update Trinity -> v2.11.0

Question

[adampepper313]

Hi,

I am working on a project and I need to use Trinity, but whenever try to run Trinity, I am constantly receiving an update message:

** NOTE: Latest version of Trinity is v2.11.0, and can be obtained at: https://github.com/trinityrnaseq/trinityrnaseq/releases

Followed by,

Trinity Trinity-v2.11.0 requires salmon to be installed.  Get it here: https://combine-lab.github.io/salmon/  at /usr/local/bin/Trinity line 3973.

I am just unsure how to add this download onto command line and how download salmon.

I am running all my commands on command-line using secure shell as my program.

Any suggestions would be kindly appreciated!

[GenoMax]

If you are unsure about how to install programs then follow this guide (just the first part that deals with conda) to install trinity: Creating workflows with snakemake and conda .

The message that you get at the beginning is just a NOTE it can be ignored. Your problem is that whoever has installed trinity on the server that you are using does not have an install of a different program called salmon available.