search

andersen-lab / Freyja

Depth-weighted De-Mixing
BSD 2-Clause "Simplified" License
100 stars 29 forks source link

pyarrow missing from conda environment in v1.5.1 #244

Closed ktmeaton closed 1 week ago

ktmeaton commented 1 week ago

Describe the bug Hi Freyja team! Really excited about the v1.5.1 release, and I've started testing the latest datasets that are provided in feather format. When running in conda, I get the following error:

ImportError: Missing optional dependency 'pyarrow'. Use pip or conda to install pyarrow.

I wonder if the bioconda recipe needs pyarrow in it's dependencies? https://github.com/bioconda/bioconda-recipes/blob/6627a6c8b9c760ed52d19151452631a296573df3/recipes/freyja/meta.yaml

To Reproduce

micromamba create --yes -n freyja-1.5.1 bioconda::freyja=1.5.1
conda activate freyja-1.5.1
freyja demix --barcodes usher_barcodes06_21_2024-00-49.feather <VARIANTS> <DEPTHS>
joshuailevy commented 1 week ago

Thanks @ktmeaton! Good catch - seems that new dependency didn't quite make it to bioconda-recipes. I've just made a PR to take care of this here: https://github.com/bioconda/bioconda-recipes/pull/48788

Josh

ktmeaton commented 1 week ago

Thank you so much! I just tested the new environment and it works perfect for the new feather datasets. Thank you!

joshuailevy commented 1 week ago

No problem! Glad that's sorted. Thanks for your help!