recipe amplicontyper

Tool for training model and classifying reads from environmental ONT amplicon sequencing.

Homepage:

https://github.com/AntonS-bio/AmpliconTyper

License:

GPL-3.0-only

Recipe:

/amplicontyper/meta.yaml

Tool for training model and classifying reads from environmental ONT amplicon sequencing.

package amplicontyper

versions:

0.1.28-0,  0.1.27-0

depends biopython:

>=1.78

depends minimap2:

depends numpy:

>=1.20.*

depends pandas:

>=2.0.0

depends pysam:

>=0.22.0

depends python:

>=3.10

depends requests:

depends samtools:

depends scikit-learn:

1.5.*

depends tqdm:

>=4.66.*

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 amplicontyper

and update with::

   mamba update amplicontyper

To create a new environment, run:

mamba create --name myenvname amplicontyper

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/amplicontyper:<tag>

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

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