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