Mercurial > repos > davidvanzessen > vidjil_with_browser
comparison vidjil.sh @ 0:fe4001bdf8d4 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Tue, 09 Dec 2014 03:55:01 -0500 |
| parents | |
| children | 7346cd210a43 |
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| -1:000000000000 | 0:fe4001bdf8d4 |
|---|---|
| 1 #!/bin/bash | |
| 2 | |
| 3 inputFile=$1 | |
| 4 outputFile=$2 | |
| 5 outputDir=$3 | |
| 6 database=$4 | |
| 7 limit_reads=$5 | |
| 8 limit_ratio=$6 | |
| 9 | |
| 10 | |
| 11 dir="$(cd "$(dirname "$0")" && pwd)" | |
| 12 mkdir $outputDir | |
| 13 | |
| 14 unzip $dir/browser.zip -d $outputDir/ > $outputDir/unziplog.log | |
| 15 | |
| 16 mkdir $outputDir/out | |
| 17 | |
| 18 if [[ "$database" == "download" ]] ; then | |
| 19 echo "Downloading up to date database from IMGT..." | |
| 20 mkdir $outputDir/tmp | |
| 21 mkdir $outputDir/tmp/germline | |
| 22 cp $dir/germline/get-germline $outputDir/tmp/germline | |
| 23 cp $dir/germline/split-from-imgt.py $outputDir/tmp/germline | |
| 24 cp $dir/vidjil $outputDir/tmp | |
| 25 cd $outputDir/tmp/germline | |
| 26 ./get-germline 2>&1 | |
| 27 cd $outputDir/tmp | |
| 28 else | |
| 29 cd $dir | |
| 30 fi | |
| 31 ./vidjil $inputFile -y all -r ${limit_reads} -% ${limit_ratio} -b data -o $outputDir | |
| 32 | |
| 33 | |
| 34 | |
| 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>" > $outputFile | |
| 36 | |
| 37 cd "$outputDir" |