comparison elastic_tool_render.R @ 1:16e0f4b7a286 draft

planemo upload commit d255df0b70677f4d5e5f2f8e240ce0b69f40d69d

0:a163532ab267

#------------------------------------------------
options_and_arguments = read.table(paste0(Sys.getenv('REPORT_FILES_PATH'), '/options_and_arguments.txt'), 
                                   sep = '|', header = TRUE)


#-----------------render Rmd--------------
render(paste0(Sys.getenv('TOOL_INSTALL_DIR'), '/elastic_tool.Rmd'),
       output_file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/report.html'))

# for some unknow reason, directly using REPORT as the input value for output_file parameter
# in the render function can cause empty report file when the tool runs in batch mode.
# the solution is to render the rmarkdown to a explicitly specified file and then copy the
# file to ${REPORT}
system(command = 'cp ${REPORT_FILES_PATH}/report.html ${REPORT}')
#------------------------------------------


##--------end of code rendering .Rmd templates----------------
sink()

1:16e0f4b7a286

#------------------------------------------------
options_and_arguments = read.table(paste0(Sys.getenv('REPORT_FILES_PATH'), '/options_and_arguments.txt'), 
                                   sep = '|', header = TRUE)

#------------------------------------------------
# create three folders within working directory
dir.create('list')
dir.create('paired')
dir.create('list_paired')
print(Sys.getenv('JOB_WORKING_DIR'))
#-----------------render Rmd--------------
# copy R markdown file to working directory and render it within the working directory.
render(paste0(Sys.getenv('TOOL_INSTALL_DIR'), '/elastic_tool.Rmd'), 
       output_file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/report.html'))

# for some unknow reason, directly using REPORT as the input value for output_file parameter
# in the render function can cause empty report file when the tool runs in batch mode.
# the solution is to render the rmarkdown to a explicitly specified file and then copy the
# file to ${REPORT}
system(command = 'cp ${REPORT_FILES_PATH}/report.html ${REPORT}')
system(command = 'sh ${REPORT_FILES_PATH}/script.sh')
#------------------------------------------


##--------end of code rendering .Rmd templates----------------
sink()