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1 #!/bin/bash
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6
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2 set -e
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3
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4 inputFile=$1
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5 outputFile=$2
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6 outputDir=$3
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7 database=$4
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8 limit_reads=$5
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9 limit_ratio=$6
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6
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10 selection=$7
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11 germline=$8
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12
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13 dir="$(cd "$(dirname "$0")" && pwd)"
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14 mkdir $outputDir
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15
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16 unzip $dir/browser.zip -d $outputDir/ > $outputDir/unziplog.log
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17
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18 mkdir $outputDir/data
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19
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20 if [[ "$database" == "download" ]] ; then
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21 echo "Downloading up to date database from IMGT..."
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22 mkdir $outputDir/tmp
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23 mkdir $outputDir/tmp/germline
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24 cp $dir/germline/get-germline $outputDir/tmp/germline
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25 cp $dir/germline/split-from-imgt.py $outputDir/tmp/germline
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26 cp $dir/vidjil $outputDir/tmp
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27 cd $outputDir/tmp/germline
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28 ./get-germline 2>&1
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29 cd $outputDir/tmp
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30 else
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31 cd $dir
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32 fi
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33
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34
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6
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35 inputFiles=$(echo "$inputFile" | tr "| " "\n")
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36 files_for_config=""
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37 last_file=""
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38 for id_file in $inputFiles
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39 do
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40 tmp=($(echo "${id_file}" | tr ";" "\n"))
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41 id=${tmp[0]}
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42 file=${tmp[1]}
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43
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44 ./vidjil -G germline/$germline -y all -r ${limit_reads} -% ${limit_ratio} -b $id -o $outputDir/data $file
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45
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46 if [[ "$files_for_config" != "" ]] ; then
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47 files_for_config="${files_for_config},"
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48 fi
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49 files_for_config="${files_for_config}'${id}.vidjil'"
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50 last_file="${id}.vidjil"
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51 done
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52
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53 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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54
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6
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55 echo -e \
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56 "var config = {\n" \
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57 " 'file_menu' : {\n" \
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58 " 'path' : 'data/',\n" \
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59 " 'file' : [\n" \
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60 " ${files_for_config}\n" \
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61 " ]\n" \
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62 " },\n" \
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63 " 'autoload' : 'data/${last_file}'\n" \
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64 "}" > $outputDir/js/conf.js;
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