:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'cnvkit' .. highlight: bash cnvkit ====== .. conda:recipe:: cnvkit :replaces_section_title: :noindex: Copy number variant detection from high\-throughput sequencing :homepage: https://github.com/etal/cnvkit :license: Apache-2.0 :recipe: /`cnvkit `_/`meta.yaml `_ :links: biotools: :biotools:`cnvkit`, doi: :doi:`10.1371/journal.pcbi.1004873` .. conda:package:: cnvkit |downloads_cnvkit| |docker_cnvkit| :versions: .. raw:: html
0.9.10-00.9.9-00.9.8-00.9.7-10.9.7-00.9.6-20.9.6-10.9.6-00.9.6a0-2 ``0.9.10-0``,  ``0.9.9-0``,  ``0.9.8-0``,  ``0.9.7-1``,  ``0.9.7-0``,  ``0.9.6-2``,  ``0.9.6-1``,  ``0.9.6-0``,  ``0.9.6a0-2``,  ``0.9.6a0-1``,  ``0.9.6a0-0``,  ``0.9.5-1``,  ``0.9.5-0``,  ``0.9.4a0-0``,  ``0.9.3-2``,  ``0.9.2-2``,  ``0.9.2a0-2``,  ``0.9.2a0-1``,  ``0.9.2a0-0``,  ``0.9.1-0``,  ``0.9.1a0-0``,  ``0.9.0-0``,  ``0.8.6a0-2``,  ``0.8.6a0-1``,  ``0.8.6a0-0``,  ``0.8.5-0``,  ``0.8.5dev0-1``,  ``0.8.5dev0-0``,  ``0.8.4-0``,  ``0.8.3a0-1``,  ``0.8.3a0-0``,  ``0.8.2-0``,  ``0.8.1-0``,  ``0.8.0-0``,  ``0.7.11-0``,  ``0.7.10-1``,  ``0.7.10-0``,  ``0.7.9-0``,  ``0.7.8-1``,  ``0.7.8-0``,  ``0.7.7-0``,  ``0.7.6-0``,  ``0.7.5-0``,  ``0.7.4-1``,  ``0.7.4-0``,  ``0.7.3-0`` .. raw:: html
:depends bioconductor-dnacopy: :depends biopython: ``>=1.62`` :depends joblib: ``<1.0`` :depends matplotlib-base: ``>=1.3.1`` :depends networkx: ``>=2.4`` :depends numpy: ``>=1.9`` :depends pandas: ``>=0.23.3`` :depends pomegranate: ``>=0.9.0`` :depends pyfaidx: ``>=0.4.7`` :depends pysam: ``>=0.16.0`` :depends python: ``>=3.5`` :depends r-base: ``>=3.4.1`` :depends r-cghflasso: :depends reportlab: ``>=3.0`` :depends scipy: ``>=0.15.0`` :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 cnvkit and update with:: mamba update cnvkit To create a new environment, run:: mamba create --name myenvname cnvkit 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/cnvkit: (see `cnvkit/tags`_ for valid values for ````) .. |downloads_cnvkit| image:: https://img.shields.io/conda/dn/bioconda/cnvkit.svg?style=flat :target: https://anaconda.org/bioconda/cnvkit :alt: (downloads) .. |docker_cnvkit| image:: https://quay.io/repository/biocontainers/cnvkit/status :target: https://quay.io/repository/biocontainers/cnvkit .. _`cnvkit/tags`: https://quay.io/repository/biocontainers/cnvkit?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/cnvkit/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/cnvkit/README.html