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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('warnings_and_errors.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 #------------import libraries--------------------
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9 options(stringsAsFactors = FALSE)
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10
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11 library(getopt)
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12 library(rmarkdown)
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13 #------------------------------------------------
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14
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15
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16 #------------get arguments into R--------------------
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17 # load helper function
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18 source(paste0(Sys.getenv('TOOL_DIR'), '/helper.R'))
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19 # import getopt specification matrix from a csv file
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20 opt = getopt(getopt_specification_matrix(specification_file = 'getopt_specification.csv',
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21 tool_dir = Sys.getenv('TOOL_DIR')))
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22 opt$X_t = Sys.getenv('TOOL_DIR')
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23 #----------------------------------------------------
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24
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25
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26 #-----------using passed arguments in R
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27 # to define system environment variables---
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28 do.call(Sys.setenv, opt[-1])
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29 #----------------------------------------------------
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30
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31 #---------- often used variables ----------------
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32 # OUTPUT_DIR: path to the output associated directory, which stores all outputs
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33 # TOOL_DIR: path to the tool installation directory
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34 OUTPUT_DIR = opt$X_d
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35 TOOL_DIR = opt$X_t
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36 OUTPUT_REPORT = opt$X_o
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37 RMD_NAME = 'interproscan.Rmd'
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38
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39 # create the output associated directory to store all outputs
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40 dir.create(OUTPUT_DIR, recursive = TRUE)
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41
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42 #-----------------render Rmd--------------
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43 # for some unknow reason, directly using REPORT as the input value for output_file parameter
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44 # in the render function can cause empty report file when the tool runs in batch mode.
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45 # the solution is to render the rmarkdown to a explicitly specified file and then copy the
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46 # file to ${REPORT}
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47 render(paste0(TOOL_DIR, '/', RMD_NAME),
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48 output_file = paste0(Sys.getenv('OUTPUT_DIR'), '/report.html'))
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49 system(command = 'cp ${OUTPUT_DIR}/report.html ${OUTPUT_REPORT}')
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50 #------------------------------------------
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51
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52 #==============the end==============
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53
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54
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55 ##--------end of code rendering .Rmd templates----------------
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56 sink()
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57 ##=========== End of sinking output============================= |
