--- title: "_systemPipeRdata_: NGS workflow templates and sample data" author: "Author: Thomas Girke (thomas.girke@ucr.edu)" date: "Last update: `r format(Sys.time(), '%d %B, %Y')`" output: BiocStyle::html_document: toc: true toc_depth: 3 fig_caption: yes fontsize: 14pt bibliography: bibtex.bib --- ```{r style, echo = FALSE, results = 'asis'} BiocStyle::markdown() options(width=100, max.print=1000) knitr::opts_chunk$set( eval=as.logical(Sys.getenv("KNITR_EVAL", "TRUE")), cache=as.logical(Sys.getenv("KNITR_CACHE", "TRUE"))) ``` ```{r setup, echo=FALSE, messages=FALSE, warnings=FALSE} suppressPackageStartupMessages({ library(systemPipeR) library(systemPipeRdata) library(BiocGenerics) }) ``` Note: the most recent version of this vignette can be found here and a short overview slide show [here](https://htmlpreview.github.io/?https://github.com/tgirke/systemPipeR/blob/master/inst/extdata/slides/systemPipeRslides.html). # Introduction [_`systemPipeRdata`_](https://github.com/tgirke/systemPipeRdata) is a helper package to generate with a single command NGS workflow templates that are intended to be used by its parent package [_`systemPipeR`_](http://www.bioconductor.org/packages/devel/bioc/html/systemPipeR.html) [@Girke2014-oy]. The latter is an environment for building *end-to-end* analysis pipelines with automated report generation for next generation sequence (NGS) applications such as RNA-Seq, Ribo-Seq, ChIP-Seq, VAR-Seq and many others. The directory structure of the workflow templates and the sample data used by _`systemPipeRdata`_ are described [here](http://bioconductor.org/packages/release/bioc/vignettes/systemPipeR/inst/doc/systemPipeR.html#load-sample-data-and-workflow-templates).
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# Getting Started ## Installation The R software for using _`systemPipeRdata`_ can be downloaded from [CRAN](http://cran.at.r-project.org). The _`systemPipeRdata`_ package can be installed from within R as follows: ```{r install, eval=FALSE} source("http://bioconductor.org/biocLite.R") # Sources the biocLite.R installation script biocLite("tgirke/systemPipeRdata", build_vignettes=TRUE, dependencies=TRUE) # Installs from github biocLite("systemPipeRdata") # Installs from Bioconductor once available there ```
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## Loading package and documentation ```{r load_systemPipeRdata, eval=TRUE} library("systemPipeRdata") # Loads the package ``` ```{r documentation_systemPipeRdata, eval=FALSE} library(help="systemPipeRdata") # Lists package info vignette("systemPipeRdata") # Opens vignette ```
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## Generate workflow template Load one of the available NGS workflows into your current working directory. The following does this for the _`varseq`_ 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. ```{r generate_workenvir, eval=FALSE} genWorkenvir(workflow="varseq", mydirname=NULL) setwd("varseq") ``` On Linux and OS X systems the same can be achieved from the command-line of a terminal with the following commands. ```{.sh generate_workenvir_from_shell, eval=FALSE} $ Rscript -e "systemPipeRdata::genWorkenvir(workflow='varseq', mydirname=NULL)" ``` The workflow templates generated by _`genWorkenvir`_ contain the following preconfigured directory structure:

```{r workflow_template_structure, eval=FALSE} workflow_name/ # *.Rnw/*.Rmd scripts and targets file param/ # parameter files for command-line software data/ # inputs e.g. FASTQ, reference, annotations results/ # analysis result files ```
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## Run workflows Next, run from within R the chosen sample workflow by executing the code provided in the corresponding _`*.Rnw`_ template file. If preferred the corresponding _`*.Rmd`_ or _`*.R`_ versions can be used instead. Alternatively, one can run an entire workflow from start to finish with a single command by executing from the command-line _`'make -B'`_ within the workflow directory (here _`'varseq'`_). Much more detailed information on running and customizing [_`systemPipeR`_](http://www.bioconductor.org/packages/devel/bioc/html/systemPipeR.html) workflows is available in its overview vignette [here](http://www.bioconductor.org/packages/devel/bioc/vignettes/systemPipeR/inst/doc/systemPipeR.html). This vignette can also be opened from R with the following command. ```{r load_systemPipeR, eval=TRUE} library("systemPipeR") # Loads systemPipeR which needs to be installed via biocLite() from Bioconductor ``` ```{r documentation_systemPipeR, eval=FALSE} vignette("systemPipeR", package = "systemPipeR") ```
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## Return paths to sample data The location of the sample data provided by _`systemPipeRdata`_ can be returned as a _`list`_. ```{r return_samplepaths, eval=TRUE} pathList() ```
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# Version information ```{r sessionInfo} sessionInfo() ```
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# Funding This project was supported by funds from the National Institutes of Health (NIH) and the National Science Foundation (NSF).
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# References