%\VignetteIndexEntry{Vignette for systemPipeRdata}
%\VignetteDepends{systemPipeR}
%\VignetteKeywords{compute cluster, pipeline, reports}
%\VignetteEngine{knitr::knitr}
%\VignettePackage{systemPipeRdata}

% Generate vignette with knitr
% R CMD Sweave --engine=knitr::knitr --pdf systemPipeRdata.Rnw

\documentclass{article}
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@

\usepackage[authoryear,round]{natbib}
\bibliographystyle{plainnat}
\def\bibsection{\section{References}}

\usepackage{graphicx}
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\usepackage{hyperref}
\usepackage{url}
\usepackage{float}

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\usepackage{fancyhdr}
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\rhead{\nouppercase{\leftmark}}
\lhead{\textit{systemPipeRdata}}
\rfoot{\thepage}

\begin{document}

<<setup, include=FALSE, cache=FALSE>>=
library(knitr)
# set global chunk options for knitr
opts_chunk$set(comment=NA, warning=FALSE, message=FALSE, fig.path='figure/systemPipeR-')
options(formatR.arrow=TRUE, width=95)
unlink("test.db")
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\title{\Rpackage{systemPipeRdata}: sample data for NGS workflows}
\author{Thomas Girke}
\maketitle

\tableofcontents

\section{Introduction}
This package provides sample data for running the NGS workflows of the \Rpackage{systemPipeR} package \citep{Girke2014-oy}. The source and usage of the data is described in the overview vignette \href{http://www.bioconductor.org/packages/devel/bioc/html/systemPipeR.html}{\textcolor{blue}{here}}.

\section{Getting Started}

\subsection{Installation}
The R software for running \Rpackage{systemPipeR} and \Rpackage{systemPipeRdata} can be downloaded from CRAN (\url{http://cran.at.r-project.org/}). The \Rpackage{systemPipeR} environment can be installed from R using the \Rfunction{biocLite} install command. 
<<eval=FALSE>>=
source("http://bioconductor.org/biocLite.R") # Sources the biocLite.R installation script 
biocLite("systemPipeR") # Installs systemPipeR from Bioconductor 
biocLite("tgirke/systemPipeRdata", build_vignettes=TRUE, dependencies=TRUE) # From github
@

\subsection{Generate workflow template}
Load one of the available NGS workflows into your current working directory (here for varseq).
<<eval=FALSE>>=
genWorkenvir(workflow="varseq")
setwd("varseq")
@

\subsection{Run workflow}
Next, run the chosen sample workflow by executing from the command-line \Rfunction{'make -B'} within the \Robject{'varseq'} directory. Alternatively, one can run the code from the provided \Robject{*.Rnw} template file from within R interactively. Much more detailed information is available in \Rpackage{systemPipeR's} overview and workflow vignettes available \href{http://www.bioconductor.org/packages/devel/bioc/html/systemPipeR.html}{\textcolor{blue}{here}}.

The BioC 2015 vignette is available \href{https://htmlpreview.github.io/?https://github.com/tgirke/systemPipeRdata/blob/master/vignettes/systemPipeR_Presentation.html}{\textcolor{blue}{here}}. It also can be opened with the following command. 
<<eval=FALSE>>=
vignette("systemPipeR_Presentation", package = "systemPipeRdata")
@

\section{Version Information}
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toLatex(sessionInfo())
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\section{Funding}
This project was supported by funds from the National Institutes of Health (NIH).

\bibliography{bibtex}

\end{document}