alevin-fry:0.3.0 or docker pull ghcr.io/alexslemonade/scpca-alevin-fry:latest.

allyhawkins commented 3 years ago

Question (not for this PR): do we also need to update salmon in the workflow to a more recent version?

The requirements for alevin-fry are to have salmon >= 1.4.0 which we have, but there are 2 docker images associated with 1.4.0 and we have the older one in our workflow now. I can update to the newer one 1.4.0--h84f40af_1 in our workflow but I don't think it should make a huge difference.

jashapiro commented 3 years ago

Question (not for this PR): do we also need to update salmon in the workflow to a more recent version?

The requirements for alevin-fry are to have salmon >= 1.4.0 which we have, but there are 2 docker images associated with 1.4.0 and we have the older one in our workflow now. I can update to the newer one 1.4.0--h84f40af_1 in our workflow but I don't think it should make a huge difference.

I don't think there is any reason to do that.. I actually noticed that salmon is now at 1.5.0, but there are no release notes I can find, so 🤷🏼 https://github.com/COMBINE-lab/salmon/releases/tag/v1.5.0