Funannotate check does not recognize samtools

Open dgslos opened this issue 2 years ago • 1 comments

The output of funannotate check shows: ERROR: samtools found but error running samtools ERROR: samtools not installed

However, samtools 1.13 is installed and working.

A quick test makes me suspect it has something to do with the UTF-8 coding of the stdout in the subprocess command of the check script. Maybe the problem is in the 'universal_newlines=True' argument. Can this be checked?

Cheers, Dieter

Oct 20 '23 09:10 dgslos

can you provide more information on the operating system, version of python, version of funannotate you are testing. This tests and works on a variety of unix and osx machines

Oct 24 '23 17:10 hyphaltip