Closed jayramr closed 1 year ago
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).
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
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/).
You may also want to look at conda-libmamba-solver, which should make the conda
command act the same as mamba
.
Thanks for the advise :)
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.
@StephanieAFlowers you may try using mamba
Thank you @apetkau
Hi Team,
conda version -> 4.14.0 rgi -> 6.0.1
I followed below steps
Please advise
Thanks Jay