Package Recipe 'bioconductor-reusedata'

recipe bioconductor-reusedata

Reusable and reproducible Data Management

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/ReUseData.html
License:: GPL-3
Recipe:: /bioconductor-reusedata/meta.yaml

ReUseData is an _R/Bioconductor_ software tool to provide a systematic and versatile approach for standardized and reproducible data management. ReUseData facilitates transformation of shell or other ad hoc scripts for data preprocessing into workflow-based data recipes. Evaluation of data recipes generate curated data files in their generic formats (e.g., VCF, bed). Both recipes and data are cached using database infrastructure for easy data management and reuse. Prebuilt data recipes are available through ReUseData portal ("https://rcwl.org/dataRecipes/") with full annotation and user instructions. Pregenerated data are available through ReUseData cloud bucket that is directly downloadable through "getCloudData()".

package bioconductor-reusedata¶

Versions:

1.10.0-0, 1.6.0-0, 1.0.0-0

Depends:

on bioconductor-basilisk >=1.22.0,<1.23.0
on bioconductor-biocfilecache >=3.0.0,<3.1.0
on bioconductor-rcwl >=1.26.0,<1.27.0
on bioconductor-rcwlpipelines >=1.26.0,<1.27.0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on r-base >=4.5,<4.6.0a0
on r-jsonlite
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-reusedata

to add into an existing workspace instead, run:

pixi add bioconductor-reusedata

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-reusedata

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-reusedata

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-reusedata:<tag>

(see bioconductor-reusedata/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-reusedata/README.html)