:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bamtocov' .. highlight: bash bamtocov ======== .. conda:recipe:: bamtocov :replaces_section_title: :noindex: 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: :biotools:`bamtocov`, doi: :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. .. conda:package:: bamtocov |downloads_bamtocov| |docker_bamtocov| :versions: .. raw:: html
2.7.0-22.7.0-12.7.0-02.6.1-12.6.1-02.6.0-02.5.0-12.5.0-02.4.0-0 ``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`` .. raw:: html
:depends htslib: ``>=1.17,<1.20.0a0`` :depends libgcc-ng: ``>=12`` :depends libzlib: ``>=1.2.13,<1.3.0a0`` :depends pcre: ``>=8.45,<9.0a0`` :requirements: .. rubric:: Installation You need a conda-compatible package manager (currently either `micromamba `_, `mamba `_, or `conda `_) and the Bioconda channel already activated (see :ref:`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: (see `bamtocov/tags`_ for valid values for ````) .. |downloads_bamtocov| image:: https://img.shields.io/conda/dn/bioconda/bamtocov.svg?style=flat :target: https://anaconda.org/bioconda/bamtocov :alt: (downloads) .. |docker_bamtocov| image:: https://quay.io/repository/biocontainers/bamtocov/status :target: https://quay.io/repository/biocontainers/bamtocov .. _`bamtocov/tags`: https://quay.io/repository/biocontainers/bamtocov?tab=tags .. raw:: html Download stats ----------------- .. raw:: html :file: ../../templates/package_dashboard.html 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) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/bamtocov/README.html