recipe megadepth

Megadepth is an efficient tool for extracting coverage related information from RNA and DNA-seq BAM and BigWig files. It supports reading whole-genome coverage from BAM files and writing either indexed TSV or BigWig files, as well as efficient region coverage summary over intervals from both types of files.

Homepage:

https://github.com/ChristopherWilks/megadepth

License:

MIT / MIT

Recipe:

/megadepth/meta.yaml

package megadepth

(downloads) docker_megadepth

versions:
1.2.0-7,  1.2.0-6,  1.2.0-5,  1.2.0-4,  1.2.0-3,  1.2.0-2,  1.2.0-1,  1.2.0-0,  1.1.3-1, 

1.2.0-7,  1.2.0-6,  1.2.0-5,  1.2.0-4,  1.2.0-3,  1.2.0-2,  1.2.0-1,  1.2.0-0,  1.1.3-1,  1.1.3-0,  1.1.2-0,  1.1.1-0,  1.1.0-1,  1.1.0-0,  1.0.9b-0

depends htslib:

>=1.21,<1.23.0a0

depends libbigwig:

>=0.4.7,<0.5.0a0

depends libgcc:

>=13

depends libstdcxx:

>=13

depends libzlib:

>=1.3.1,<2.0a0

requirements:

additional platforms:

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 megadepth

and update with::

   mamba update megadepth

To create a new environment, run:

mamba create --name myenvname megadepth

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/megadepth:<tag>

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

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Link to this page

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