- recipe scmap-cli
CLI scripts for the scmap package
- Homepage:
- License:
GPL / Apache 2.0
- Recipe:
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¶
- Versions:
0.1.0-0,0.0.11-1,0.0.11-0,0.0.10-0,0.0.9-0,0.0.8-0,0.0.5-0,0.0.4-0,0.0.3-0,0.1.0-0,0.0.11-1,0.0.11-0,0.0.10-0,0.0.9-0,0.0.8-0,0.0.5-0,0.0.4-0,0.0.3-0,0.0.2-1,0.0.2-0,0.0.1-0- Depends:
on bioconductor-biobase
on bioconductor-loomexperiment
on bioconductor-scmap
>=1.6.0,<1.7on bioconductor-singlecellexperiment
on r-optparse
on r-workflowscriptscommon
- Additional platforms:
Installation¶
You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).
Pixi¶
With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:
pixi global install scmap-cli
to add into an existing workspace instead, run:
pixi add scmap-cli
In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:
pixi workspace channel add conda-forge
pixi workspace channel add bioconda
Conda¶
With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:
conda install scmap-cli
Alternatively, to install into a new environment, run:
conda create -n envname scmap-cli
with envname being the name of the desired environment.
Container¶
Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:
docker pull quay.io/biocontainers/scmap-cli:<tag>
(see scmap-cli/tags for valid values for <tag>).
Integrated deployment¶
Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/scmap-cli/README.html)
