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bingmann / cobs

COBS - Compact Bit-Sliced Signature Index (for Genomic k-Mer Data or q-Grams)
https://panthema.net/cobs
MIT License
83 stars 15 forks source link

conda package #15

Open graceblackwell opened 4 years ago

graceblackwell commented 4 years ago

Hi Timo, Would it be possible to get a conda package for cobs? I am having trouble compiling on my Mac and being able to access cobs through conda would make it easy to get working. Thanks, Grace

bingmann commented 4 years ago

Hmm. I have no idea what a conda package is. Maybe someone knows how to make them?

luizirber commented 4 years ago

I'll try it, I think all deps are available in conda-forge

luizirber commented 4 years ago

https://github.com/bioconda/bioconda-recipes/pull/24326

issues to solve:

shenwei356 commented 3 years ago

Thank you @bingmann for this algorithm. I've rewriten cobs in Golang and like to compare them. But it's difficult to compile on our server cause the old compilers.

Looking forward @luizirber 's bioconda recipes.

I think all deps are available in conda-forge

Yes but some manual operations are needed. I spent two hours finguring out how to compile cobs on our server (CentOS 7.9 with gcc 4.8.5) using conda. May this helps.

Steps: https://github.com/bingmann/cobs/issues/16

johnlees commented 3 years ago

This would be useful for us too. @luizirber I've made a fresh attempt here which I think works, if you want to review: https://github.com/bioconda/bioconda-recipes/pull/27701

luizirber commented 3 years ago

The package is now available on bioconda. It would still be good to have tagged releases here and fix the bioconda recipe to use them, but thanks @johnlees for picking it up and submitting the bioconda recipe!

iqbal-lab commented 3 years ago

I'll have a chat with @bingmann about a release and see how he's doing more generally

iqbal-lab commented 3 years ago

Thanks so much for the contributions and work @luizirber @johnlees

johnlees commented 3 years ago

No problem at all!

Just to note from a conda perspective in case someone else updates the recipe after a release is made: I think the best way to update it would be to point the git_rev at the release tag and bump the build, but otherwise leave the recipe as-is (using git_url and uses_vcs_url rather than url). It would be a lot more difficult to rely on or build all of the submodules used through conda dependencies of their own, and the bioconda team have advised me against this before on a previous recipe which was similar to this one.