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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 library(genefilter)
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18 library(RColorBrewer)
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19 #------------------------------------------------
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20
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21
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22 #------------get arguments into R--------------------
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23 # getopt_specification_matrix(extract_short_flags('fastqc_report.xml')) %>%
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24 # write.table(file = 'spec.txt', sep = ',', row.names = FALSE, col.names = TRUE, quote = FALSE)
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25
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26
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27 spec_matrix = as.matrix(
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28 data.frame(stringsAsFactors=FALSE,
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29 long_flags = c("X_e", "X_o", "X_d", "X_s", "X_t", "X_P", "X_N",
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30 "X_S", "X_p", "X_w"),
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31 short_flags = c("e", "o", "d", "s", "t", "P", "N", "S", "p", "w"),
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32 argument_mask_flags = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L),
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33 data_type_flags = c("character", "character", "character", "character",
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34 "character", "character", "character",
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35 "character", "character", "character")
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36 )
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37 )
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38 opt = getopt(spec_matrix)
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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_REPORT: path to galaxy output report
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49 # OUTPUT_DIR: path to the output associated directory, which stores all outputs
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50 # TOOL_DIR: path to the tool installation directory
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51 OUTPUT_DIR = opt$X_d
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52 TOOL_DIR = opt$X_t
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53 OUTPUT_REPORT = opt$X_o
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54
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55
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56 # create the output associated directory to store all outputs
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57 dir.create(OUTPUT_DIR, recursive = TRUE)
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58
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59 #-----------------render site--------------
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60 # copy site generating materials into OUTPUT_DIR
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61 dir.create(paste0(OUTPUT_DIR, '/site_generator'), recursive = TRUE)
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62 command_cp = paste0('cp -r ', TOOL_DIR, '/DESeq_0*.Rmd ', OUTPUT_DIR, '/site_generator')
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63 system(command_cp)
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64 system(paste0('cp -r ', TOOL_DIR, '/DESeq_site.yml ', OUTPUT_DIR, '/site_generator/_site.yml'))
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65 system(paste0('cp -r ', TOOL_DIR, '/DESeq_index.Rmd ', OUTPUT_DIR, '/site_generator/index.Rmd'))
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66 # render site to OUTPUT_DIR/_site, this is configured in the "_site.yml" file
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67 dir.create(paste0(OUTPUT_DIR, '/_site'))
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68 render_site(input = paste0(OUTPUT_DIR, '/site_generator'))
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69 # remove site generating materials from output associated directory
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70 print(unlink(paste0(OUTPUT_DIR, '/site_generator'), recursive = TRUE))
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71 # move _site/* into output associated directory
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72 move_cmd = paste0('mv ', OUTPUT_DIR, '/_site/* ', OUTPUT_DIR)
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73 system(move_cmd)
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74 #------------------------------------------
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75
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76 #-----link index.html to output-----
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77 cp_index = paste0('cp ', OUTPUT_DIR, '/index.html ', OUTPUT_REPORT)
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78 system(cp_index)
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79 #-----------------------------------
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80
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81 #==============the end==============
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82
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83
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84 ##--------end of code rendering .Rmd templates----------------
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85 sink()
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86 ##=========== End of sinking output============================= |
