sbx-metaphlan

Sunbeam extension for running MetaPhlAn2, adapted from zhaoc1's sunbeam_neutrino.

Installation

git clone https://github.com/sunbeam-labs/sbx_metaphlan
cat sunbeam/extensions/sbx_metaphlan/config.yml >> sunbeam_config.yml

Running

This extension uses an isolated Conda environment for the MetaPhlAn2 installation, so you need to include the --use-conda argument when running Sunbeam:

sunbeam run --configfile=sunbeam_config.yml --use-conda all_metaphlan

The default MetaPhlAn2 database will be downloaded and stored inside the original Sunbeam Conda environment in $CONDA_PREFIX/opt/metaphlan_databases.