Pangolin dependency checker flags missing usher even if not using --usher mode

[niemasd]

I'm trying to build a minimal Docker image for Pangolin using the Alpine base (without using conda), and I ran into issues setting up UShER while successfully setting up everything else, so given that I wasn't planning on using --usher mode for now, I gave up on trying to build UShER from scratch for now. However, when I try to run Pangolin as follows:

pangolin my_sequences.fasta

I still get an error from Pangolin's dependency checker saying that I'm missing the usher dependency, and the error prevents me from executing Pangolin, even though I'm not using --usher mode. It would be good to update the dependency checker to check which dependencies are actually being used based on the user's arguments, and only check for those specific dependencies.

Just in case anyone else runs into this, for now, my hacky workaround is that I just deleted "usher" from the list of dependencies in this file:

/usr/lib/python3.8/site-packages/pangolin/utils/dependency_checks.py

If you want something headless without manual editing, the following should work:

sed -i 's/,"usher"]/]#,"usher"]/g' /usr/lib/python3.8/site-packages/pangolin/utils/dependency_checks.py

(the exact path may differ based on how you installed pangolin)

[aineniamh]

Should be resolved now!