:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'refgenie' .. highlight: bash refgenie ======== .. conda:recipe:: refgenie :replaces_section_title: :noindex: Refgenie creates a standardized folder structure for reference genome files and indexes. You can download pre\-built genomes or build your own for any fasta file :homepage: http://refgenie.databio.org :license: BSD / BSD-2-Clause :recipe: /`refgenie `_/`meta.yaml `_ .. conda:package:: refgenie |downloads_refgenie| |docker_refgenie| :versions: .. raw:: html
0.12.1-00.12.0-00.11.0-00.10.0-00.9.3-00.9.2-10.9.2-00.9.1-00.9.0-0 ``0.12.1-0``,  ``0.12.0-0``,  ``0.11.0-0``,  ``0.10.0-0``,  ``0.9.3-0``,  ``0.9.2-1``,  ``0.9.2-0``,  ``0.9.1-0``,  ``0.9.0-0``,  ``0.8.2-0``,  ``0.8.1-0``,  ``0.8.0-0``,  ``0.7.2-0`` .. raw:: html
:depends logmuse: ``>=0.2.6`` :depends piper: ``>=0.12.1`` :depends pyfaidx: ``>=0.5.5.2`` :depends python: ``>=3.6`` :depends refgenconf: ``>=0.10.0`` :depends yacman: ``>=0.8.0`` :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 refgenie and update with:: mamba update refgenie To create a new environment, run:: mamba create --name myenvname refgenie 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/refgenie: (see `refgenie/tags`_ for valid values for ````) .. |downloads_refgenie| image:: https://img.shields.io/conda/dn/bioconda/refgenie.svg?style=flat :target: https://anaconda.org/bioconda/refgenie :alt: (downloads) .. |docker_refgenie| image:: https://quay.io/repository/biocontainers/refgenie/status :target: https://quay.io/repository/biocontainers/refgenie .. _`refgenie/tags`: https://quay.io/repository/biocontainers/refgenie?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/refgenie/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/refgenie/README.html