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1 ---
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2 title: 'Dynamic tool'
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3 output: html_document
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4 ---
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5
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6 ```{r setup, include=FALSE, warning=FALSE, message=FALSE}
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7 knitr::opts_chunk$set(error = TRUE)
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8 ```
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9
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10 ## User input
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11
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12 ```{r, echo=FALSE}
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13 ##-------- build script files -----------
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14
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15 # build script file: script.sh
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16 df = read.table(paste0(Sys.getenv('REPORT_FILES_PATH'), '/options_and_arguments.txt'),
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17 sep = '|', header = TRUE)
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18
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19 # get tool name
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20 tool_name = df[df$type == 'tool_name', 'value']
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21 # build script for displaying help messages (this probably should be tool specific)
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22 write(paste0(tool_name, ' -h'),
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23 file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/help.sh'))
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24
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25 knitr::kable(df[, c('flag', 'value')])
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26
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27 # if the number of option/argument pairs is larger than 0, build script file
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28 df2 = df[df$type != 'tool_name', ]
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29 if (nrow(df2) > 0) {
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30 # write tool name as the first line of the script.sh
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31 # before running the job, cd into the ${REPORT_FILES_PATH} directory
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32 write(paste0(tool_name, ' \\'),
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33 paste0(Sys.getenv('REPORT_FILES_PATH'), '/script.sh'))
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34 df2 = df[df$type != 'tool_name', ]
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35 write(paste(' ', df2$flag, df2$value, '\\', sep = ' '),
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36 file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/script.sh'),
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37 append = TRUE )
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38 # remember that after writing option/argument lines to the script.sh, the last line
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39 # has an extra newline character '\' which causes a problem. We can either remove that extra
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40 # '\' or add a new line to the end. We choose to add a new line.
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41
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42 # add an extra line to the end to redirect stdout to stdout.txt and stderr to stderr.txt
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43 write(' > ${REPORT_FILES_PATH}/stdout.txt 2>${REPORT_FILES_PATH}/stderr.txt',
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44 paste0(Sys.getenv('REPORT_FILES_PATH'), '/script.sh'), append = TRUE)
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45 } else {
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46 # if no option/argument input, simply display the help message
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47 write(paste0(tool_name, ' -h'),
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48 file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/script.sh'))
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49 }
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50
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51 ```
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52
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53
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54 ```{bash, echo=FALSE}
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55 ## code to open help documentation
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56 sh ${REPORT_FILES_PATH}/help.sh > ${TOOL_HELP_DOC}
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57 ```
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58
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59 ```{bash, results='asis', echo=FALSE}
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60 echo '## Show help documentation'
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61 echo ''
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62 echo ''
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63 echo '```bash'
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64 cat ${REPORT_FILES_PATH}/help.sh
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65 echo '```'
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66 ```
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67
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68
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69 ```{bash, echo=FALSE}
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70 # run job script
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71 # it's important to run the job within the REPORT_FILES_PATH
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72 cd ${REPORT_FILES_PATH} && sh script.sh
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73 ```
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74
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75 ```{bash, results='asis', echo=FALSE}
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76 echo '## Job script'
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77 echo ''
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78 echo ''
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79 echo '```bash'
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80 cat ${REPORT_FILES_PATH}/script.sh
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81 echo '```'
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82 ```
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83
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84
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85 ```{r, results='asis', echo=FALSE}
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86 cat('##All output files')
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87 cat('\n\n')
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88 all_files = list.files(path = Sys.getenv('REPORT_FILES_PATH'),
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89 full.names = TRUE,
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90 recursive = TRUE)
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91
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92 for (f in sub(Sys.getenv('REPORT_FILES_PATH'), '.', all_files) ) {
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93 cat('* [', f, '](', f, ')\n')
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94 }
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95 cat('\n')
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96 ```
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97
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