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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(DESeq2)
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14 library(pheatmap)
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15 library(DT)
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16 library(ggplot2)
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17 #------------------------------------------------
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18
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19
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20 #------------get arguments into R--------------------
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21 # getopt_specification_matrix(extract_short_flags('DESeq_results.xml')) %>%
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22 # write.table(file = 'spec.txt', sep = ',', row.names = FALSE, col.names = TRUE, quote = FALSE)
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23
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24
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25 spec_matrix = as.matrix(
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26 data.frame(stringsAsFactors=FALSE,
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27 long_flags = c("X_e", "X_W", "X_C", "X_T", "X_K", "X_M", "X_o",
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28 "X_d", "X_s", "X_R", "X_t"),
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29 short_flags = c("e", "W", "C", "T", "K", "M", "o", "d", "s", "R",
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30 "t"),
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31 argument_mask_flags = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L),
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32 data_type_flags = c("character", "character", "character", "character",
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33 "character", "character", "character",
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34 "character", "character", "character", "character")
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35 )
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36 )
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37 opt = getopt(spec_matrix)
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38 opt
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39 #----------------------------------------------------
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40
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41
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42 #-----------using passed arguments in R
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43 # to define system environment variables---
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44 do.call(Sys.setenv, opt[-1])
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45 #----------------------------------------------------
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46
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47 #---------- often used variables ----------------
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48 # OUTPUT_DIR: path to the output associated directory, which stores all outputs
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49 # TOOL_DIR: path to the tool installation directory
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50 # RMD_NAME: name of Rmd file to be rendered
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51 # OUTPUT_REPORT: path to galaxy output report
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52 OUTPUT_DIR = opt$X_d
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53 TOOL_DIR = opt$X_t
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54 RMD_NAME = 'DESeq_results.Rmd'
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55 OUTPUT_REPORT = opt$X_o
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56
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57 # create the output associated directory to store all outputs
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58 dir.create(OUTPUT_DIR, recursive = TRUE)
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59
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60 #-----------------render Rmd--------------
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61 render(paste0(TOOL_DIR, '/', RMD_NAME), output_file = OUTPUT_REPORT)
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62 #------------------------------------------
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63
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64 #==============the end==============
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65
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66
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67 ##--------end of code rendering .Rmd templates----------------
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68 sink()
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69 ##=========== End of sinking output============================= |
