Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

adding medaka version 2.0.1 #1093

Merged
merged 2 commits into from
Nov 9, 2024
Merged

adding medaka version 2.0.1 #1093

merged 2 commits into from
Nov 9, 2024

Conversation

erinyoung
Copy link
Contributor

There's a new version of medaka!

According to the release notes, this fixes a bug in medaka smolecule.

I copied the files from 2.0.0, updated the version arg, removed some unnecessary ls lines, and removed the -vv flags.

The full diff:

< ARG MEDAKA_VER="2.0.0"
---
> ARG MEDAKA_VER="2.0.1"
77d76
<     ls && \
127,128c126,127
< RUN pip install medaka-cpu==${MEDAKA_VER} --extra-index-url https://download.pytorch.org/whl/cpu -vv --no-cache-dir && \
<     pip install pyabpoa==${PYABPOA_VER} -vv --no-cache-dir
---
> RUN pip install medaka-cpu==${MEDAKA_VER} --extra-index-url https://download.pytorch.org/whl/cpu --no-cache-dir && \
>     pip install pyabpoa==${PYABPOA_VER} --no-cache-dir

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

erinyoung and others added 2 commits October 30, 2024 22:44
…larity.yml to use a different runner and more importantly apptainer github action to see if it will appropriately test singularity/apptainer functionality
@kapsakcj
Copy link
Collaborator

kapsakcj commented Nov 9, 2024

OK I made some minor changes to silence some warnings and such to the dockerfile and readme for medaka

FYI I also updated the run-singularity.yml github actions workflow to see if we can get the singularity/apptainer test to run appropriately when deploying docker images.

I won't know if it works until I try deploying this docker image, but if it's broken then it shouldn't matter as it's the last step in the manual-deploy GHActions workflow and the images should already be pushed to dockerhub and quay prior to the singularity/apptainer test running 🤞

It's now using this pre-built action from the marketplace: https://github.com/marketplace/actions/setup-apptainer

Copy link
Collaborator

@kapsakcj kapsakcj left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

will merge and deploy now. Hopefully the update to the singularity/apptainer ghactions workflow works!

@kapsakcj kapsakcj merged commit eaefbcf into master Nov 9, 2024
2 checks passed
@kapsakcj kapsakcj deleted the erin-medaka branch November 9, 2024 17:34
@kapsakcj
Copy link
Collaborator

kapsakcj commented Nov 9, 2024

deploy workflow here: https://github.com/StaPH-B/docker-builds/actions/runs/11758179241

thank you for the PR!

@kapsakcj
Copy link
Collaborator

kapsakcj commented Nov 9, 2024

OK! It worked! The Github action downloaded the staphb/medaka:latest docker image, converted it into a SIF (singularity image format) and then ran the pwd command.

We could further improve this and perhaps try to run tests via the singularity image, but at least we got the github actions workflow fixed and at least showing that we can convert the docker image to SIF

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

2 participants