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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(paste0(Sys.getenv('REPORT_FILES_PATH'), '/.r_rendering.log.txt'))
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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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7
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8 #============== preparation ====================================
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9 options(stringsAsFactors = FALSE)
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10 # import libraries
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11 #------------------------------------------------------------------
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12 # ADD MORE LIBRARIES HERE IF YOUR TOOL DEPENDS ON OTHER R LIBRARIES
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13 #------------------------------------------------------------------
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14 library('getopt')
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15 library('rmarkdown')
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16 library('htmltools')
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17
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18
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19 # load helper functions
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20 source(paste0(Sys.getenv('TOOL_INSTALL_DIR'), '/helper.R'))
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21 # import getopt specification matrix from a csv file
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22 opt = getopt(getopt_specification_matrix('getopt_specification.csv',
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23 tool_dir=Sys.getenv('TOOL_INSTALL_DIR')))
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24 # define environment variables for all input values. this is useful when we
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25 # want to use input values by other programming language in r markdown
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26 do.call(Sys.setenv, opt[-1])
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27 #===============================================================
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28
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29
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30 #======================== render Rmd files =========================
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31 # NOTICE:
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32 # we should copy all rmarkdown files from tool install directory to REPORT_FILES_PATH directory.
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33 # and render rmarkdown files in the REPORT_FILES_PATH directory.
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34 file.copy(from = paste0(Sys.getenv('TOOL_INSTALL_DIR'), '/vakata-jstree-3.3.5'),
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35 to = Sys.getenv('REPORT_FILES_PATH'), recursive = TRUE)
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36 system(command = 'cp -r ${TOOL_INSTALL_DIR}/*.Rmd ${REPORT_FILES_PATH}')
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37 # for rendering a site
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38 system(command = 'cp -r ${TOOL_INSTALL_DIR}/_site.yml ${REPORT_FILES_PATH}')
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39
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40 #----------------BELOW IS WHERE YOU NEED TO CUSTOMIZE ---------------------
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41 render(input = paste0(Sys.getenv('REPORT_FILES_PATH'), '/rmarkdown_report.Rmd'))
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42 # add more lines below if there are more Rmd files to be rendered
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43
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44 #===============================================================
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45
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46
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47 #============== expose outputs to galaxy history ===============
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48 system(command = 'sh ${TOOL_INSTALL_DIR}/expose-outputs.sh')
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49 #===============================================================
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50
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51
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52 ##--------end of code rendering .Rmd templates----------------
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53 sink()
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54 ##=========== End of sinking output=============================
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