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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
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
systemPipeRdata are described here.
To install the package, please use the
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.
Detailed user manuals are available here: