recipe mgatk

Mitochondrial genome analysis toolkit.

Homepage:

https://github.com/caleblareau/mgatk

Documentation:

https://github.com/caleblareau/mgatk/wiki

License:

MIT / MIT

Recipe:

/mgatk/meta.yaml

package mgatk

versions:

0.7.0-2,  0.7.0-1,  0.7.0-0

depends bioconductor-genomicranges:

depends bioconductor-summarizedexperiment:

depends biopython:

depends click:

depends numpy:

depends openjdk:

depends optparse-pretty:

depends pandas:

depends picard-slim:

depends pulp:

<2.8

depends pysam:

depends pytest:

depends python:

>=3

depends r-base:

depends r-data.table:

depends r-dplyr:

depends r-matrix:

depends regex:

depends ruamel.yaml:

0.16.12.*

depends snakemake-minimal:

<8

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 mgatk

and update with::

   mamba update mgatk

To create a new environment, run:

mamba create --name myenvname mgatk

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/mgatk:<tag>

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

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