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I searched for the package 'snakemake' on my SLURM cluster using:

conda search --channel bioconda snakemake

and I get many versions, up to 5.4.2.

I then try to install it using:

conda install --channel bioconda --yes snakemake=5.4.2

but it fails with the following message:

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

  - snakemake

Current channels:

  - https://repo.anaconda.com/pkgs/main/linux-64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/free/linux-64
  - https://repo.anaconda.com/pkgs/free/noarch
  - https://repo.anaconda.com/pkgs/r/linux-64
  - https://repo.anaconda.com/pkgs/r/noarch
  - https://repo.anaconda.com/pkgs/pro/linux-64
  - https://repo.anaconda.com/pkgs/pro/noarch

Why?

Why is the bioconda channel not included in the current channels? I thought that was what the --channel bioconda did in my install command.

Note that conda install --channel bioconda --yes samtools=1.9 worked fine and installed samtools successfully.

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    $\begingroup$ I've heard some folks warn that conda is sensitive to the order in which channels are set/configured. I'm not exactly sure what the details are, but maybe that gives you somewhere to start troubleshooting? $\endgroup$
    – Daniel Standage
    Feb 25, 2019 at 14:52

1 Answer 1

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I created a file .condarc in my home directory with the following content:

channels:
  - conda-forge
  - bioconda
  - defaults

and it works now. I don't understand why this is necessary though. I thought the channels in the .condarc file would be used if I did not specify them in my command.

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    $\begingroup$ This seems to be a bug in the version of conda you're using, it works in 4.6.4. Note, however, that you needed to add -c conda-forge to your original command anyway, since many of the snakemake dependencies come from there. $\endgroup$
    – Devon Ryan
    Feb 26, 2019 at 22:21
  • $\begingroup$ good point about the dependencies. I didn't know about that. I just always give the channel of the package I want to install but it sounds like I also need to give the channel of dependencies. So I'll keep using -c conda-forge -c bioconda -c r in all my conda install commands. $\endgroup$
    – Biomagician
    Feb 27, 2019 at 11:05

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