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transcript / samsa2

SAMSA pipeline, version 2.0. An open-source metatranscriptomics pipeline for analyzing microbiome data, built around DIAMOND and customizable reference databases.
GNU General Public License v3.0
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Help with scripts #38

Closed mradz19 closed 4 years ago

mradz19 commented 4 years ago

I'm new to running bash scripts so I was hoping to get some advice...

I downloaded samsa2 and have tried following the guidelines for installation using the scripts in the setup_and_test folder.

I have used gmod +x to give executable permission to the scripts and I try to run them using:

bash pathway_to_script.sh

When doing this I get the following error:

package_installation.bash: line 32: package_installation.bash/../bash_scripts/lib/common.sh: Not a directory

When looking at the script I see this line:

Set pathway for SAMSA to location of samsa2 GitHub download:

IGNORE_DEPS=1 source "${BASH_SOURCE%/*}/../bash_scripts/lib/common.sh"

What is the correct way to set this pathway? Do I need to delete the whole line as it is and add in the path to the samsa2 download or is there another way to do it?

Thanks for your help!

transcript commented 4 years ago

Simple fix - run the command as follows (note the slash for location):

bash ./package_installation.bash

Longer fix - it looks like if the path (including current directory) isn't provided, this line throws an error. I'll see if I can write an error handling fix for this and update the repo.

transcript commented 4 years ago

Added an error handler in commit #63519f45c05ac22c7b19b19d77890a50f1312a7a.