:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'garnett-cli' .. highlight: bash garnett-cli =========== .. conda:recipe:: garnett-cli :replaces_section_title: :noindex: Collection of wrapper scripts for the Garnett scRNAseq cell type classification tool. :homepage: https://github.com/ebi-gene-expression-group/garnett-cli :license: Apache / Apache-2.0 :recipe: /`garnett-cli `_/`meta.yaml `_ .. conda:package:: garnett-cli |downloads_garnett-cli| |docker_garnett-cli| :versions: ``0.0.5-1``,  ``0.0.5-0``,  ``0.0.4-0``,  ``0.0.3-2``,  ``0.0.3-1``,  ``0.0.3-0``,  ``0.0.2-0``,  ``0.0.1-0``,  ``v0.0.1-0`` :depends bioconductor-org.hs.eg.db: :depends bioconductor-org.mm.eg.db: :depends monocle3-cli: ``0.0.7.*`` :depends r-garnett: ``0.2.8.*`` :depends r-glmnet: ``2.0_18.*`` :depends r-optparse: :depends r-workflowscriptscommon: :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 garnett-cli and update with:: mamba update garnett-cli To create a new environment, run:: mamba create --name myenvname garnett-cli 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/garnett-cli: (see `garnett-cli/tags`_ for valid values for ````) .. |downloads_garnett-cli| image:: https://img.shields.io/conda/dn/bioconda/garnett-cli.svg?style=flat :target: https://anaconda.org/bioconda/garnett-cli :alt: (downloads) .. |docker_garnett-cli| image:: https://quay.io/repository/biocontainers/garnett-cli/status :target: https://quay.io/repository/biocontainers/garnett-cli .. _`garnett-cli/tags`: https://quay.io/repository/biocontainers/garnett-cli?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/garnett-cli/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/garnett-cli/README.html