:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'picard' .. highlight: bash picard ====== .. conda:recipe:: picard :replaces_section_title: :noindex: Java tools for working with NGS data in the BAM format :homepage: http://broadinstitute.github.io/picard/ :developer docs: https://github.com/broadinstitute/picard :license: MIT / MIT :recipe: /`picard `_/`meta.yaml `_ :links: usegalaxy-eu: :usegalaxy-eu:`picard_MarkDuplicates` Java tools for working with NGS data in the BAM format. This package depends on \'r\-base\' because Picard requires R to run some of its metrics commands. The \'picard\-slim\' package offers an installation of Picard without the \'r\-base\' dependency. .. conda:package:: picard |downloads_picard| |docker_picard| :versions: .. raw:: html
3.1.1-03.1.0-03.0.0-13.0.0-02.27.5-02.27.4-02.27.3-02.27.2-02.27.1-0 ``3.1.1-0``,  ``3.1.0-0``,  ``3.0.0-1``,  ``3.0.0-0``,  ``2.27.5-0``,  ``2.27.4-0``,  ``2.27.3-0``,  ``2.27.2-0``,  ``2.27.1-0``,  ``2.27.0-0``,  ``2.26.11-0``,  ``2.26.10-0``,  ``2.26.9-0``,  ``2.26.8-0``,  ``2.26.7-0``,  ``2.26.6-0``,  ``2.26.5-0``,  ``2.26.4-0``,  ``2.26.3-0``,  ``2.26.2-0``,  ``2.26.1-0``,  ``2.26.0-0``,  ``2.25.7-0``,  ``2.25.6-0``,  ``2.25.5-0``,  ``2.25.4-0``,  ``2.25.3-0``,  ``2.25.2-0``,  ``2.25.1-1``,  ``2.25.1-0``,  ``2.25.0-1``,  ``2.25.0-0``,  ``2.24.2-0``,  ``2.24.1-0``,  ``2.24.0-0``,  ``2.23.9-0``,  ``2.23.8-0``,  ``2.23.7-0``,  ``2.23.6-0``,  ``2.23.5-0``,  ``2.23.4-0``,  ``2.23.3-0``,  ``2.23.2-0``,  ``2.23.1-0``,  ``2.23.0-0``,  ``2.22.9-0``,  ``2.22.8-0``,  ``2.22.7-0``,  ``2.22.6-0``,  ``2.22.5-0``,  ``2.22.4-0``,  ``2.22.3-0``,  ``2.22.2-0``,  ``2.22.1-0``,  ``2.22.0-0``,  ``2.21.9-0``,  ``2.21.8-0``,  ``2.21.7-0``,  ``2.21.6-0``,  ``2.21.5-0``,  ``2.21.4-0``,  ``2.21.3-0``,  ``2.21.2-1``,  ``2.21.2-0``,  ``2.21.1-0``,  ``2.20.8-0``,  ``2.20.7-0``,  ``2.20.6-0``,  ``2.20.5-0``,  ``2.20.4-1``,  ``2.20.4-0``,  ``2.20.3-0``,  ``2.20.2-0``,  ``2.20.1-0``,  ``2.20.0-0``,  ``2.19.2-0``,  ``2.19.1-0``,  ``2.19.0-0``,  ``2.18.29-0``,  ``2.18.27-0``,  ``2.18.26-0``,  ``2.18.25-0``,  ``2.18.23-0``,  ``2.18.22-0``,  ``2.18.21-0``,  ``2.18.20-0``,  ``2.18.17-0``,  ``2.18.16-0``,  ``2.18.15-0``,  ``2.18.14-0``,  ``2.18.13-0``,  ``2.18.12-0``,  ``2.18.11-0``,  ``2.18.10-0``,  ``2.18.9-0``,  ``2.18.7-2``,  ``2.18.7-0``,  ``2.18.6-0``,  ``2.18.5-0``,  ``2.18.4-0``,  ``2.18.3-0``,  ``2.18.2-0``,  ``2.18.1-0``,  ``2.18.0-0``,  ``2.17.11-0``,  ``2.17.10-0``,  ``2.17.8-0``,  ``2.17.6-0``,  ``2.17.5-0``,  ``2.17.4-0``,  ``2.17.3-0``,  ``2.17.2-0``,  ``2.17.0-0``,  ``2.16.0-0``,  ``2.15.0-0``,  ``2.14.1-0``,  ``2.14-0``,  ``2.13-1``,  ``2.13-0``,  ``2.11.0-0``,  ``2.10.6-0``,  ``2.9.2-2``,  ``2.9.2-1``,  ``2.9.2-0``,  ``2.9.0-0``,  ``2.7.1-2``,  ``2.7.1-1``,  ``2.7.1-0``,  ``2.5.0-2``,  ``2.5.0-1``,  ``2.5.0-0``,  ``2.3.0-0``,  ``2.0.1-1``,  ``2.0.1-0``,  ``1.141-6``,  ``1.141-5``,  ``1.141-4``,  ``1.141-3``,  ``1.141-1``,  ``1.141-0``,  ``1.139-0``,  ``1.126-5``,  ``1.126-4``,  ``1.126-3``,  ``1.126-2``,  ``1.97-0``,  ``1.56-1``,  ``1.56-0`` .. raw:: html
:depends openjdk: ``>=17`` :depends r-base: :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 picard and update with:: mamba update picard To create a new environment, run:: mamba create --name myenvname picard 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/picard: (see `picard/tags`_ for valid values for ````) .. |downloads_picard| image:: https://img.shields.io/conda/dn/bioconda/picard.svg?style=flat :target: https://anaconda.org/bioconda/picard :alt: (downloads) .. |docker_picard| image:: https://quay.io/repository/biocontainers/picard/status :target: https://quay.io/repository/biocontainers/picard .. _`picard/tags`: https://quay.io/repository/biocontainers/picard?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/picard/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/picard/README.html