## ----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")))

## ----setup, echo=FALSE, messages=FALSE, warnings=FALSE-------------------
suppressPackageStartupMessages({
    library(systemPipeR)
    library(systemPipeRdata)
    library(BiocGenerics)
})

## ----load_systemPipeRdata, eval=TRUE-------------------------------------
library("systemPipeRdata") # Loads the package

## ----documentation_systemPipeRdata, eval=FALSE---------------------------
## library(help="systemPipeRdata") # Lists package info
## vignette("systemPipeRdata") # Opens vignette

## ----generate_workenvir, eval=FALSE--------------------------------------
## genWorkenvir(workflow="varseq", mydirname=NULL)
## setwd("varseq")

## ----generate_workenvir_from_shell, eval=FALSE, engine="sh"--------------
## $ Rscript -e "systemPipeRdata::genWorkenvir(workflow='varseq', mydirname=NULL)"

## ----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

## ----load_systemPipeR, eval=TRUE-----------------------------------------
library("systemPipeR") # Loads systemPipeR which needs to be installed via biocLite() from Bioconductor 

## ----documentation_systemPipeR, eval=FALSE-------------------------------
## vignette("systemPipeR", package = "systemPipeR")

## ----return_samplepaths, eval=TRUE---------------------------------------
pathList()

## ----sessionInfo---------------------------------------------------------
sessionInfo()