:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'covtobed' .. highlight: bash covtobed ======== .. conda:recipe:: covtobed :replaces_section_title: :noindex: covtobed \- generate a BED file of covered regions from a BAM file :homepage: https://github.com/telatin/covtobed/ :license: MIT :recipe: /`covtobed `_/`meta.yaml `_ .. conda:package:: covtobed |downloads_covtobed| |docker_covtobed| :versions: .. raw:: html
1.3.5-21.3.5-11.3.5-01.3.3-01.3.1-01.3.0-01.2.0-11.2.0-01.1.4-0 ``1.3.5-2``,  ``1.3.5-1``,  ``1.3.5-0``,  ``1.3.3-0``,  ``1.3.1-0``,  ``1.3.0-0``,  ``1.2.0-1``,  ``1.2.0-0``,  ``1.1.4-0``,  ``1.1.2-0``,  ``1.1.0-0``,  ``1.0.1-0``,  ``1.0.0-0``,  ``0.6-0``,  ``0.4-0``,  ``0.3-0``,  ``0.1-0`` .. raw:: html
:depends bamtools: ``>=2.5.1,<2.5.2.0a0`` :depends libgcc-ng: ``>=12`` :depends libstdcxx-ng: ``>=12`` :depends libzlib: ``>=1.2.13,<1.3.0a0`` :depends zlib: :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 covtobed and update with:: mamba update covtobed To create a new environment, run:: mamba create --name myenvname covtobed 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/covtobed: (see `covtobed/tags`_ for valid values for ````) .. |downloads_covtobed| image:: https://img.shields.io/conda/dn/bioconda/covtobed.svg?style=flat :target: https://anaconda.org/bioconda/covtobed :alt: (downloads) .. |docker_covtobed| image:: https://quay.io/repository/biocontainers/covtobed/status :target: https://quay.io/repository/biocontainers/covtobed .. _`covtobed/tags`: https://quay.io/repository/biocontainers/covtobed?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/covtobed/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/covtobed/README.html