systemPipeRdata

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systemPipeRdata: Workflow templates and sample data

systemPipeRdata is a helper package to generate with a single command workflow templates that are intended to be used by its parent package systemPipeR. The systemPipeR project provides a suite of R/Bioconductor packages for designing, building and running end-to-end analysis workflows on local machines, HPC clusters and cloud systems, while generating at the same time publication quality analysis reports.

To test workflows quickly or design new ones from existing templates, users can generate with a single command workflow instances fully populated with sample data and parameter files required for running a chosen workflow. Pre-configured directory structure of the workflow environment and the sample data used by systemPipeRdata are described here.

Installation

To install the package, please use the BiocManager::install command:

if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install("systemPipeRdata")

To obtain the most recent updates immediately, one can install it directly from github as follow:

if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install("tgirke/systemPipeRdata", build_vignettes=TRUE, dependencies=TRUE)

Due to the large size of the sample data (~320 MB) provided by systemPipeRdata, its download/install may take some time.

To install the parent package systemPipeR itself, please use the BiocManager::install method as instructed here.

Usage

Detailed user manuals are available here: