:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'mtb-snp-it' .. highlight: bash mtb-snp-it ========== .. conda:recipe:: mtb-snp-it :replaces_section_title: :noindex: SNP\-IT\: Whole genome SNP based identification of members of the Mycobacterium tuberculosis complex. :homepage: https://github.com/samlipworth/snpit :license: MIT :recipe: /`mtb-snp-it `_/`meta.yaml `_ :links: doi: :doi:`10.3201/eid2503.180894` Whole genome SNP based identification of members of the Mycobacterium tuberculosis complex. Based on code originally written by Samuel Lipworth and turned into a package by Philip Fowler. SNP\-IT allows rapid Mycobacterial speciation of VCF or FASTA files aligned to NC000962 \(H37rV\). .. conda:package:: mtb-snp-it |downloads_mtb-snp-it| |docker_mtb-snp-it| :versions: ``1.1-1``,  ``1.1-0``,  ``0.1.0-0`` :depends biopython: :depends python: :depends pyvcf: :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 mtb-snp-it and update with:: mamba update mtb-snp-it To create a new environment, run:: mamba create --name myenvname mtb-snp-it 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/mtb-snp-it: (see `mtb-snp-it/tags`_ for valid values for ````) .. |downloads_mtb-snp-it| image:: https://img.shields.io/conda/dn/bioconda/mtb-snp-it.svg?style=flat :target: https://anaconda.org/bioconda/mtb-snp-it :alt: (downloads) .. |docker_mtb-snp-it| image:: https://quay.io/repository/biocontainers/mtb-snp-it/status :target: https://quay.io/repository/biocontainers/mtb-snp-it .. _`mtb-snp-it/tags`: https://quay.io/repository/biocontainers/mtb-snp-it?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/mtb-snp-it/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/mtb-snp-it/README.html