:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'shigatyper' .. highlight: bash shigatyper ========== .. conda:recipe:: shigatyper :replaces_section_title: :noindex: Typing tool for Shigella spp. from WGS Illumina sequencing :homepage: https://github.com/CFSAN-Biostatistics/shigatyper :license: Public Domain / Public Domain :recipe: /`shigatyper `_/`meta.yaml `_ .. conda:package:: shigatyper |downloads_shigatyper| |docker_shigatyper| :versions: ``2.0.5-0``,  ``2.0.4-0``,  ``2.0.3-0``,  ``2.0.2-0``,  ``2.0.1-1``,  ``2.0.1-0``,  ``1.0.7-0``,  ``1.0.6-0``,  ``1.0.5-3`` :depends bcftools: ``>=1.9`` :depends minimap2: ``>=2.16`` :depends pandas: ``>=0.24.2`` :depends python: ``>=3.7`` :depends samtools: ``>=1.9`` :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 shigatyper and update with:: mamba update shigatyper To create a new environment, run:: mamba create --name myenvname shigatyper 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/shigatyper: (see `shigatyper/tags`_ for valid values for ````) .. |downloads_shigatyper| image:: https://img.shields.io/conda/dn/bioconda/shigatyper.svg?style=flat :target: https://anaconda.org/bioconda/shigatyper :alt: (downloads) .. |docker_shigatyper| image:: https://quay.io/repository/biocontainers/shigatyper/status :target: https://quay.io/repository/biocontainers/shigatyper .. _`shigatyper/tags`: https://quay.io/repository/biocontainers/shigatyper?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/shigatyper/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/shigatyper/README.html