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1 ---
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2 title: 'Tool Report'
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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$set(error = TRUE)
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17 ```
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18
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19 ## User input
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20
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21 ```{r, 'display user input'}
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22 # get user input and save it into a data frame.
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23 df = read.table(paste0(Sys.getenv('REPORT_FILES_PATH'), '/options_and_arguments.txt'),
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24 sep = '|', header = TRUE)
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25
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26 # if the input type is 'path_relative_to_a_tool', prepend A_TOOL_OUTPUT_PATH to the value to make
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27 # the value a full path.
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28 if (nrow(df[df$type == 'path_relative_to_a_tool', ]) > 0) {
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29 for (i in 1:nrow(df[df$type == 'path_relative_to_a_tool', ])) {
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30 root_path = readLines(df[df$type == 'path_relative_to_a_tool', ][i, 'path_type'])[1]
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31 df[df$type == 'path_relative_to_a_tool', ][i, 'value'] = paste(root_path,
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32 df[df$type == 'path_relative_to_a_tool', ][i, 'value'],
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33 sep = '/')
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34 }
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35 }
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36
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37 ## display user input as a table
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38 knitr::kable(df)
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39 ```
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40
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41
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42 ```{r, 'build script', echo=FALSE}
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43 ##-------- build script files -----------
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44
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45 # get tool name, the first line of the script is always the tool name.
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46 tool_name = df[df$type == 'tool_name', 'value']
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47
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48 # if the number of option/argument pairs is larger than 0, build script file
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49 df2 = df[df$type != 'tool_name', ]
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50 if (nrow(df2) > 0) {
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51 # write tool name as the first line of the script.sh
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52 # before running the job, cd into the ${REPORT_FILES_PATH} directory
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53 write(paste0(tool_name, ' \\'),
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54 paste0(Sys.getenv('REPORT_FILES_PATH'), '/script.sh'))
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55 df2 = df[df$type != 'tool_name', ]
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56 write(paste(' ', df2$flag, df2$value, '\\', sep = ' '),
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57 file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/script.sh'),
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58 append = TRUE )
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59 # remember that after writing option/argument lines to the script.sh, the last line
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60 # has an extra newline character '\' which causes a problem. We can either remove that extra
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61 # '\' or add a new line to the end. We choose to add a new line.
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62
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63 # add an extra line to the end to redirect stdout to stdout.txt and stderr to stderr.txt
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64 write(' > ${REPORT_FILES_PATH}/stdout.txt 2>${REPORT_FILES_PATH}/stderr.txt',
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65 paste0(Sys.getenv('REPORT_FILES_PATH'), '/script.sh'), append = TRUE)
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66 } else {
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67 # if no option/argument input, simply display the help message
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68 write(paste0(tool_name, ' -h'),
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69 file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/script.sh'))
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70 }
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71 ```
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72
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73
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74 ```{r, 'create paths if they do not exist', echo=FALSE}
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75 ## if the input type is 'path_relative_to_this_tool', that means
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76 ## we need to create a directory or file path.
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77
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78 # create paths before running the job script
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79 df_paths = df[df$type == 'path_relative_to_this_tool', ]
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80
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81 if (nrow(df_paths) > 0) {
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82 for (i in 1:nrow(df_paths)) {
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83 path = paste0(Sys.getenv('REPORT_FILES_PATH'), '/', df_paths[i, 'value'])
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84 path_type = df_paths[i, 'path_type']
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85
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86 # create file paths
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87 if ((path_type == 'file_path') & !file.exists(path)) {
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88 dir_path = paste(head(strsplit(path, '/')[[1]], -1), collapse = '/' )
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89 if (!dir.exists(dir_path)) {
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90 dir.create(dir_path, recursive = TRUE)
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91 }
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92 file.create(path)
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93 }
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94
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95 # create dir paths
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96 if ((path_type == 'dir_path') & !dir.exists(path)) {
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97 dir.create(path, recursive = TRUE)
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98 }
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99 }
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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 ```{bash, 'run jobs', echo=FALSE}
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105 # run job script, always use absolute path.
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106 # we want to run all jobs within the working path.
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107 sh ${REPORT_FILES_PATH}/script.sh
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108 ```
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109
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110
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111 ```{bash, 'display script', results='asis', echo=FALSE}
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112 echo '## Job script'
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113 echo ''
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114 echo ''
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115 echo '```bash'
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116 cat ${REPORT_FILES_PATH}/script.sh
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117 echo '```'
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118 ```
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119
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120
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121 ```{r, 'display output directory contents', results='asis', echo=FALSE}
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122 ## after the job is done, we list all files from the output directory.
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123 ## full relative path to the output directory needs to be displayed.
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124
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125 cat('##All output files')
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126 cat('\n\n')
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127 all_files = list.files(path = Sys.getenv('REPORT_FILES_PATH'),
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128 full.names = TRUE,
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129 recursive = TRUE)
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130
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131 for (f in sub(Sys.getenv('REPORT_FILES_PATH'), '.', all_files) ) {
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132 cat('* [', f, '](', f, ')\n')
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133 }
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134 cat('\n')
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135 ```
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136
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137
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138 ```{r, 'save output directory of this tool', echo=FALSE}
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139 ## each elastic tool has a galaxy history output which contains the REPORT_FILES_PATH of this tool
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140 ## so that other tools can reference the outputs from this tool.
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141
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142 ## obtain REPORT_FILES_PAHT and save it to a galaxy output.
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143 database_root = paste(head(strsplit(Sys.getenv('TOOL_LOG'), '/')[[1]], -1), collapse = '/')
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144 tool_output_dir_id = tail(strsplit(Sys.getenv('REPORT_FILES_PATH'), '/')[[1]], 1)
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145 tool_output_dir = paste0(database_root, '/', tool_output_dir_id)
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146 write(tool_output_dir, Sys.getenv('TOOL_OUTPUT_DIR'))
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147 ```
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