:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'shigeifinder' .. highlight: bash shigeifinder ============ .. conda:recipe:: shigeifinder :replaces_section_title: :noindex: Cluster informed Shigella and EIEC serotyping tool from Illumina reads and assemblies :homepage: https://github.com/LanLab/ShigEiFinder :license: GPL3 :recipe: /`shigeifinder `_/`meta.yaml `_ .. conda:package:: shigeifinder |downloads_shigeifinder| |docker_shigeifinder| :versions: ``1.3.5-0``,  ``1.3.4-0``,  ``1.3.3-0``,  ``1.3.2-0``,  ``1.3.1-0``,  ``1.2.0-0``,  ``1.1.0-0`` :depends blast: ``>=2.9.0`` :depends bwa: ``>=0.7.17`` :depends python: ``>=3.7`` :depends samtools: ``>=1.10`` :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 shigeifinder and update with:: mamba update shigeifinder To create a new environment, run:: mamba create --name myenvname shigeifinder 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/shigeifinder: (see `shigeifinder/tags`_ for valid values for ````) .. |downloads_shigeifinder| image:: https://img.shields.io/conda/dn/bioconda/shigeifinder.svg?style=flat :target: https://anaconda.org/bioconda/shigeifinder :alt: (downloads) .. |docker_shigeifinder| image:: https://quay.io/repository/biocontainers/shigeifinder/status :target: https://quay.io/repository/biocontainers/shigeifinder .. _`shigeifinder/tags`: https://quay.io/repository/biocontainers/shigeifinder?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/shigeifinder/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/shigeifinder/README.html