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sii-companion / companion

A genome annotation tool for more than just protists
https://companion.ac.uk/
ISC License
6 stars 3 forks source link

/usr/bin/env: ‘gt’: No such file or directory #50

Closed anearman closed 8 months ago

anearman commented 8 months ago

Hello! I have installed and run the example project with no issues. When adjusting config files and directories for my own project, everything goes well up until ../../bin/update_references.lua where I receive the following error:

/usr/bin/env: ‘gt’: No such file or directory

"gt" is listed in the shebang for that script but I can find no reference to it that I understand. Can you help troubleshoot this issue?

Ubuntu 22.04.03 LTS 13th Gen Intel® Core™ i9-13900K × 32

haessar commented 8 months ago

Hi, thanks for using Companion. Can you ensure you have genometools installed (see https://github.com/genometools/genometools?tab=readme-ov-file#building-and-installation) and following this that you can now call "gt --version" in the command line?

anearman commented 8 months ago

That was it, thanks! The script worked and the annotation is running now. I read GenomeTools as a requirement in the preparing references wiki and thought I had it installed. Must be on my work machine.

Appreciate the quick reply!