Package Recipe 'bioconductor-rcwl'

recipe bioconductor-rcwl

An R interface to the Common Workflow Language

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/Rcwl.html
License:: GPL-2 | file LICENSE
Recipe:: /bioconductor-rcwl/meta.yaml

The Common Workflow Language (CWL) is an open standard for development of data analysis workflows that is portable and scalable across different tools and working environments. Rcwl provides a simple way to wrap command line tools and build CWL data analysis pipelines programmatically within R. It increases the ease of usage, development, and maintenance of CWL pipelines.

package bioconductor-rcwl¶

Versions:

1.26.0-0, 1.22.0-0, 1.18.0-0, 1.16.0-0, 1.14.0-0, 1.10.0-0, 1.8.0-0, 1.6.0-0, 1.4.2-0

Depends:

on bioconductor-basilisk >=1.22.0,<1.23.0
on bioconductor-biocparallel >=1.44.0,<1.45.0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on r-base >=4.5,<4.6.0a0
on r-batchtools
on r-codetools
on r-diagrammer
on r-r.utils
on r-shiny
on r-yaml

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 bioconductor-rcwl

to add into an existing workspace instead, run:

pixi add bioconductor-rcwl

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 bioconductor-rcwl

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-rcwl

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/bioconductor-rcwl:<tag>

(see bioconductor-rcwl/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:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-rcwl/README.html)