## ----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) }) ## ----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 ## ----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") ## ----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()