KwanLab / Autometa

Autometa: Automated Extraction of Genomes from Shotgun Metagenomes
https://autometa.readthedocs.io
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Replace `conda` commands with `mamba` and add `-c conda-forge` channel to `mamba install autometa` #331

Closed evanroyrees closed 10 months ago

evanroyrees commented 11 months ago

Some users do not have conda-forge as a channel for their conda configuration. Many tools available via conda rely on the conda-forge channel.

For example:

conda create -n autometa -c bioconda autometa ```console Collecting package metadata (current_repodata.json): done Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: / Found conflicts! Looking for incompatible packages. This can take several minutes. Press CTRL-C to abort. failed UnsatisfiableError: ```

results in an UnsatisfiableError

To avoid conda errors for these users, we should explicitly specify -c conda-forge during the install (or mention adding the bioconda and conda-forge channels in the user's conda configuration.

I.e.

conda config --append channels bioconda
conda config --append channels conda-forge

We should also replace conda commands with mamba (also including mamba installation prior to mamba commands) to decrease the time it takes for the user to get started.

conda install -n base -c conda-forge mamba

https://github.com/KwanLab/Autometa/blob/baf61c04dddf5b33bb825dba2841de1e38dffefe/docs/source/bash-workflow.rst?plain=1#L24