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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 # library(dplyr)
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18 # getopt_specification_matrix(extract_short_flags('')) %>%
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19 # write.table(file = 'spec.txt', sep = ',', row.names = FALSE, col.names = TRUE, quote = FALSE)
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20
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21
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22 spec_matrix = as.matrix(
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23 data.frame(stringsAsFactors=FALSE,
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24 long_flags = c("X_e", "X_o", "X_d", "X_s", "X_t", "X_A", "X_B", "X_G",
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25 "X_f", "X_r", "X_S", "X_a", "X_T", "X_i", "X_m", "X_c", "X_O"),
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26 short_flags = c("e", "o", "d", "s", "t", "A", "B", "G", "f", "r", "S",
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27 "a", "T", "i", "m", "c", "O"),
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28 argument_mask_flags = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
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29 1L, 1L, 1L, 1L),
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30 data_type_flags = c("character", "character", "character", "character",
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31 "character", "character", "character", "character",
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32 "character", "character", "character", "character",
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33 "character", "character", "character", "character",
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34 "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 #----------------------------------------------------
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39
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40
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41 #-----------using passed arguments in R
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42 # to define system environment variables---
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43 do.call(Sys.setenv, opt[-1])
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44 #----------------------------------------------------
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45
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46 #---------- often used variables ----------------
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47 # OUTPUT_REPORT: path to galaxy output report
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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 OUTPUT_DIR = opt$X_d
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51 TOOL_DIR = opt$X_t
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52 OUTPUT_REPORT = opt$X_o
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53
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54
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55 # create the output associated directory to store all outputs
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56 dir.create(OUTPUT_DIR, recursive = TRUE)
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57
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58 #-----------------render site--------------
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59 # copy site generating materials into OUTPUT_DIR
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60 dir.create(paste0(OUTPUT_DIR, '/site_generator'), recursive = TRUE)
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61 system(paste0('cp -r ', TOOL_DIR, '/htseq_count.Rmd ', OUTPUT_DIR, '/site_generator/htseq_count.Rmdd'))
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62 system(paste0('cp -r ', TOOL_DIR, '/htseq_count_site.yml ', OUTPUT_DIR, '/site_generator/_site.yml'))
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63 system(paste0('cp -r ', TOOL_DIR, '/htseq_count_index.Rmd ', OUTPUT_DIR, '/site_generator/index.Rmd'))
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64 # render site to OUTPUT_DIR/_site, this is configured in the "_site.yml" file
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65 render_site(input = paste0(OUTPUT_DIR, '/site_generator'))
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66 # remove site generating materials from output associated directory
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67 unlink(paste0(OUTPUT_DIR, '/site_generator'), recursive = TRUE)
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68 # move _site/* into output associated directory
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69 move_cmd = paste0('mv ', OUTPUT_DIR, '/_site/* ', OUTPUT_DIR)
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70 system(move_cmd)
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71 #------------------------------------------
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72
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73 #-----link index.html to output-----
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74 cp_index = paste0('cp ', OUTPUT_DIR, '/index.html ', OUTPUT_REPORT)
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75 system(cp_index)
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76 #-----------------------------------
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77
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78 #==============the end==============
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79
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80
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81 ##--------end of code rendering .Rmd templates----------------
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82 sink()
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83 ##=========== End of sinking output============================= |
