Question

update salmon with conda

2

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4.0 years ago

eridanus ▴ 40

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 • 7.0k views

ADD COMMENT • link updated 2.2 years ago by jpcourneya • 0 • written 4.0 years ago by eridanus ▴ 40

score 4 · Answer 1 · 2020-10-16

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4.0 years ago

Devon Ryan 104k

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.

ADD COMMENT • link 4.0 years ago by Devon Ryan 104k

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Hi thanks for this answer Devon Ryan as it ultimately led to the solution to my salmon update. however i am wondering why conda update salmon without salmon=1.9.0 doesnt look for the current version or update to the current version. Trying to understand bioconda better. Thanks!

ADD REPLY • link 2.2 years ago by jpcourneya • 0

score 2 · Answer 2 · 2020-10-16

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4.0 years ago

Rob 6.9k

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.

ADD COMMENT • link 4.0 years ago by Rob 6.9k

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

ADD REPLY • link 4.0 years ago by eridanus ▴ 40

2

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

ADD REPLY • link 4.0 years ago by Rob 6.9k

score 1 · Answer 3 · 2020-10-16

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)