:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'pneumocat' .. highlight: bash pneumocat ========= .. conda:recipe:: pneumocat :replaces_section_title: :noindex: PneumoCaT \(Pneumococcal Capsular Typing\) uses a two\-step step approach to assign capsular type to S.pneumoniae genomic data \(Illumina\) :homepage: https://github.com/phe-bioinformatics/pneumocat :license: GPL / GPL-3.0 :recipe: /`pneumocat `_/`meta.yaml `_ .. conda:package:: pneumocat |downloads_pneumocat| |docker_pneumocat| :versions: ``1.2.1-1``,  ``1.2.1-0``,  ``1.2-3``,  ``1.2-2``,  ``1.2-0``,  ``1.1-0`` :depends biopython: :depends bowtie2: :depends lxml: :depends numpy: :depends pysam: :depends python: ``<3`` :depends pyyaml: :depends samtools: ``>1.3`` :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 pneumocat and update with:: mamba update pneumocat To create a new environment, run:: mamba create --name myenvname pneumocat 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/pneumocat: (see `pneumocat/tags`_ for valid values for ````) .. |downloads_pneumocat| image:: https://img.shields.io/conda/dn/bioconda/pneumocat.svg?style=flat :target: https://anaconda.org/bioconda/pneumocat :alt: (downloads) .. |docker_pneumocat| image:: https://quay.io/repository/biocontainers/pneumocat/status :target: https://quay.io/repository/biocontainers/pneumocat .. _`pneumocat/tags`: https://quay.io/repository/biocontainers/pneumocat?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/pneumocat/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/pneumocat/README.html