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Teichlab / bracer

BraCeR - reconstruction of B cell receptor sequences from single-cell RNAseq data
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Dockerfile needs to change Phylip download link #81

Closed ulyssebaruchel closed 1 month ago

ulyssebaruchel commented 2 months ago

Hi, The Phylip link in the Dockerfile does not work anymore. I think it must be replaced by https://phylipweb.github.io/phylip/download/phylip-3.697.tar.gz.

And I think this has been raised before, but I was wondering if there was any plan to make a bioconda package for BraCeR, please? Or at least a Singularity biocontainer maybe?

Thank you

NickEngland commented 1 month ago

Hi @ulyssebaruchel,

Thank you for bringing this to my attention, I've fixed the Phylip download link in the docker file.

We don't currently have plans to make a bioconda package, would a singularity biocontainer be more useful than the current docker container which can be converted to singularity?

ulyssebaruchel commented 1 month ago

Dear @NickEngland, thank you for your answer. A functional and ready-made singularity biocontainer would amazing, please, especially because a colleague and I have not been able to build the Docker image from the Docker file even after fixing the Phylip link and trying to fix other errors that popped up. And our HPC cluster does not support Docker for safety reasons (root / sudo access needed I believe).

NickEngland commented 1 month ago

Hi @ulyssebaruchel , I've pushed https://github.com/Teichlab/bracer/releases/tag/v0.2.1 with an attached Singularity container for now. It's not biocontainer compliant, but I don't have the time to make those changes right now. If you do, feel free to issue a pull request!

ulyssebaruchel commented 1 month ago

Dear @NickEngland, thank you so much! Will try to do it if a pipeline using it gets deployed or published.

NickEngland commented 1 month ago

Great! Let me know how you get on. I'll close this issue now.