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1
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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 library(stringr)
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14 #------------------------------------------------
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15
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16
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17 #------------get arguments into R--------------------
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18 # load helper function
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19 source(paste0(Sys.getenv('TOOL_DIR'), '/helper.R'))
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20 # import getopt specification matrix from a csv file
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21 opt = getopt(getopt_specification_matrix('getopt_specification.csv'))
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22 opt$X_t = Sys.getenv('TOOL_DIR')
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23 working_dir = getwd()
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24 Sys.setenv(WORKING_DIR = working_dir)
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25 #----------------------------------------------------
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26
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27
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28 #-----------using passed arguments in R
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29 # to define system environment variables---
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30 do.call(Sys.setenv, opt[-1])
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31 #----------------------------------------------------
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32
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33 #---------- often used variables ----------------
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34 # OUTPUT_DIR: path to the output associated directory, which stores all outputs
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35 # TOOL_DIR: path to the tool installation directory
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36 OUTPUT_DIR = opt$X_d
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37 TOOL_DIR = opt$X_t
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38 OUTPUT_REPORT = opt$X_o
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39 RMD_NAME = 'fastq_dump.Rmd'
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40
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41
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42 # create the output associated directory to store all outputs
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43 dir.create(OUTPUT_DIR, recursive = TRUE)
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44
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45 #-----------------render Rmd--------------
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46 render(paste0(TOOL_DIR, '/', RMD_NAME), output_file = OUTPUT_REPORT)
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47 #------------------------------------------
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48
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49 #==============the end==============
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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============================= |
