- recipe gmwi2
Enhanced Health Status Prediction from Gut Microbiome Taxonomic Profiles
- Homepage:
- License:
MIT / MIT
- Recipe:
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:
1.6-0,1.5-0- Depends:
on bbmap
on bedtools
on fastqc
on halo
on metaphlan
3.0.13.*on pandas
on python
>=3.7on samtools
on scikit-learn
1.2.2.*on trimmomatic
- Additional platforms:
Installation¶
You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).
Pixi¶
With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:
pixi global install gmwi2
to add into an existing workspace instead, run:
pixi add gmwi2
In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:
pixi workspace channel add conda-forge
pixi workspace channel add bioconda
Conda¶
With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:
conda install gmwi2
Alternatively, to install into a new environment, run:
conda create -n envname gmwi2
with envname being the name of the desired environment.
Container¶
Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:
docker pull quay.io/biocontainers/gmwi2:<tag>
(see gmwi2/tags for valid values for <tag>).
Integrated deployment¶
Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/gmwi2/README.html)
