Conda install fail?

[Morgan McCarthy]

Hi All, 

Is anyone having problems with the conda install of stacks v.2.61? 

I've been using the command conda install stacks and get the output pasted down below. I've tried installing it on two separate clusters and get the same error. It is possible to install version 1.44 with conda install -c bioconda/label/cf201901 stacks but this version lacks the gstacks function. Due to cluster permissions I can't install it directly myself which is why I'm trying to use conda install. Let me know if you've run into this error/have found a work around. Thanks in advance!

Cheers, Morgan

Collecting package metadata (current_repodata.json): done

Solving environment: failed with initial frozen solve. Retrying with flexible solve.

Collecting package metadata (repodata.json): done

Solving environment: failed with initial frozen solve. Retrying with flexible solve.

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

  - stacks

Current channels:

  - https://repo.anaconda.com/pkgs/main/linux-64

  - https://repo.anaconda.com/pkgs/main/noarch

  - https://repo.anaconda.com/pkgs/r/linux-64

  - https://repo.anaconda.com/pkgs/r/noarch

To search for alternate channels that may provide the conda package you're

looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.

[Rita Afonso]

Hi Morgan,

I already had the same issue but I don't know if the problem is the same.

In my case, I was not being able to install the newest version of stacks via conda because the conda environment I was using didn't have the needed versions of the stacks dependencies.
You can check stacks dependencies using this:

conda search -c bioconda --info stacks

Stacks v.61 needs python>3 and r-base>4 and I had older versions of these two. You can choose the versions you want when you create the conda environment:

conda create -n <name> python=x r-base=x

Hope it helps.

Cheers,

Rita