search

rrwick / Trycycler

A tool for generating consensus long-read assemblies for bacterial genomes
GNU General Public License v3.0
306 stars 28 forks source link

FileNotFoundError: [Errno 2] No such file or directory: 'minimap2' #58

Closed yusator closed 1 year ago

yusator commented 1 year ago

I have minimap2 installed in my Linux Ubuntu desktop. However, it is not on PATH, so I have to go directly into the folder to launch it. Despite executing trycycler in the minimap2 folder itself, it says it cannot locate it.

rrwick commented 1 year ago

If you can, I'd recommend copying the minimap2 executable file to somewhere in your PATH variable - that will make it easier to run in general. But if that's not an option, you can temporarily add it like this before running Trycycler:

export PATH=/your/path:"$PATH"

Replace /your/path with the full path of where your minimap2 file is.

Hope that helps!

yusator commented 1 year ago

Thank you for the advice. I did that but then a new error showed up of "PermissionError: [Errno 13] Permission denied: 'minimap2'". Im not sure how trycycler accesses permissions of the file

rrwick commented 1 year ago

You could give it maximum permissions like this:

chmod 777 minimap2

Does that fix it?