search

maxplanck-ie / snakepipes

Customizable workflows based on snakemake and python for the analysis of NGS data
http://snakepipes.readthedocs.io
381 stars 85 forks source link

Develop #977

Closed katsikora closed 8 months ago

katsikora commented 8 months ago

I had to drop the speedup version as it resulted in the package not being included in the build and snakePipes erroring out later on.

WardDeb commented 8 months ago

Does this also warrant the same change in the action env ? (snakePipesEnvCI.yml)

katsikora commented 8 months ago

Does this also warrant the same change in the action env ? (snakePipesEnvCI.yml)

Good question... The tests ran through, so I guess this can be now left as is. I wonder if it's the difference in python version, or in the solver. The GHA workflow uses micromamba, I'm using conda build locally. There is also a difference in the channels, I'll test briefly if adding defaults would fix the build issue. Thanks for your help :pray:

katsikora commented 8 months ago

Running conda build -c conda-forge -c bioconda -c defaults conda-recipe instead of conda build -c conda-forge -c bioconda conda-recipe doesn't solve the issue, I still get ModuleNotFoundError: No module named 'thefuzz' Tests failed for snakepipes-2.8.0-py_0.tar.bz2 .

I'll go ahead with the PR then.