rgi v6.0.1 unable to install using conda

[jayramr]

Hi Team,

conda version -> 4.14.0 rgi -> 6.0.1

I followed below steps

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda create --name rgi rgi=6.0.1

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): -

Please advise

Thanks Jay

[apetkau]

So I have a similar issue to you @jayramr. Running the installation using mamba gives more information:

mamba create --name rgi --channel conda-forge --channel bioconda --channel defaults rgi=6.0.1
...
Looking for: ['rgi=6.0.1']

conda-forge/linux-64                                        Using cache
conda-forge/noarch                                          Using cache
bioconda/linux-64                                           Using cache
bioconda/noarch                                             Using cache
pkgs/main/noarch                                              No change
pkgs/r/linux-64                                               No change
pkgs/main/linux-64                                            No change
pkgs/r/noarch                                                 No change
Encountered problems while solving:
  - package rgi-6.0.1-pyha8f3691_0 requires lxml 4.6.5, but none of the providers can be installed

However, I did notice if I removed conda channel priorities (--no-channel-priority) it would install:

# This succeeds
mamba create --name rgi --channel conda-forge --channel bioconda --channel defaults --no-channel-priority rgi=6.0.1

I suspect there's incompatibilities with the package lxml version 4.6.5 that is available through different conda channels. You can remove the strict channel priorities when installing directly through conda, but this still remains an issue if installing the rgi tool in Galaxy (which uses it's own conda package and command to install).

[jayramr]

Thanks @apetkau i tried mamba which resolves the issue.

In my automation pipeline, it never looks for mamba binary. this i need to manually update. But for me without passing --no-channel-priority this succeeded.

Jay

[apetkau]

For --no-channel-priority it would only be needed if you have configured strict channel priority before conda config --set channel_priority strict (as described in the bioconda documentation: https://bioconda.github.io/).

[apetkau]

You may also want to look at conda-libmamba-solver, which should make the conda command act the same as mamba.

[jayramr]

Thanks for the advise :)

[StephanieAFlowers]

New user here. I am having the same issue, but need to designate a channel to use this on our University cluster. I have also tried to install older versions and am running into the same issue.

[jayramr]

@StephanieAFlowers you may try using mamba

[raphenya]

Thank you @apetkau