Running Biobakery tools from the QIB Cloud

Prerequisites

You need access to a VM at QIB Cloud! Follow these instructions if you don't have yet a running VM.

Installation

The tools can be either:

• installed using Conda

• Ran directly using one of the shared singularity images made available by the QIB Core Bioinformatics [TUTORIAL COMING SOON].

Access to the databases

To access the shared databases (and the singularity images), you will need to mount the "outgoing" Core bioinformatics folder to your VM.

mkdir ~/transfer

sudo mount.cifs  //smb.qib-hpc-data.ciscloud/Informatics/transfer ~/transfer -o domain=nr4,user=<YOUR NBI LOGIN>,uid=$(id -u),gid=$(id -g),mfsymlinks

Once mounted, the Metaphlan4 databases will be accessible at :

DB_DIR : "~/transfer/outgoing/databases/metaphlan4/metaphlan4"

- mpa_vJan21_CHOCOPhlAnSGB_202103
- mpa_vOct22_CHOCOPhlAnSGB_202403
- mpa_vJun23_CHOCOPhlAnSGB_202307

and the Humann3 databases will be accessible at :

MPA="~/transfer/outgoing/databases/humann_db/mpa/mpa_vOct22_CHOCOPhlAnSGB_202212"
HUMANN_NUC="~/transfer/outgoing/databases/humann_db/2023/chocophlan"
HUMANN_PROT="~/transfer/outgoing/databases/humann_db/uniref"

Running the tools on your VM

If you installed the tools using Conda, follow this tutorial for MetaphlAn4 and this tutorial for Humann3 to run the tools on your VM.

If you want to use the singularity images, this tutorial is the way to go [COMING SOON].