recipe hymet

HYMET provides hybrid Mash+minimap2 metagenomic classification with benchmark and case-study tooling.

Homepage:

https://github.com/ieeta-pt/HYMET

License:

MIT / MIT

Recipe:

/hymet/meta.yaml

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:

1.2.1-0,  1.2.0-0,  1.0.0-0

depends biopython:

depends csvkit:

depends mash:

depends matplotlib-base:

depends minimap2:

depends numpy:

depends pandas:

depends perl:

depends python:

>=3.9

depends seaborn:

depends taxonkit:

depends wget:

requirements:

additional platforms:

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 hymet

and update with::

   mamba update hymet

To create a new environment, run:

mamba create --name myenvname hymet

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/hymet:<tag>

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

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