Manual Installation of kneaddata_db_human_genome

Infrastructure and utilities bioBakery workflows
1

Dear all,

I think this is a simple fix, but the proper code isn’t apparent to this newbie.

I am currently attempting to use bioBakery Workflows in my Universities research computing cluster. I have successfully installed biobakery_workflows (v.3.1) with the core requirements, KneadData (v.0.12.0), MetaPhlAn (v.4.0.6), HUMAnN (v.3.6), and botie2 (v.2.5.1). StrainPhlAn was unsuccessful, but I don’t need this tool and will just quiet when implementing the workflow (i.e., --bypass-strain-profiling).

Issue: I attempted to run with some sequences; however it appears not all of the shotgun databases were installed (i.e., wmgx). Upon assessing my ‘biobakery_workflows_databases’ directory I noticed I only have the following:

humann/ strainphlan_db_markers/ strainphlan_db_reference/

I do not have: kneaddata_db_human_genome

Error Message:

ERROR: Unable to find bowtie2 index files in directory: /home/aemohr/biobakery_workflows_databases/kneaddata_db_human_genome

I understand this can be installed manually as described here (GitHub - biobakery/biobakery_workflows: bioBakery workflows is a collection of workflows and tasks for executing common microbial community analyses using standardized, validated tools and parameters.) but I’m not understanding how to generate the code.

Also, I am aware this has been discussed before (How to install biobakery_workflows database manually), but it is still not clear to me. Apologies!

Thank you for your help!

2

Hello @Alexander ,
Thank you for reaching out to the biobakery lab. It seems like only half of the workflow databases have been installed on your side. Can you try following steps to get the full database installed please?

$ biobakery_workflows_databases --install $WORKFLOW

- Replace $WORKFLOW with the workflow name (ie wmgx, 16s, wmgx_wmtx, or wmgx_demo, isolate_assembly).

Regards,
Sagun

3

Thanks, Sagun.

Yes, I have already run this general command using the below and the databases I listed in the op still didn’t load.

$ biobakery_workflows_databases --install wmgx