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3
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1 ##============ Sink warnings and errors to a file ==============
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2 ## use the sink() function to wrap all code within it.
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3 ##==============================================================
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4 zz = file(Sys.getenv('TOOL_LOG'))
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5 sink(zz)
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6 sink(zz, type = 'message')
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7
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8 #------------import libraries--------------------
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9 options(stringsAsFactors = FALSE)
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10
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11 library(rmarkdown)
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12 #------------------------------------------------
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13
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14 #------------------------------------------------
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15 options_and_arguments = read.table(paste0(Sys.getenv('REPORT_FILES_PATH'), '/options_and_arguments.txt'),
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16 sep = '|', header = TRUE)
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17
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18 #------------------------------------------------
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19 # create three folders within working directory
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20 dir.create('individual_outputs')
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21
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22 #-----------------render Rmd--------------
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23 # copy R markdown file to working directory and render it within the working directory.
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24 render(paste0(Sys.getenv('TOOL_INSTALL_DIR'), '/paired.Rmd'),
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25 output_file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/report.html'))
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26
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27 # for some unknow reason, directly using REPORT as the input value for output_file parameter
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28 # in the render function can cause empty report file when the tool runs in batch mode.
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29 # the solution is to render the rmarkdown to a explicitly specified file and then copy the
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30 # file to ${REPORT}
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31 system(command = 'cp ${REPORT_FILES_PATH}/report.html ${REPORT}')
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32 # system(command = 'sh ${REPORT_FILES_PATH}/script.sh')
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33 #------------------------------------------
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34
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35
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36 ##--------end of code rendering .Rmd templates----------------
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37 sink()
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38 ##=========== End of sinking output============================= |
