update salmon with conda
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12 months ago
eridanus ▴ 30

I have installed Salmon with conda. However, I think that an old version has been installed (I get some errors). How could I update with conda? I have tried conda update salmon but nothing happened. I could not install manually that s the reason I used conda. Any solutions? Thank you!

RNA-Seq • 1.2k views
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3
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12 months ago

Make sure conda-forge and bioconda are in your channels: conda install -c conda-forge -c bioconda salmon=1.3.0. I assume you're not running this on Windows, since we (Bioconda) only ship for Linux and OSX at the moment.

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12 months ago
Rob 4.9k

Have you tried conda install salmon=1.3.0, to specifically request the latest version? Sometimes, there are strange package conflicts, and so the other thing you can try is to create a new, blank, environment, and install salmon there.

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thank you for your answer! I tried your suggestion and it says PackagesNotFoundError..hmm maybe should I try docker..?

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Let me tag @Devon Ryan here as well, since he may have an idea what's going on with bioconda.

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12 months ago

PackagesNotFoundError: Do you have the bioconda channel available? You can check with:

conda config --show channels

Which should print something like:

channels:
  - conda-forge
  - bioconda
  - defaults

If you don't see bioconda there, check the installation instructions to fix it.

Also, I would suggest switching to mamba for installing packages (consider that snakemake recommends installing with mamba so it should be pretty reliable)

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