Entering edit mode
4.7 years 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!
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?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).
I am on Windows... can you recommend another alignment tool that will allow me to continue along the DESeq2 workflow in R?
Docker or WSL would probably be the easiest route.
thanks! I'll give it a shot
I'm a total beginner with Linux, is Ubuntu a good place to start or should I try a different distro?
Yea, I'd say Ubuntu is a good place to start.
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.