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1 #!/bin/bash
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2
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3 inputFile=$1
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4 outputFile=$2
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5 outputDir=$3
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6 database=$4
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7 limit_reads=$5
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8 limit_ratio=$6
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9
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10
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11 dir="$(cd "$(dirname "$0")" && pwd)"
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12 mkdir $outputDir
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13
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14 unzip $dir/browser.zip -d $outputDir/ > $outputDir/unziplog.log
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15
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16 mkdir $outputDir/out
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17
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18 if [[ "$database" == "download" ]] ; then
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19 echo "Downloading up to date database from IMGT..."
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20 mkdir $outputDir/tmp
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21 mkdir $outputDir/tmp/germline
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22 cp $dir/germline/get-germline $outputDir/tmp/germline
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23 cp $dir/germline/split-from-imgt.py $outputDir/tmp/germline
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24 cp $dir/vidjil $outputDir/tmp
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25 cd $outputDir/tmp/germline
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26 ./get-germline 2>&1
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27 cd $outputDir/tmp
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28 else
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29 cd $dir
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30 fi
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31 ./vidjil $inputFile -y all -r ${limit_reads} -% ${limit_ratio} -b data -o $outputDir
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32
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33
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34
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35 echo "<html><center><h1><a href='index.html'>Click here for the results</a></h1>Tip: Open it in a new tab (middle mouse button or right mouse button -> 'open in new tab' on the link above)</center></html>" > $outputFile
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36
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37 cd "$outputDir"
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