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DecodeGenetics / Ratatosk

Hybrid error correction of long reads using colored de Bruijn graphs
BSD 2-Clause "Simplified" License
94 stars 7 forks source link

Remove bifrost from code and add it as a requirement #45

Closed loraine-gueguen closed 1 year ago

loraine-gueguen commented 1 year ago

Hello! Do you think that it would it be possible to remove bifrost from the code (and from build) and add it as a requirement ? Using the bioconda package maybe ? (https://bioconda.github.io/recipes/bifrost/README.html) It would be a "best practice" for conda packaging, in particular. See https://github.com/bioconda/bioconda-recipes/pull/37864 Regards, Loraine

GuillaumeHolley commented 1 year ago

Hi @loraine-gueguen

Thank you for your work on the conda recipe, I really appreciate it. I see one major problem to removing Bifrost as a submodule from this repository and from the installation: Bifrost's bioconda package is compiled for k<32 while Ratatosk needs Bifrost to enable k<64. It would also become an issue to have Bifrost as a requirement in the source install: it happens that some users have Bifrost already installed with k<32 but k<63 is needed for Ratatosk. So compiling and linking Ratatosk with Bifrost k<32 would fail with errors that would be hard to solve for anyone.

I don't see an easy solution to this but I am all ears if you have an idea in mind.

Guillaume

loraine-gueguen commented 1 year ago

ok, thanks for the explanation: the cloning and build steps for bifrost have been kept in the conda recipe.

The PR has been merged and Ratatosk is now available as a bioconda package: https://anaconda.org/bioconda/ratatosk