:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'resfinder' .. highlight: bash resfinder ========= .. conda:recipe:: resfinder :replaces_section_title: :noindex: ResFinder identifies acquired antimicrobial resistance genes in total or partial sequenced isolates of bacteria. :homepage: https://bitbucket.org/genomicepidemiology/resfinder :license: APACHE / Apache-2.0 :recipe: /`resfinder `_/`meta.yaml `_ :links: doi: :doi:`10.1093/jac/dkaa345` .. conda:package:: resfinder |downloads_resfinder| |docker_resfinder| :versions: ``4.5.0-0``,  ``4.4.3-0``,  ``4.4.2-1``,  ``4.4.2-0``,  ``4.1.11-0`` :depends biopython: ``>=1.79`` :depends blast: ``>=2.8.1`` :depends cgecore: ``1.5.6`` :depends cgelib: ``>=0.7.3`` :depends git: :depends kma: :depends pandas: ``>=1.4.2`` :depends python: ``>=3.8`` :depends python-dateutil: :depends tabulate: ``>=0.8.9`` :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 resfinder and update with:: mamba update resfinder To create a new environment, run:: mamba create --name myenvname resfinder 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/resfinder: (see `resfinder/tags`_ for valid values for ````) .. |downloads_resfinder| image:: https://img.shields.io/conda/dn/bioconda/resfinder.svg?style=flat :target: https://anaconda.org/bioconda/resfinder :alt: (downloads) .. |docker_resfinder| image:: https://quay.io/repository/biocontainers/resfinder/status :target: https://quay.io/repository/biocontainers/resfinder .. _`resfinder/tags`: https://quay.io/repository/biocontainers/resfinder?tab=tags .. raw:: html Notes ----- ResFinder requires databases that can be downloaded with download\-db.sh. 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/resfinder/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/resfinder/README.html