recipe mutamr

Stripped down tool for generation of annotated vcf from paired-end reads in a CPHL.

Homepage:

https://github.com/MDU-PHL/mutamr

License:

GPL3 / GPL-3.0-or-later

Recipe:

/mutamr/meta.yaml

package mutamr

versions:

0.0.1-0

depends bcftools:

1.20.*

depends bwa:

0.7.18.*

depends delly:

1.2.8.*

depends freebayes:

1.3.8.*

depends python:

>=3.10

depends samclip:

0.4.0.*

depends samtools:

1.20.*

depends snpeff:

5.2.*

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 mutamr

and update with::

   mamba update mutamr

To create a new environment, run:

mamba create --name myenvname mutamr

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/mutamr:<tag>

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

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