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Salmon update on Linux

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.

linux salmon wsl
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updated by Antonio R. Franco Antonio R. Franco • written by Soumajit • Soumajit

bioconda or a docker container would be my go-to

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written by Asaf Asaf

2 answers

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.

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written by ATpoint ATpoint

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

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written by Antonio R. Franco Antonio R. Franco

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