Mercurial > repos > mingchen0919 > aurora_fastqc
view fastqc_render.R @ 2:5f00aef42904 draft
planemo upload commit 58ac10c63c4cc51b4122de0fa07b887ace6df657-dirty
author | mingchen0919 |
---|---|
date | Wed, 25 Apr 2018 15:55:23 -0400 |
parents | 2fbb7d627af1 |
children |
line wrap: on
line source
##============ Sink warnings and errors to a file ============== ## use the sink() function to wrap all code within it. ##============================================================== zz = file(paste0(Sys.getenv('REPORT_FILES_PATH'), '/.r_rendering.log.txt')) sink(zz) sink(zz, type = 'message') #============== preparation ==================================== options(stringsAsFactors = FALSE) # import libraries #------------------------------------------------------------------ # ADD MORE LIBRARIES HERE IF YOUR TOOL DEPENDS ON OTHER R LIBRARIES #------------------------------------------------------------------ library('getopt') library('rmarkdown') library('htmltools') library(plyr) library(dplyr) library(stringr) library(DT) library(reshape2) library(plotly) # load helper functions source(paste0(Sys.getenv('TOOL_INSTALL_DIR'), '/helper.R')) # import getopt specification matrix from a csv file opt = getopt(getopt_specification_matrix('getopt_specification.csv', tool_dir=Sys.getenv('TOOL_INSTALL_DIR'))) # define environment variables for all input values. this is useful when we # want to use input values by other programming language in r markdown do.call(Sys.setenv, opt[-1]) #=============================================================== #======================== render Rmd files ========================= # NOTICE: # we should copy all rmarkdown files from tool install directory to REPORT_FILES_PATH directory. # and render rmarkdown files in the REPORT_FILES_PATH directory. file.copy(from = paste0(Sys.getenv('TOOL_INSTALL_DIR'), '/vakata-jstree-3.3.5'), to = Sys.getenv('REPORT_FILES_PATH'), recursive = TRUE) system(command = 'cp -r ${TOOL_INSTALL_DIR}/*.Rmd ${REPORT_FILES_PATH}') #----------------BELOW IS WHERE YOU NEED TO CUSTOMIZE --------------------- render(input = paste0(Sys.getenv('REPORT_FILES_PATH'), '/fastqc.Rmd')) # add more lines below if there are more Rmd files to be rendered #=============================================================== #============== expose outputs to galaxy history =============== system(command = 'sh ${TOOL_INSTALL_DIR}/expose-outputs.sh') #=============================================================== ##--------end of code rendering .Rmd templates---------------- sink() ##=========== End of sinking output=============================