recipe mosdepth

Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing.

Homepage:

https://github.com/brentp/mosdepth

License:

MIT

Recipe:

/mosdepth/meta.yaml

Links:

doi: 10.1093/bioinformatics/btx699, biotools: mosdepth

package mosdepth

versions:

0.3.10-1,  0.3.10-0,  0.3.8-0,  0.3.7-0,  0.3.6-0,  0.3.5-0,  0.3.4-0,  0.3.3-3,  0.3.3-2, 

0.3.10-1,  0.3.10-0,  0.3.8-0,  0.3.7-0,  0.3.6-0,  0.3.5-0,  0.3.4-0,  0.3.3-3,  0.3.3-2,  0.3.3-1,  0.3.3-0,  0.3.2-1,  0.3.2-0,  0.3.1-2,  0.3.1-1,  0.3.1-0,  0.2.9-1,  0.2.9-0,  0.2.7-0,  0.2.6-0,  0.2.5-0,  0.2.4-0,  0.2.3-1,  0.2.3-0,  0.2.2-1,  0.2.1-1,  0.2.1-0,  0.2.0-0,  0.1.9-0,  0.1.7-0,  0.1.6-0,  0.1.5-0,  0.1.4a-0,  0.1.3-0,  0.1.1-0

depends htslib:

>=1.21,<1.22.0a0

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 mosdepth

and update with::

   mamba update mosdepth

To create a new environment, run:

mamba create --name myenvname mosdepth

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/mosdepth:<tag>

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

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