recipe bioconductor-reusedata

Reusable and reproducible Data Management

Homepage:

https://bioconductor.org/packages/3.18/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

(downloads) docker_bioconductor-reusedata

versions:

1.6.0-0,  1.0.0-0

depends bioconductor-basilisk:

>=1.18.0,<1.19.0

depends bioconductor-biocfilecache:

>=2.14.0,<2.15.0

depends bioconductor-rcwl:

>=1.22.0,<1.23.0

depends bioconductor-rcwlpipelines:

>=1.22.0,<1.23.0

depends bioconductor-s4vectors:

>=0.44.0,<0.45.0

depends r-base:

>=4.4,<4.5.0a0

depends r-jsonlite:

depends r-yaml:

requirements:

additional platforms:

Installation

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 bioconductor-reusedata

and update with::

   mamba update bioconductor-reusedata

To create a new environment, run:

mamba create --name myenvname bioconductor-reusedata

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/bioconductor-reusedata:<tag>

(see `bioconductor-reusedata/tags`_ for valid values for ``<tag>``)

Download stats

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/bioconductor-reusedata/README.html)