:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'megadepth' .. highlight: bash megadepth ========= .. conda:recipe:: megadepth :replaces_section_title: :noindex: 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 `_ .. conda:package:: megadepth |downloads_megadepth| |docker_megadepth| :versions: .. raw:: html
1.2.0-51.2.0-41.2.0-31.2.0-21.2.0-11.2.0-01.1.3-11.1.3-01.1.2-0 ``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`` .. raw:: html
:depends htslib: ``>=1.17,<1.20.0a0`` :depends libbigwig: ``>=0.4.7,<0.5.0a0`` :depends libgcc-ng: ``>=12`` :depends libstdcxx-ng: ``>=12`` :depends libzlib: ``>=1.2.13,<1.3.0a0`` :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 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: (see `megadepth/tags`_ for valid values for ````) .. |downloads_megadepth| image:: https://img.shields.io/conda/dn/bioconda/megadepth.svg?style=flat :target: https://anaconda.org/bioconda/megadepth :alt: (downloads) .. |docker_megadepth| image:: https://quay.io/repository/biocontainers/megadepth/status :target: https://quay.io/repository/biocontainers/megadepth .. _`megadepth/tags`: https://quay.io/repository/biocontainers/megadepth?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/megadepth/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/megadepth/README.html