## ----style, echo = FALSE, results = 'asis'----------------
BiocStyle::markdown()
options(width=60, max.print=1000)
knitr::opts_chunk$set(
    eval=as.logical(Sys.getenv("KNITR_EVAL", "TRUE")),
    cache=as.logical(Sys.getenv("KNITR_CACHE", "TRUE")), 
    tidy.opts=list(width.cutoff=60), tidy=TRUE)

## ----setup, echo=FALSE, messages=FALSE, warnings=FALSE----
suppressPackageStartupMessages({
    library(systemPipeR)
    library(BiocParallel)
    library(Biostrings)
    library(Rsamtools)
    library(GenomicRanges)
    library(ggplot2)
    library(GenomicAlignments)
    library(ShortRead)
    library(ape)
    library(batchtools)
})

## ----genRibo_workflow_single, eval=FALSE------------------
#  library(systemPipeRdata)
#  genWorkenvir(workflow="riboseq")
#  setwd("riboseq")

## ----render_report, eval=FALSE----------------------------
#  rmarkdown::render("systemPipeRIBOseq.Rmd", "html_document")
#  rmarkdown::render("systemPipeRIBOseq.Rmd", "pdf_document")

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