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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 <style>
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7 pre code, pre, code {
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8 white-space: pre !important;
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9 overflow-x: scroll !important;
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10 word-break: keep-all !important;
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11 word-wrap: initial !important;
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12 }
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13 </style>
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14
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15 ```{r setup, include=FALSE, warning=FALSE, message=FALSE}
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16 knitr::opts_chunk$set(error = TRUE)
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17 ```
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18
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19 ## User input
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20
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21 ```{r, echo=FALSE}
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22 ##-------- build script files -----------
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23
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24 # build script file: script.sh
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25 df = read.table(paste0(Sys.getenv('REPORT_FILES_PATH'), '/options_and_arguments.txt'),
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26 sep = '|', header = TRUE)
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27
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28 # prepend A_TOOL_OUTPUT_PATH
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29 if (nrow(df[df$type == 'path_relative_to_a_tool', ]) > 0) {
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30 for (i in 1:nrow(df[df$type == 'path_relative_to_a_tool', ])) {
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31 root_path = readLines(df[df$type == 'path_relative_to_a_tool', ][i, 'path_type'])[1]
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32 df[df$type == 'path_relative_to_a_tool', ][i, 'value'] = paste(root_path,
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33 df[df$type == 'path_relative_to_a_tool', ][i, 'value'],
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34 sep = '/')
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35 }
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36 }
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37
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38 # get tool name
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39 tool_name = df[df$type == 'tool_name', 'value']
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40 # build script for displaying help messages (this probably should be tool specific)
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41 write(paste0(tool_name, ' -h'),
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42 file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/help.sh'))
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43
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44 knitr::kable(df)
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45
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46 # if the number of option/argument pairs is larger than 0, build script file
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47 df2 = df[df$type != 'tool_name', ]
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48 if (nrow(df2) > 0) {
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49 # write tool name as the first line of the script.sh
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50 # before running the job, cd into the ${REPORT_FILES_PATH} directory
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51 write(paste0(tool_name, ' \\'),
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52 paste0(Sys.getenv('REPORT_FILES_PATH'), '/script.sh'))
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53 df2 = df[df$type != 'tool_name', ]
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54 write(paste(' ', df2$flag, df2$value, '\\', sep = ' '),
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55 file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/script.sh'),
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56 append = TRUE )
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57 # remember that after writing option/argument lines to the script.sh, the last line
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58 # has an extra newline character '\' which causes a problem. We can either remove that extra
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59 # '\' or add a new line to the end. We choose to add a new line.
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60
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61 # add an extra line to the end to redirect stdout to stdout.txt and stderr to stderr.txt
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62 write(' > ${REPORT_FILES_PATH}/stdout.txt 2>${REPORT_FILES_PATH}/stderr.txt',
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63 paste0(Sys.getenv('REPORT_FILES_PATH'), '/script.sh'), append = TRUE)
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64 } else {
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65 # if no option/argument input, simply display the help message
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66 write(paste0(tool_name, ' -h'),
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67 file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/script.sh'))
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68 }
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69
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70 ```
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71
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72
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73 ```{bash, echo=FALSE}
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74 ## code to open help documentation
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75 sh ${REPORT_FILES_PATH}/help.sh > ${TOOL_HELP_DOC}
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76 ```
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77
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78
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79 ```{r, echo=FALSE}
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80 # create paths before running the job script
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81 df_paths = df[df$type == 'path_relative_to_this_tool', ]
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82
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83 if (nrow(df_paths) > 0) {
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84 for (i in 1:nrow(df_paths)) {
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85 path = paste0(Sys.getenv('REPORT_FILES_PATH'), '/', df_paths[i, 'value'])
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86 path_type = df_paths[i, 'path_type']
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87
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88 # create file paths
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89 if ((path_type == 'file_path') & !file.exists(path)) {
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90 dir_path = paste(head(strsplit(path, '/')[[1]], -1), collapse = '/' )
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91 if (!dir.exists(dir_path)) {
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92 dir.create(dir_path, recursive = TRUE)
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93 }
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94 file.create(path)
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95 }
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96
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97 # create dir paths
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98 if ((path_type == 'dir_path') & !dir.exists(path)) {
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99 dir.create(path, recursive = TRUE)
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100 }
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101 }
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102 }
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103 ```
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104
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105
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106 ```{bash, echo=FALSE}
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107 # run job script
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108 # it's important to run the job within the REPORT_FILES_PATH
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109 cd ${REPORT_FILES_PATH} && sh script.sh
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110 ```
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111
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112
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113
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114 ```{bash, results='asis', echo=FALSE}
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115 echo '## Job script'
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116 echo ''
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117 echo ''
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118 echo '```bash'
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119 cat ${REPORT_FILES_PATH}/script.sh
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120 echo '```'
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121 ```
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122
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123
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124 ```{r, echo=FALSE}
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125 ## obtain REPORT_FILES_PAHT and save it to a galaxy output.
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126 database_root = paste(head(strsplit(Sys.getenv('TOOL_LOG'), '/')[[1]], -1), collapse = '/')
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127 tool_output_dir_id = tail(strsplit(Sys.getenv('REPORT_FILES_PATH'), '/')[[1]], 1)
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128 tool_output_dir = paste0(database_root, '/', tool_output_dir_id)
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129 write(tool_output_dir, Sys.getenv('TOOL_OUTPUT_DIR'))
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130 ```
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131
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132
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133 ```{r, results='asis', echo=FALSE}
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134 cat('##All output files')
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135 cat('\n\n')
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136 all_files = list.files(path = Sys.getenv('REPORT_FILES_PATH'),
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137 full.names = TRUE,
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138 recursive = TRUE)
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139
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140 for (f in sub(Sys.getenv('REPORT_FILES_PATH'), '.', all_files) ) {
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141 cat('* [', f, '](', f, ')\n')
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142 }
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143 cat('\n')
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144 ```
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145
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