Mercurial > repos > davidvanzessen > vidjil_with_browser
diff vidjil.sh @ 0:fe4001bdf8d4 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Tue, 09 Dec 2014 03:55:01 -0500 |
| parents | |
| children | 7346cd210a43 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/vidjil.sh Tue Dec 09 03:55:01 2014 -0500 @@ -0,0 +1,37 @@ +#!/bin/bash + +inputFile=$1 +outputFile=$2 +outputDir=$3 +database=$4 +limit_reads=$5 +limit_ratio=$6 + + +dir="$(cd "$(dirname "$0")" && pwd)" +mkdir $outputDir + +unzip $dir/browser.zip -d $outputDir/ > $outputDir/unziplog.log + +mkdir $outputDir/out + +if [[ "$database" == "download" ]] ; then + echo "Downloading up to date database from IMGT..." + mkdir $outputDir/tmp + mkdir $outputDir/tmp/germline + cp $dir/germline/get-germline $outputDir/tmp/germline + cp $dir/germline/split-from-imgt.py $outputDir/tmp/germline + cp $dir/vidjil $outputDir/tmp + cd $outputDir/tmp/germline + ./get-germline 2>&1 + cd $outputDir/tmp +else + cd $dir +fi +./vidjil $inputFile -y all -r ${limit_reads} -% ${limit_ratio} -b data -o $outputDir + + + +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>" > $outputFile + +cd "$outputDir"