Description
I encountered a database installation issue when running:
biobakery_workflows_databases --install wmgx --location biobakery_workflows_databases
The installation failed during the HUMAnN UniRef database download step.
Environment
biobakery_workflows v4.0.0a1
humann v4.0.0.alpha.1
OS:
Ubuntu Linux
Error
The workflow internally runs:
humann_databases --download uniref uniref90_diamond biobakery_workflows_databases/humann
which produces:
ERROR: Please select an available build.
Investigation
Running:
humann_databases --available
shows:
uniref : uniref90_ec_filtered_diamond
but NOT:
uniref90_diamond
So it appears that biobakery_workflows still references an older HUMAnN database build name.
Inside biobakery_workflows/biobakery_workflows_databases.py, the following is currently used in line 180:
run_command(["humann_databases","--download","uniref","uniref90_diamond",humann_install_folder])
However, current HUMAnN v4 alpha only exposes:
uniref90_ec_filtered_diamond
Workaround
Manual installation succeeds with:
humann_databases --download uniref uniref90_ec_filtered_diamond biobakery_workflows_databases/humann
Suggested Fix
Update:
"uniref90_diamond"
to:
"uniref90_ec_filtered_diamond"
inside:
biobakery_workflows/biobakery_workflows_databases.py