salmon command not found from shell

Question

[martijnhoes5]

Hi all, I'm using Salmon to align fastq files to an index genome and I've installed all associated packages (as far as I know). When I call salmon from the terminal, everything runs fine. I previously used a shell script to automate alignment for multiple files, but I suddenly get the error messages "salmon: command not found" and "gzip: command not found".

The command I use in terminal (single files) is:

salmon quant -i human_index --libType A -r /Rprojects/Sweet_et_al/fastq/SRR7426123.fastq -o /Rprojects/Sweet_et_al/quant/SRR7426123

The shell script I use looks like this:

#!/bin/bash
PATH="/media/manager/HDD_Martijn/RNAseq"
for i in {123..130}
do
salmon quant -i ${PATH}/salmon/human_index --libType A -r ${PATH}/Rprojects/Sweet_et_al/fastq/SRR7426${i}.fastq -o ${PATH}/Rprojects/Sweet_et_al/quant/SRR7426${i}
gzip ${PATH}/Rprojects/Sweet_et_al/quant/SRR7426${i}/quant.sf
done

It used to work just fine, but I haven't used it in a while. Something is wrong and I'm not very familiar with Linux. Can anyone help me figure this out? Any and all suggestions would be greatly appreciated! Thank you.

Answer 1

[WouterDeCoster]

You should not use PATH as a variable, as you are overwriting the $PATH environmental variable which tells your shell where to find executables (such as gzip and salmon)

[martijnhoes5]

Hi Wouter, this is great! Thanks for your help. That fixed it I wasn't aware that I was overwriting the PATH variable.