Salmon update on Linux

Question

[Soumajit]

Hello,

I am using windows subsystem Linux for sequencing analysis purposes on a Windows machine. With sudo apt install salmon the version installed is 0.12.0., which is quite an old release and lacks a few upgraded options (such as the decoy option). I have used sudo apt upgrade salmon as the result says salmon is already the newest version (0.12.0+ds1-1)

Can anyone please recommend how to get or install v1.9.0 on Linux or at least the version which is capable of understanding decoy commands?

Thanks a lot.

[Asaf]

bioconda or a docker container would be my go-to

Answer 1

[ATpoint]

I would go for the official Linux binary:

wget -q https://github.com/COMBINE-lab/salmon/releases/download/v1.9.0/salmon-1.9.0_linux_x86_64.tar.gz
tar zxf salmon-1.9.0_linux_x86_64.tar.gz
export PATH=$PATH:path/to/salmon-1.9.0_linux_x86_64/bin

I personally had trouble with conda as it (depending on what else is in the env) downgrades salmon to ancient versions, the binary is easier.

Answer 2

[Antonio R. Franco]

This is a widespread problem when trying to install packages. I mean that it is not advisable to install programs or binaries using sudo apt install