:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'gatk-framework' .. highlight: bash gatk-framework ============== .. conda:recipe:: gatk-framework :replaces_section_title: :noindex: The core MIT\-licensed Genome Analysis Toolkit \(GATK\) framework\, free for all uses :homepage: https://github.com/chapmanb/gatk :license: MIT :recipe: /`gatk-framework `_/`meta.yaml `_ .. conda:package:: gatk-framework |downloads_gatk-framework| |docker_gatk-framework| :versions: .. raw:: html
3.6.24-63.6.24-53.6.24-43.6.24-33.6.24-23.6.24-13.6.24-03.5.21-03.4.46-3 ``3.6.24-6``,  ``3.6.24-5``,  ``3.6.24-4``,  ``3.6.24-3``,  ``3.6.24-2``,  ``3.6.24-1``,  ``3.6.24-0``,  ``3.5.21-0``,  ``3.4.46-3``,  ``3.4.46-2``,  ``3.4.46-1``,  ``3.4.46-0`` .. raw:: html
:depends openjdk: ``>=8,<9`` :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 gatk-framework and update with:: mamba update gatk-framework To create a new environment, run:: mamba create --name myenvname gatk-framework 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/gatk-framework: (see `gatk-framework/tags`_ for valid values for ````) .. |downloads_gatk-framework| image:: https://img.shields.io/conda/dn/bioconda/gatk-framework.svg?style=flat :target: https://anaconda.org/bioconda/gatk-framework :alt: (downloads) .. |docker_gatk-framework| image:: https://quay.io/repository/biocontainers/gatk-framework/status :target: https://quay.io/repository/biocontainers/gatk-framework .. _`gatk-framework/tags`: https://quay.io/repository/biocontainers/gatk-framework?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/gatk-framework/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/gatk-framework/README.html