recipe gmwi2

Enhanced Health Status Prediction from Gut Microbiome Taxonomic Profiles

Homepage:

https://github.com/danielchang2002/GMWI2

License:

MIT / MIT

Recipe:

/gmwi2/meta.yaml

GMWI2 (Gut Microbiome Wellness Index 2) is a robust and biologically interpretable predictor of health status based on gut microbiome taxonomic profiles. On a stool metagenome sample, this command-line tool performs four major steps: (1) Quality control; (2) Taxonomic profiling using MetaPhlAn3 (v3.0.13) with the mpa\_v30\_CHOCOPhlAn_201901 marker database; (3) Transformation of taxonomic relative abundances into a binary presence/absence profile; (4) Computation of the GMWI2 score using a Lasso-penalized logistic regression model trained on a meta-dataset of 8,069 health status labeled stool shotgun metagenomes.

package gmwi2

versions:

1.5-0

depends bbmap:

depends bedtools:

depends fastqc:

depends halo:

depends metaphlan:

3.0.13.*

depends pandas:

depends python:

>=3.7

depends samtools:

depends scikit-learn:

1.2.2.*

depends trimmomatic:

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install gmwi2

and update with::

   mamba update gmwi2

To create a new environment, run:

mamba create --name myenvname gmwi2

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/gmwi2:<tag>

(see `gmwi2/tags`_ for valid values for ``<tag>``)

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