Conda install

[ndeimler99]

For some reason I am having issues with the conda install command "conda install -c bioconda agat". It is not a conda issue as other bioconda packages install perfectly fine. However, with agat I get the solving environment: and then it will just sit there and spin for hours.

According to the bioconda website this would be AGAT v1.0.0 with conda version 23.1.0.

I have also run the following commands to ensure the proper channels are established.

conda config --add channels defaults conda config --add channels bioconda conda config --add channels conda-forge conda config --set channel_priority strict

Thanks for any advice.

[Juke34]

Force the version you want to install I.e agat=1.0.0 it might help

[Rafaelsoler13]

Same problem here. Also with force

PackagesNotFoundError: The following packages are not available from current channels:

• agat=1.0.0

[Juke34]

Apparently there is an annoying dependency. Are you on MacOS, linux? Did you try to install it via mamba? (to make it faster) Remove the strict priority it can help: conda config --set channel_priority false

[eduardo-pizarro]

I faced the same issue. The only way I could resolve it was install AGAT using mamba mamba create -n agat -c bioconda agat

[kdm9]

I faced the same issue. The only way I could resolve it was install AGAT using mamba mamba create -n agat -c bioconda agat

Even this didn't work for me, but I think the issue is with a dependency: the version of perl-lwp-simple agat=1.0.0 requires isn't available for any installable version of perl. I've bumped the build numbers of both agat and perl-lwp-simple in https://github.com/bioconda/bioconda-recipes/pull/40365 which hopefully fixes it, but the problem might be in more dependencies (or deeper still)

[Juke34]

Thank you for the feedbacks, let's have a look

[Juke34]

Could it be linked to libgcc-ng and the python version used by conda the problem as in https://github.com/NBISweden/AGAT/issues/330?

Currently on my OSX the recipe is working (using python 3.10.9 )... Could you share your conflict / error messages?

[kdm9]

$ mamba create -n agat1 -c bioconda -c conda-forge agat=1.0

                  __    __    __    __
                 /  \  /  \  /  \  /  \
                /    \/    \/    \/    \
███████████████/  /██/  /██/  /██/  /████████████████████████
              /  / \   / \   / \   / \  \____
             /  /   \_/   \_/   \_/   \    o \__,
            / _/                       \_____/  `
            |/
        ███╗   ███╗ █████╗ ███╗   ███╗██████╗  █████╗
        ████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
        ██╔████╔██║███████║██╔████╔██║██████╔╝███████║
        ██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
        ██║ ╚═╝ ██║██║  ██║██║ ╚═╝ ██║██████╔╝██║  ██║
        ╚═╝     ╚═╝╚═╝  ╚═╝╚═╝     ╚═╝╚═════╝ ╚═╝  ╚═╝

        mamba (0.16.0) supported by @QuantStack

        GitHub:  https://github.com/mamba-org/mamba
        Twitter: https://twitter.com/QuantStack

█████████████████████████████████████████████████████████████

Looking for: ['agat=1.0']

bioconda/linux-64        [====================] (00m:00s) No change
bioconda/noarch          [====================] (00m:00s) No change
pkgs/r/linux-64          [====================] (00m:00s) No change
pkgs/r/noarch            [====================] (00m:00s) No change
pkgs/main/linux-64       [====================] (00m:00s) No change
pkgs/main/noarch         [====================] (00m:00s) No change
kdm801/noarch            [====================] (00m:00s) No change
kdm801/linux-64          [====================] (00m:00s) No change
conda-forge/noarch       [====================] (00m:02s) Done
conda-forge/linux-64     [====================] (00m:06s) Done
Encountered problems while solving:
  - package agat-1.0.0-pl5321hdfd78af_0 requires perl-lwp-simple >=6.39, but none of the providers can be installed

It's unlikely the exact same issue, as I'm not installing python and am using conda-forge already.

[Juke34]

Specifying a version of perl (not the latest) does not help?

[kdm9]

I did try that, but then there was a different version of the same phenomenon on a different dependency (which required the latest perl)

[kdm9]

the version bumps in the above bioconda PR seem to have fixed this for me. @Juke34 can you please test on OSX?

[Juke34]

I confirm on OSX it is still working. Thank you for your help @kdm9

[alexbougdour]

Same problem to install agat using conda on a fresh install of ubuntu 22.04.

conda install -c bioconda agat=1.0.0 Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: / is running forever Thank you in advance for anything you can do, Alex

[kdm9]

Try using mamba? I gave up on conda itself a while ago for this reason among others -- it is slow to find solutions, and often fails to in strange cases.

I'd also try creating a fresh environment: mamba create -n agat bioconda::agat

[kcmtest]

I faced the same issue. The only way I could resolve it was install AGAT using mamba mamba create -n agat -c bioconda agat

this worked conda installation somehow doesn't work