view deseq2_render.R @ 9:f8c7138cfc35 draft

planemo upload commit 92144072ce2bd29bf437bde994b9700e03d79f1b-dirty

##============ 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('ggplot2')
library('plotly')
library('DESeq2')
library('pheatmap')
library('DT')

# 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'), '/deseq2.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=============================