:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'cnv_facets' .. highlight: bash cnv_facets ========== .. conda:recipe:: cnv_facets :replaces_section_title: :noindex: Detect somatic copy number variants \(CNV\) in tumour\-normal samples using next generation sequencing data :homepage: https://github.com/dariober/cnv_facets :license: MIT / MIT :recipe: /`cnv_facets `_/`meta.yaml `_ .. conda:package:: cnv_facets |downloads_cnv_facets| |docker_cnv_facets| :versions: .. raw:: html
0.16.0-10.16.0-00.15.0-10.15.0-00.14.0-10.13.0-10.12.1-10.12.1-00.12.0-0 ``0.16.0-1``,  ``0.16.0-0``,  ``0.15.0-1``,  ``0.15.0-0``,  ``0.14.0-1``,  ``0.13.0-1``,  ``0.12.1-1``,  ``0.12.1-0``,  ``0.12.0-0``,  ``v0.11.3-2``,  ``v0.11.3-1``,  ``v0.11.2-1`` .. raw:: html
:depends bcftools: ``>=1.9`` :depends bioconductor-rsamtools: :depends htslib: ``>=1.9,<1.10.0a0`` :depends libgcc-ng: ``>=7.3.0`` :depends libgfortran-ng: ``>=7,<8.0a0`` :depends libstdcxx-ng: ``>=7.3.0`` :depends python: ``>=3.8,<3.9.0a0`` :depends r-base: ``>=3.6,<3.7.0a0`` :depends r-data.table: :depends r-ggplot2: :depends r-gridextra: :depends r-jsonlite: :depends samtools: :depends snp-pileup: :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 cnv_facets and update with:: mamba update cnv_facets To create a new environment, run:: mamba create --name myenvname cnv_facets 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/cnv_facets: (see `cnv_facets/tags`_ for valid values for ````) .. |downloads_cnv_facets| image:: https://img.shields.io/conda/dn/bioconda/cnv_facets.svg?style=flat :target: https://anaconda.org/bioconda/cnv_facets :alt: (downloads) .. |docker_cnv_facets| image:: https://quay.io/repository/biocontainers/cnv_facets/status :target: https://quay.io/repository/biocontainers/cnv_facets .. _`cnv_facets/tags`: https://quay.io/repository/biocontainers/cnv_facets?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/cnv_facets/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/cnv_facets/README.html