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.
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.
Some users do not have
conda-forge
as a channel for their conda configuration. Many tools available viaconda
rely on theconda-forge
channel.For example:
```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: ```conda create -n autometa -c bioconda autometa
results in an
UnsatisfiableError
To avoid conda errors for these users, we should explicitly specify
-c conda-forge
during the install (or mention adding thebioconda
andconda-forge
channels in the user'sconda
configuration.I.e.
We should also replace
conda
commands withmamba
(also includingmamba
installation prior tomamba
commands) to decrease the time it takes for the user to get started.https://github.com/KwanLab/Autometa/blob/baf61c04dddf5b33bb825dba2841de1e38dffefe/docs/source/bash-workflow.rst?plain=1#L24