Having trouble running Salmon in Anaconda prompt
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17 months ago
zal4002 • 0

I have un/reinstalled anaconda entirely several times but no matter what I do I keep getting an error message about how Salmon is not available from the channels I have open - even though I have conda-forge and bioconda as my first channels.

I even tried to download the .tar.gz file from GitHub and I cannot run the program or create an environment like they do in the Salmon documentation. I have a suspicion that this has something to do with running McAffee on my computer but am hoping to be proven wrong or to get some advice about how to get around/replace McAffee.

Please help!

software error anaconda Salmon python • 848 views
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Are you on Windows? If so then you cannot run salmon, it is a Unix-based tool. In that case a dual-boot setup or VM would be an option.

If not, what is the exact output when you run conda install -c bioconda salmon?

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I believe it also works under WSL, but I'm not sure about the combination of conda+WSL.

Regarding the VM solution, we also provide an official docker image on dockerhub (combinelab/salmon).

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I am on Windows... can you recommend another alignment tool that will allow me to continue along the DESeq2 workflow in R?

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Docker or WSL would probably be the easiest route.

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thanks! I'll give it a shot

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I'm a total beginner with Linux, is Ubuntu a good place to start or should I try a different distro?

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Yea, I'd say Ubuntu is a good place to start.

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The other thing to try if you can't get things installed on your system is to go to usegalaxy.org. They have a lot of tools, including salmon, though you'll have to upload your fastqs to their site.

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