recipe locityper

Targeted genotyper for complex polymorphic loci from short and long read WGS.

Homepage:

https://github.com/tprodanov/locityper

License:

MIT / MIT

Recipe:

/locityper/meta.yaml

package locityper

versions:

0.17.5-0,  0.17.4-1,  0.17.4-0,  0.17.3-0,  0.16.12-0,  0.16.11-0,  0.16.10-0,  0.16.9-0,  0.16.8-0, 

0.17.5-0,  0.17.4-1,  0.17.4-0,  0.17.3-0,  0.16.12-0,  0.16.11-0,  0.16.10-0,  0.16.9-0,  0.16.8-0,  0.16.7-0,  0.16.6-0,  0.16.5-0,  0.16.0-0,  0.15.3-0,  0.15.2-0,  0.15.1-0,  0.15.0-0,  0.14.5-0,  0.14.4-0,  0.13.4-0

depends _openmp_mutex:

>=4.5

depends kmer-jellyfish:

>=1.0

depends libgcc:

>=13

depends libstdcxx:

>=13

depends minimap2:

>=2.25

depends pysam:

depends python:

depends samtools:

>=1.18

depends strobealign:

>=0.12

requirements:

additional platforms:

linux-aarch64

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 locityper

and update with::

   mamba update locityper

To create a new environment, run:

mamba create --name myenvname locityper

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/locityper:<tag>

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

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Render an badge with the following MarkDown:

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