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balabanmetin / uDance

BSD 3-Clause "New" or "Revised" License
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Add Dockerfile + RAxML-NG #10

Closed niemasd closed 3 months ago

niemasd commented 3 months ago

Hey, Metin! I'm helping Rob Knight's lab run uDance on their cluster, and as part of that, I wanted to create a Docker container for it.

This PR includes the Dockerfile (as well as .devcontainer stuff needed to set up the environment automatically in VS Code / GitHub Codespaces).

It also adds raxml-ng to the install.sh script since RAxML-NG is on bioconda now without any conflicts.

balabanmetin commented 3 months ago

Hi Niema this pull request is very useful, thanks a lot. I will push this as soon as my tests finish. OSX installation (arm chip) is not working due to conda conflicts but it is not because of the changes you made. I am trying to address that now.

niemasd commented 3 months ago

No problem; happy to help! Sounds good; no rush

balabanmetin commented 3 months ago

CONDA_SUBDIR=osx-64 conda create -y -c bioconda -c conda-forge --channel smirarab --name udance python pip scipy pandas snakemake

even the Conda environment described above cannot be created in osx arm64 architecture anymore. I will add a notice to README for the users with Mac arm chip. I will approve these changes. I noticed that I introduced a bug in my last commit that prevents using raxml-ng. I will address that right after the merge.

balabanmetin commented 3 months ago

the bug is fixed. if you have created a docker image before the fix please redo using the latest version (1.6.5). Did you upload the image somewhere? I can add that to the README.

niemasd commented 3 months ago

I have a Docker image here (niemasd/udance):

https://hub.docker.com/r/niemasd/udance

It builds from this Dockerfile:

https://github.com/Niema-Docker/udance/blob/main/Dockerfile

The existing Docker image was built 4 days ago, so I just kicked off a new build of the Docker image based on your most recent updates (including this merged PR), and it should be ready in ~15 min

balabanmetin commented 3 months ago

the dockerfile in Niema-Docker repository is not up-to-date. rsync package is missing in that one. The docker file in the pull request has rsync package. I tested the image, it works after installing rsync via apt. Once you rebuild the Docker image with rsync I will add the link to the README.

niemasd commented 3 months ago

Woops, thanks for catching that! I just pushed the updated Dockerfile, and I just triggered another build. It should be ready in ~20 minutes (same link)

balabanmetin commented 3 months ago

OK I added the image link and instructions to the README. Thanks a lot Niema!

niemasd commented 3 months ago

No problem 😄