search

cdanielmachado / carveme

CarveMe: genome-scale metabolic model reconstruction
Other
149 stars 51 forks source link

Bioconda recipe #9

Closed SilasK closed 3 years ago

SilasK commented 6 years ago

Do you think you can make a bioconda recipe? It is very straight forward and handles also the dependencies.. thanks

cdanielmachado commented 6 years ago

Sure, I think that can be done. It would handle the diamond installation, but not cplex unfortunately.

darwinbandoy commented 5 years ago

same request- would it be possible to have it in miniconda

vinisalazar commented 3 years ago

Hi, is there any progress on this? I've submitted a couple of recipes to Bioconda before and would be happy to draft one for this package. However, it would be necessary for a core dev to step up as maintainer for the recipe.

cdanielmachado commented 3 years ago

To be honest this hasn't really been a priority. But I can do it if people think it really necessary, and I'd be happy to receive any help. What would be the advantage of the conda installer compared to the pip installer ?

vinisalazar commented 3 years ago

I believe the main advantage of a conda distribution is the automatic handling of dependencies, as mentioned by the original comment that started the issue. Apparently there is a conda distribution for cplex, so maybe it can also include that?

The conda recipe can be configured to download the tarball from PyPI, this way when you update the PyPI version, the conda distribution is automatically updated.

cdanielmachado commented 3 years ago

The only dependencies not handled by the pip installer are CPLEX and diamond, and CPLEX should not be installed via pip or conda, because that is the community edition, which does not support problems with more than 1000 variables.

vinisalazar commented 3 years ago

I see, thanks for clearing that :)