:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'scmap-cli' .. highlight: bash scmap-cli ========= .. conda:recipe:: scmap-cli :replaces_section_title: :noindex: CLI scripts for the scmap package :homepage: https://github.com/ebi-gene-expression-group/scmap-cli :license: GPL / Apache 2.0 :recipe: /`scmap-cli `_/`meta.yaml `_ A set of wrappers for operations associated with the scmap package. Functions in R packages are hard to call when building workflows outside of R\, so this package adds a set of simple wrappers with robust argument parsing. Intermediate steps are currently mainly serialized R objects\, but the ultimate objective is to have language\-agnostic intermediate formats allowing composite workflows using a variety of software packages. .. conda:package:: scmap-cli |downloads_scmap-cli| |docker_scmap-cli| :versions: .. raw:: html
0.1.0-00.0.11-10.0.11-00.0.10-00.0.9-00.0.8-00.0.5-00.0.4-00.0.3-0 ``0.1.0-0``,  ``0.0.11-1``,  ``0.0.11-0``,  ``0.0.10-0``,  ``0.0.9-0``,  ``0.0.8-0``,  ``0.0.5-0``,  ``0.0.4-0``,  ``0.0.3-0``,  ``0.0.2-1``,  ``0.0.2-0``,  ``0.0.1-0`` .. raw:: html
:depends bioconductor-biobase: :depends bioconductor-loomexperiment: :depends bioconductor-scmap: ``>=1.6.0,<1.7`` :depends bioconductor-singlecellexperiment: :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 scmap-cli and update with:: mamba update scmap-cli To create a new environment, run:: mamba create --name myenvname scmap-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/scmap-cli: (see `scmap-cli/tags`_ for valid values for ````) .. |downloads_scmap-cli| image:: https://img.shields.io/conda/dn/bioconda/scmap-cli.svg?style=flat :target: https://anaconda.org/bioconda/scmap-cli :alt: (downloads) .. |docker_scmap-cli| image:: https://quay.io/repository/biocontainers/scmap-cli/status :target: https://quay.io/repository/biocontainers/scmap-cli .. _`scmap-cli/tags`: https://quay.io/repository/biocontainers/scmap-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/scmap-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/scmap-cli/README.html