Mercurial > repos > davidvanzessen > vidjil_with_browser
diff vidjil.sh @ 6:7346cd210a43 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Thu, 12 Feb 2015 09:54:07 -0500 |
| parents | fe4001bdf8d4 |
| children | e55dfd9a8c00 |
line wrap: on
line diff
--- a/vidjil.sh Tue Dec 09 04:14:03 2014 -0500 +++ b/vidjil.sh Thu Feb 12 09:54:07 2015 -0500 @@ -1,4 +1,5 @@ #!/bin/bash +set -e inputFile=$1 outputFile=$2 @@ -6,14 +7,15 @@ database=$4 limit_reads=$5 limit_ratio=$6 - +selection=$7 +germline=$8 dir="$(cd "$(dirname "$0")" && pwd)" mkdir $outputDir unzip $dir/browser.zip -d $outputDir/ > $outputDir/unziplog.log -mkdir $outputDir/out +mkdir $outputDir/data if [[ "$database" == "download" ]] ; then echo "Downloading up to date database from IMGT..." @@ -28,10 +30,35 @@ else cd $dir fi -./vidjil $inputFile -y all -r ${limit_reads} -% ${limit_ratio} -b data -o $outputDir +inputFiles=$(echo "$inputFile" | tr "| " "\n") +files_for_config="" +last_file="" +for id_file in $inputFiles +do + tmp=($(echo "${id_file}" | tr ";" "\n")) + id=${tmp[0]} + file=${tmp[1]} + + ./vidjil -G germline/$germline -y all -r ${limit_reads} -% ${limit_ratio} -b $id -o $outputDir/data $file + + if [[ "$files_for_config" != "" ]] ; then + files_for_config="${files_for_config}," + fi + files_for_config="${files_for_config}'${id}.vidjil'" + last_file="${id}.vidjil" +done 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" +echo -e \ +"var config = {\n" \ +" 'file_menu' : {\n" \ +" 'path' : 'data/',\n" \ +" 'file' : [\n" \ +" ${files_for_config}\n" \ +" ]\n" \ +" },\n" \ +" 'autoload' : 'data/${last_file}'\n" \ +"}" > $outputDir/js/conf.js;