:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'galru' .. highlight: bash galru ===== .. conda:recipe:: galru :replaces_section_title: :noindex: Rapid spoligotyping for Mycobacterium tuberculosis directly from long read sequencing :homepage: https://github.com/quadram-institute-bioscience/galru :license: GPL3 :recipe: /`galru `_/`meta.yaml `_ .. conda:package:: galru |downloads_galru| |docker_galru| :versions: ``1.0.0-0``,  ``0.0.2-1``,  ``0.0.2-0`` :depends bedtools: :depends biopython: ``>=1.68`` :depends blast: :depends cd-hit: :depends minced: :depends minimap2: :depends mlst: :depends ncbi-genome-download: :depends pyfastaq: ``>=3.12`` :depends python: ``>=3`` :depends pyyaml: :depends samtools: :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 galru and update with:: mamba update galru To create a new environment, run:: mamba create --name myenvname galru 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/galru: (see `galru/tags`_ for valid values for ````) .. |downloads_galru| image:: https://img.shields.io/conda/dn/bioconda/galru.svg?style=flat :target: https://anaconda.org/bioconda/galru :alt: (downloads) .. |docker_galru| image:: https://quay.io/repository/biocontainers/galru/status :target: https://quay.io/repository/biocontainers/galru .. _`galru/tags`: https://quay.io/repository/biocontainers/galru?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/galru/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/galru/README.html