- recipe hymet
HYMET provides hybrid Mash+minimap2 metagenomic classification with benchmark and case-study tooling.
- Homepage:
- License:
MIT / MIT
- Recipe:
- Links:
biotools: hymet
HYMET couples Mash candidate filtering, minimap2 alignment, and a weighted LCA resolver to classify contigs and reads. The project bundles the new Python CLI (`bin/hymet`), the legacy Perl pipeline, CAMI benchmark harnesses, and case-study analysis scripts so users can reproduce the published experiments directly.
- package hymet¶
- Versions:
1.3.0-0,1.2.1-0,1.2.0-0,1.0.0-0- Depends:
on biopython
on csvkit
on mash
on matplotlib-base
on minimap2
on numpy
on pandas
on perl
on python
>=3.9on seaborn
on taxonkit
on wget
- 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 hymet
to add into an existing workspace instead, run:
pixi add hymet
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 hymet
Alternatively, to install into a new environment, run:
conda create -n envname hymet
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/hymet:<tag>
(see hymet/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/hymet/README.html)
