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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 docker image for Alevin-fry to v0.4.0 #112

Closed allyhawkins closed 3 years ago

allyhawkins commented 3 years ago

Closes #103. This PR updates the Dockerfile for alevin-fry to build the image with the most current version, 0.4.0, of alevin-fry. I've tested that the image contains the correct version by running the image interactively and testing alevin-fry --version.

I have also pushed this to github and tested that it can be pulled using: docker pull ghcr.io/alexslemonade/scpca-alevin-fry:latest or docker pull ghcr.io/alexslemonade/scpca-alevin-fry:0.4.0

rob-p commented 3 years ago

Since the salmon and fry containers are different, any salmon related bumps are probably done on a separate branch, but I just want to suggest bumping to salmon 1.5.1 while you're upgrading fry. The are some small but synergistic changes between the two tools in the latest version that leads to a little sensitivity boost (at leas in our testing on simulated data).

P.S. Somehow, @jashapiro, I am just learning about biocontainers. This is amazing!!!

allyhawkins commented 3 years ago

Since the salmon and fry containers are different, any salmon related bumps are probably done on a separate branch, but I just want to suggest bumping to salmon 1.5.1 while you're upgrading fry.

Yup! We reference the container for salmon in our nextflow workflow, so that is a separate update that is happening and is on our list.