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1 ######### each aurora tool generates a html file and have an files path directory associated with it.
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2 mkdir -p $report.files_path &&
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3
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4 ######### three important paths:
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5 ######### 1. path to tool installation directory
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6 ######### 2. path to report html
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7 ######### 3. path to files_path directory associated with the report output.
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8 export TOOL_INSTALL_DIR='${__tool_directory__}' &&
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9 export REPORT='$report' &&
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10 export REPORT_FILES_PATH='$report.files_path' &&
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11
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12 ############ create a hidden file to store r markdown rendering log
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13 touch $report.files_path/r_rendering.log.txt &&
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14
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15 ############ finally run the render.R script
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16 Rscript '${__tool_directory__}/rmarkdown_report_render.R'
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17
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18 -o $report
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19 -d $report.files_path
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20
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21 -f $fasta_file
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22 -m $masked_file
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23
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24 -F $ssr_fasta
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25 -S $ssr_stats
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26 -R $ssr_report
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27
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28
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