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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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5
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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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8 #-------------------preparation -----------------
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9 options(stringsAsFactors = FALSE)
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5
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10 # import libraries
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11 library(getopt)
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12 library(rmarkdown)
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13 library(htmltools)
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14 # load helper functions
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15 source(paste0(Sys.getenv('TOOL_INSTALL_DIR'), '/helper.R'))
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16 # import getopt specification matrix from a csv file
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17 opt = getopt(getopt_specification_matrix('getopt_specification.csv',
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18 tool_dir=Sys.getenv('TOOL_INSTALL_DIR')))
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19 # define a unix variable versions for all input values. this is useful when we
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20 # want to use input values by other programming language in r markdown
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21 do.call(Sys.setenv, opt[-1])
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22 #------------------------------------------------
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23
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24
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25 #-----------------render Rmd files --------------
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26 # NOTICE:
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27 # we should copy all rmarkdown files from tool install directory to REPORT_FILES_PATH directory.
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28 # and render rmarkdown files in the REPORT_FILES_PATH directory.
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29 file.copy(from = paste0(Sys.getenv('TOOL_INSTALL_DIR'), '/vakata-jstree-3.3.5'),
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30 to = Sys.getenv('REPORT_FILES_PATH'), recursive = TRUE)
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31 system(command = 'cp -r ${TOOL_INSTALL_DIR}/*.Rmd ${REPORT_FILES_PATH}')
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32 # render Rmd files in order
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33 render(input = paste0(Sys.getenv('REPORT_FILES_PATH'), '/htseq_count.Rmd'))
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34 # add more lines below if there are more Rmd files to be rendered
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35
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36 #------------------------------------------
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37
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38
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39 #---------------- copy the output html to REPORT ----
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40 system(command = 'cp ${REPORT_FILES_PATH}/htseq_count.html ${REPORT}')
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41 # add more lines below if there are more output html files
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42
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43 #==============the end==============
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44
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45
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46 ##--------end of code rendering .Rmd templates----------------
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47 sink()
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48 ##=========== End of sinking output============================= |
