:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'scagaire' .. highlight: bash scagaire ======== .. conda:recipe:: scagaire :replaces_section_title: :noindex: Scagaire allows you to take in gene predictions from a metagenomic sample and filter them by bacterial\/pathogenic species :homepage: https://github.com/quadram-institute-bioscience/scagaire :license: GPLv3 :recipe: /`scagaire `_/`meta.yaml `_ .. conda:package:: scagaire |downloads_scagaire| |docker_scagaire| :versions: ``0.0.4-0`` :depends biopython: ``>=1.68`` :depends mash: :depends python: ``>=3`` :depends pyyaml: :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 scagaire and update with:: mamba update scagaire To create a new environment, run:: mamba create --name myenvname scagaire 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/scagaire: (see `scagaire/tags`_ for valid values for ````) .. |downloads_scagaire| image:: https://img.shields.io/conda/dn/bioconda/scagaire.svg?style=flat :target: https://anaconda.org/bioconda/scagaire :alt: (downloads) .. |docker_scagaire| image:: https://quay.io/repository/biocontainers/scagaire/status :target: https://quay.io/repository/biocontainers/scagaire .. _`scagaire/tags`: https://quay.io/repository/biocontainers/scagaire?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/scagaire/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/scagaire/README.html