:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'biopet' .. highlight: bash biopet ====== .. conda:recipe:: biopet :replaces_section_title: :noindex: Biopet \(Bio Pipeline Execution Toolkit\) is the main pipeline development framework of the LUMC Sequencing Analysis Support Core team. :homepage: https://github.com/biopet/biopet :license: https://github.com/biopet/biopet/blob/develop/biopet-core/src/main/resources/nl/lumc/sasc/biopet/License.txt :recipe: /`biopet `_/`meta.yaml `_ .. conda:package:: biopet |downloads_biopet| |docker_biopet| :versions: ``0.9.0-2``,  ``0.9.0-1``,  ``0.9.0-0``,  ``0.8.0-1``,  ``0.8.0-0``,  ``0.7.0-0`` :depends openjdk: :depends python: :depends r-argparse: :depends r-base: :depends r-ggplot2: :depends r-reshape: :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 biopet and update with:: mamba update biopet To create a new environment, run:: mamba create --name myenvname biopet 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/biopet: (see `biopet/tags`_ for valid values for ````) .. |downloads_biopet| image:: https://img.shields.io/conda/dn/bioconda/biopet.svg?style=flat :target: https://anaconda.org/bioconda/biopet :alt: (downloads) .. |docker_biopet| image:: https://quay.io/repository/biocontainers/biopet/status :target: https://quay.io/repository/biocontainers/biopet .. _`biopet/tags`: https://quay.io/repository/biocontainers/biopet?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/biopet/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/biopet/README.html