:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'srst2' .. highlight: bash srst2 ===== .. conda:recipe:: srst2 :replaces_section_title: :noindex: Short Read Sequence Typing for Bacterial Pathogens :homepage: https://github.com/katholt/srst2 :license: BSD :recipe: /`srst2 `_/`meta.yaml `_ .. conda:package:: srst2 |downloads_srst2| |docker_srst2| :versions: ``0.2.0-4``,  ``0.2.0-3``,  ``0.2.0-2``,  ``0.2.0-1``,  ``0.2.0-0``,  ``0.1.6-1``,  ``0.1.6-0``,  ``0.1.4.6-1``,  ``0.1.4.6-0`` :depends bowtie2: ``<=2.2.9`` :depends numpy: ``>=1.7.1`` :depends python: ``<3`` :depends samtools: ``0.1.18`` :depends scipy: ``>=0.12.0`` :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 srst2 and update with:: mamba update srst2 To create a new environment, run:: mamba create --name myenvname srst2 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/srst2: (see `srst2/tags`_ for valid values for ````) .. |downloads_srst2| image:: https://img.shields.io/conda/dn/bioconda/srst2.svg?style=flat :target: https://anaconda.org/bioconda/srst2 :alt: (downloads) .. |docker_srst2| image:: https://quay.io/repository/biocontainers/srst2/status :target: https://quay.io/repository/biocontainers/srst2 .. _`srst2/tags`: https://quay.io/repository/biocontainers/srst2?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/srst2/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/srst2/README.html