search

franciscozorrilla / metaGEM

:gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
https://franciscozorrilla.github.io/metaGEM/
MIT License
189 stars 41 forks source link

maintenance: check env installation recipes #90

Closed franciscozorrilla closed 2 years ago

franciscozorrilla commented 2 years ago

The metagem env recipe seems to not work properly when installing locally, with mamba unable to resolve dependencies for concoct and gtdbtk.

Currently testing the following: remove gtdbtk & concoct from mamba install/metagem recipe file, instead install in subsequent pip installations along with SMETANA etc.

Note that the recipe file works perfectly fine when setting up on the Cambridge cluster.

franciscozorrilla commented 2 years ago

Moving gtdbtk & concoct from mamba to pip installation seems to resolve the issue, however pip only has concoct version 0.4, whereas conda has the latest 1.1.0 version.