HumanN2 Databases on VirtualBox VM

Microbial community profiling HUMAnN
1

I have a question for you regarding the VirtualBox VM for the BioBakery suite of tools. I am trying to run HumanN2, but I do not have the ability to add the full chocophlan or uniref directories beyond the included demo files-- I get a permission denied error (see below):

vagrant@biobakery:/usr/local/lib/python2.7/dist-packages/humann/data$
humann_databases --download chocophlan full /usr/local/lib/python2.7/dist-packages/humann/data
Creating subdirectory to install database: /usr/local/lib/python2.7/dist-packages/humann/data/chocophlan
CRITICAL ERROR: Unable to create directory: /usr/local/lib/python2.7/dist-packages/humann/data/chocophlan

Is there any way that this could be updated to add additional functionality? As always, thank you very much for your time and consideration, and thank you for developing/maintaining this great set of tools with such care.

Best,

LRB

2

Hello LRB, If you add “sudo” to the beginning of your command it will give you permission to write to the install folder. Sorry we can’t include the full databases in the VM by default because it would make the image very large.

Thank you,
Lauren