ERROR:vcontact2: Could not find Diamond in $PATH.

[Former user]

When running vcontact2: ERROR:vcontact2: Could not find Diamond in $PATH. ERROR:vcontact2: Could not find MCL (specifically mcxload) in $PATH.

however both commands are in $PATH when I try either:

echo $PATH
which diamond

or

import os
import shutil

print(os.environ["PATH"])

locate = shutil.which('diamond')
print(locate)

the vcontact2 script looks fine to me, so I do not know what to do

[Ben Bolduc]

I’m assuming vConTACT2 was installed via Anaconda? or is it bleeding edge? (via bitbucket?)

Looks like they’re in your PATH and available to the system, but not vConTACT2…

Which version of vConTACT2 are you using? I admit I need to update the Bioconda package with the latest version.

-Ben

[Ben Bolduc]

Should be resolved with recent update(s) to setup.py, recommended Anaconda install instructions, and/or Singularity definition file.

Please re-open if issue persists!