:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'varscan' .. highlight: bash varscan ======= .. conda:recipe:: varscan :replaces_section_title: :noindex: variant detection in massively parallel sequencing data :homepage: http://dkoboldt.github.io/varscan/ :license: The Non-Profit Open Software License version 3.0 (NPOSL-3.0) :recipe: /`varscan `_/`meta.yaml `_ :links: biotools: :biotools:`varscan` .. conda:package:: varscan |downloads_varscan| |docker_varscan| :versions: .. raw:: html
2.4.6-02.4.4-12.4.4-02.4.3-22.4.3-12.4.3-02.4.2-22.4.2-12.4.2-0 ``2.4.6-0``,  ``2.4.4-1``,  ``2.4.4-0``,  ``2.4.3-2``,  ``2.4.3-1``,  ``2.4.3-0``,  ``2.4.2-2``,  ``2.4.2-1``,  ``2.4.2-0``,  ``2.4.1-0``,  ``2.4.0-1``,  ``2.4.0-0``,  ``2.3.7-4``,  ``2.3.7-3``,  ``2.3.7-2``,  ``2.3.7-0`` .. raw:: html
:depends openjdk: :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 varscan and update with:: mamba update varscan To create a new environment, run:: mamba create --name myenvname varscan 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/varscan: (see `varscan/tags`_ for valid values for ````) .. |downloads_varscan| image:: https://img.shields.io/conda/dn/bioconda/varscan.svg?style=flat :target: https://anaconda.org/bioconda/varscan :alt: (downloads) .. |docker_varscan| image:: https://quay.io/repository/biocontainers/varscan/status :target: https://quay.io/repository/biocontainers/varscan .. _`varscan/tags`: https://quay.io/repository/biocontainers/varscan?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/varscan/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/varscan/README.html