:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'ariba' .. highlight: bash ariba ===== .. conda:recipe:: ariba :replaces_section_title: :noindex: ARIBA\: Antibiotic Resistance Identification By Assembly :homepage: https://github.com/sanger-pathogens/ariba :license: GPL / GNU General Public License v3 (GPL-3.0) :recipe: /`ariba `_/`meta.yaml `_ .. conda:package:: ariba |downloads_ariba| |docker_ariba| :versions: .. raw:: html
2.14.6-52.14.6-42.14.6-32.14.6-22.14.6-02.14.5-22.14.5-12.14.5-02.14.4-0 ``2.14.6-5``,  ``2.14.6-4``,  ``2.14.6-3``,  ``2.14.6-2``,  ``2.14.6-0``,  ``2.14.5-2``,  ``2.14.5-1``,  ``2.14.5-0``,  ``2.14.4-0``,  ``2.14.3-1``,  ``2.14.3-0``,  ``2.14.1-0``,  ``2.13.5-0``,  ``2.13.3-0``,  ``2.13.2-0``,  ``2.12.1-0``,  ``2.12.0-2``,  ``2.12.0-0``,  ``2.11.1-0``,  ``2.11.0-0``,  ``2.10.1-0``,  ``2.10.0-0``,  ``2.5.1-0``,  ``0.6.0-0`` .. raw:: html
:depends bcftools: ``>=1.2,<=1.14`` :depends beautifulsoup4: ``>=4.1.0`` :depends biopython: :depends bowtie2: ``<2.4.0`` :depends cd-hit: ``>=4.6.5`` :depends dendropy: ``>=4.2.0`` :depends libgcc-ng: ``>=12`` :depends libstdcxx-ng: ``>=12`` :depends libzlib: ``>=1.2.13,<1.3.0a0`` :depends matplotlib-base: ``>=3.1.0`` :depends mummer: ``>=3.23`` :depends pyfastaq: ``>=3.12.0`` :depends pymummer: ``>=0.11.0`` :depends pysam: ``>=0.15.3,<=0.18.0`` :depends python: ``>=3.8,<3.9.0a0`` :depends python_abi: ``3.8.* *_cp38`` :depends samtools: ``>=1.2`` :depends spades: ``>=3.5.0`` :depends wget: :depends zlib: :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 ariba and update with:: mamba update ariba To create a new environment, run:: mamba create --name myenvname ariba 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/ariba: (see `ariba/tags`_ for valid values for ````) .. |downloads_ariba| image:: https://img.shields.io/conda/dn/bioconda/ariba.svg?style=flat :target: https://anaconda.org/bioconda/ariba :alt: (downloads) .. |docker_ariba| image:: https://quay.io/repository/biocontainers/ariba/status :target: https://quay.io/repository/biocontainers/ariba .. _`ariba/tags`: https://quay.io/repository/biocontainers/ariba?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/ariba/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/ariba/README.html