Introduction

systemPipeR is an R/Bioconductor package for building and running automated end-to-end analysis workflows for a wide range of research applications, including next-generation sequencing (NGS) experiments, such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq. Important features include a uniform workflow interface across different data analysis applications, automated report generation, and support for running both R and command-line software, such as NGS aligners or peak/variant callers, on local computers or compute clusters. The latter supports interactive job submissions and batch submissions to queuing systems of clusters. Efficient handling of complex sample sets and experimental designs is facilitated by a well-defined sample annotation infrastructure which improves reproducibility and user-friendliness of many typical analysis workflows in the NGS area.

Installation

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

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

To obtain the systemPipeR and systemPipeRdata, please run as follow:

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

Usage

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.

Load one of the available workflows into your current working directory. The following does this for the systemPipeR/SPchipseq workflow template. The name of the resulting workflow directory can be specified under the mydirname argument. The default NULL uses the name of the chosen workflow. An error is issued if a directory of the same name and path exists already.

library("systemPipeRdata") 
genWorkenvir(workflow="systemPipeR/SPchipseq", mydirname=NULL)
setwd("SPchipseq")

On Linux and OS X systems the same can be achieved from the command-line of a terminal with the following commands.

$ Rscript -e "systemPipeRdata::genWorkenvir(workflow='systemPipeR/SPchipseq', mydirname=NULL)"