recipe scmap-cli

CLI scripts for the scmap package



GPL / Apache 2.0



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.

package scmap-cli

(downloads) docker_scmap-cli



depends bioconductor-biobase:

depends bioconductor-loomexperiment:

depends bioconductor-scmap:


depends bioconductor-singlecellexperiment:

depends r-optparse:

depends r-workflowscriptscommon:



You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see 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<tag>

(see `scmap-cli/tags`_ for valid values for ``<tag>``)

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