recipe handyreadgenotyper

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

Homepage:

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

License:

GPL-3.0-only

Recipe:

/handyreadgenotyper/meta.yaml

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

package handyreadgenotyper

(downloads) docker_handyreadgenotyper

versions:
0.1.24-0,  0.1.22-0,  0.1.21-1,  0.1.21-0,  0.1.20-0,  0.1.18-0,  0.1.14-1,  0.1.14-0,  0.1.13-0, 

0.1.24-0,  0.1.22-0,  0.1.21-1,  0.1.21-0,  0.1.20-0,  0.1.18-0,  0.1.14-1,  0.1.14-0,  0.1.13-0,  0.1.9-0

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 samtools:

depends scikit-learn:

>=1.3.*

depends tqdm:

>=4.66.*

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 handyreadgenotyper

and update with::

   mamba update handyreadgenotyper

To create a new environment, run:

mamba create --name myenvname handyreadgenotyper

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/handyreadgenotyper:<tag>

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

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Link to this page

Render an install-with-bioconda badge with the following MarkDown:

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