inst/doc/RGalaxy-vignette.R

In RGalaxy: Make an R function available in the Galaxy web platform

## ----setup, echo=FALSE---------------------------------------------------
options(width = 75)
options(useFancyQuotes=FALSE)

## ----hook-printfun, echo=FALSE-------------------------------------------
library(knitr)
library(formatR)
knit_hooks$set(printfun = function(before, options, envir) {
  if (before) return()
  txt = capture.output(dump(options$printfun, '', envir = envir))
  ## reformat if tidy=TRUE
  if (options$tidy)
  	txt = tidy.source(text=txt, output=FALSE,
  		width.cutoff=30L, keep.comment=TRUE,
  		keep.blank.line=FALSE)$text.tidy
  paste(c('\n```r\n', txt, '\n```\n'), collapse="\n")
})

## ----hook-printmanpage, echo=FALSE---------------------------------------
knit_hooks$set(printmanpage = function(before, options, envir) {
  if (before) return()
    manpage <- file.path("..", "man",
      sprintf("%s.Rd", options$printmanpage))
  lines <- readLines(manpage)
  ret <- "\n"
  for (line in lines)
  {
      ret <- paste(ret, "\t", line, "\n", sep="")
  }
  ret
})

## ----library_RGalaxy_fake, eval=FALSE------------------------------------
#  library(RGalaxy)

## ----library_RGalaxy_real, echo=FALSE, results="hide"--------------------
suppressPackageStartupMessages(library(RGalaxy))

## ----addTwoNumbers, printfun='addTwoNumbers', echo=FALSE, tidy=FALSE-----
#source code goes here

## ----run_addTwoNumbers---------------------------------------------------
t <- tempfile()
addTwoNumbers(2, 2, t)
readLines(t, warn=FALSE)

## ----addTwoNumbers_man, printmanpage='addTwoNumbers', echo=FALSE, tidy=FALSE----
#source code goes here

## ----galaxyHomeSetup, echo=FALSE, results="hide"-------------------------
if (!exists("galaxyHome"))
  galaxyHome <- getwd()
toolDir <- "RGalaxy_test_tool"
funcName <- "functionToGalaxify"

file.copy(system.file("galaxy", "tool_conf.xml", package="RGalaxy"),
    file.path(galaxyHome, "tool_conf.xml"), overwrite=FALSE)
 if(!file.exists("test-data")) dir.create("test-data", )

## ----run_galaxy, tidy=FALSE----------------------------------------------
galaxy("addTwoNumbers",
    galaxyConfig=
      GalaxyConfig(galaxyHome, "mytool", "Test Section",
        "testSectionId")
    )

## ----addTwoNumbersWithTest, printfun='addTwoNumbersWithTest', echo=FALSE, tidy=FALSE----
#source code goes here

## ----runFunctionalTest---------------------------------------------------
runFunctionalTest(addTwoNumbersWithTest)

## ----withRserve, tidy=FALSE, eval=FALSE----------------------------------
#  galaxy("addTwoNumbersWithTest",
#      galaxyConfig=
#        GalaxyConfig(galaxyHome, "mytool", "Test Section",
#          "testSectionId"),
#      RserveConnection=RserveConnection()
#      )

## ----install_RSclient, eval=FALSE----------------------------------------
#  if (!requireNamespace("BiocManager", quietly = TRUE))
#      install.packages("BiocManager")
#  BiocManager::install("RSclient", site_repository="http://www.rforge.net")

## ----RserveConnection----------------------------------------------------
RserveConnection(host="mymachine", port=2012L)

## ----probeLookup, printfun='probeLookup', echo=FALSE, tidy=FALSE---------
#source code goes here

## ----test_probeLookup----------------------------------------------------
runFunctionalTest(probeLookup)