Mercurial > repos > mingchen0919 > elastic_expose_data
annotate list_paired.Rmd @ 6:52ecc1cfd205 draft
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author | mingchen0919 |
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date | Mon, 02 Apr 2018 10:21:30 -0400 |
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2 title: 'Expose data (list:paired)' |
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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, eval=TRUE} |
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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 |
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29 knitr::kable(df) |
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30 ``` |
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32 ```{r, echo=FALSE} |
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33 write('', file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/script.sh')) |
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34 if (nrow(df) > 0) { |
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35 for (i in 1:nrow(df)) { |
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36 tool_output_dir = readLines(df[i, 'tool_output_dir'])[1] |
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37 full_path = paste0(tool_output_dir, '/', df[i, 'relative_path']) |
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38 # if it is a directory path, add '/*' to the end. |
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39 if (dir.exists(full_path)) { |
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40 full_path = paste0(full_path, '/*') |
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41 } |
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42 command_line = paste0('cp -r ', full_path, ' list_paired') |
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43 write(command_line, append = TRUE, |
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44 file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/script.sh')) |
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45 } |
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46 } |
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47 ``` |
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49 |