:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'plasmidfinder' .. highlight: bash plasmidfinder ============= .. conda:recipe:: plasmidfinder :replaces_section_title: :noindex: PlasmidFinder allows identification of plasmids in total or partial sequenced isolates of bacteria. :homepage: https://bitbucket.org/genomicepidemiology/plasmidfinder :license: APACHE / Apache-2.0 :recipe: /`plasmidfinder `_/`meta.yaml `_ :links: doi: :doi:`10.1128/AAC.02412-14` .. conda:package:: plasmidfinder |downloads_plasmidfinder| |docker_plasmidfinder| :versions: ``2.1.6-1``,  ``2.1.6-0``,  ``2.1.1-1``,  ``2.1.1-0``,  ``2.1-1``,  ``2.1-0``,  ``2.0.1-0`` :depends biopython: :depends blast: :depends cgecore: :depends kma: :depends python: ``>=3`` :depends tabulate: :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 plasmidfinder and update with:: mamba update plasmidfinder To create a new environment, run:: mamba create --name myenvname plasmidfinder 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/plasmidfinder: (see `plasmidfinder/tags`_ for valid values for ````) .. |downloads_plasmidfinder| image:: https://img.shields.io/conda/dn/bioconda/plasmidfinder.svg?style=flat :target: https://anaconda.org/bioconda/plasmidfinder :alt: (downloads) .. |docker_plasmidfinder| image:: https://quay.io/repository/biocontainers/plasmidfinder/status :target: https://quay.io/repository/biocontainers/plasmidfinder .. _`plasmidfinder/tags`: https://quay.io/repository/biocontainers/plasmidfinder?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/plasmidfinder/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/plasmidfinder/README.html