recipe bamtocov

Extract coverage information from BAM files, supporting stranded and physical coverage and streams.

Homepage:

https://github.com/telatin/bamtocov

License:

MIT

Recipe:

/bamtocov/meta.yaml

Links:

biotools: bamtocov, doi: 10.3390/bioengineering8050059

A collection of tools to extract coverage information from BAM and CRAM files, supporting target (BED, GFF) and reporting the output in bedGraph (BED) or WIG format.

package bamtocov

(downloads) docker_bamtocov

versions:
2.7.0-2,  2.7.0-1,  2.7.0-0,  2.6.1-1,  2.6.1-0,  2.6.0-0,  2.5.0-1,  2.5.0-0,  2.4.0-0, 

2.7.0-2,  2.7.0-1,  2.7.0-0,  2.6.1-1,  2.6.1-0,  2.6.0-0,  2.5.0-1,  2.5.0-0,  2.4.0-0,  2.3.0-0,  2.2.0-1,  2.2.0-0,  2.1.0-1,  2.1.0-0,  2.0.4-0,  2.0.2-1,  2.0.2-0,  2.0.001-0,  2.0.000-0

depends htslib:

>=1.17,<1.22.0a0

depends libgcc-ng:

>=12

depends libzlib:

>=1.2.13,<1.3.0a0

depends pcre:

>=8.45,<9.0a0

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 bamtocov

and update with::

   mamba update bamtocov

To create a new environment, run:

mamba create --name myenvname bamtocov

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/bamtocov:<tag>

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

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Link to this page

Render an install-with-bioconda badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bamtocov/README.html)