Mercurial > repos > davidvanzessen > vidjil_with_browser
comparison vidjil.sh @ 6:7346cd210a43 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Thu, 12 Feb 2015 09:54:07 -0500 |
| parents | fe4001bdf8d4 |
| children | e55dfd9a8c00 |
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| 5:b94a4ec63d12 | 6:7346cd210a43 |
|---|---|
| 1 #!/bin/bash | 1 #!/bin/bash |
| 2 set -e | |
| 2 | 3 |
| 3 inputFile=$1 | 4 inputFile=$1 |
| 4 outputFile=$2 | 5 outputFile=$2 |
| 5 outputDir=$3 | 6 outputDir=$3 |
| 6 database=$4 | 7 database=$4 |
| 7 limit_reads=$5 | 8 limit_reads=$5 |
| 8 limit_ratio=$6 | 9 limit_ratio=$6 |
| 9 | 10 selection=$7 |
| 11 germline=$8 | |
| 10 | 12 |
| 11 dir="$(cd "$(dirname "$0")" && pwd)" | 13 dir="$(cd "$(dirname "$0")" && pwd)" |
| 12 mkdir $outputDir | 14 mkdir $outputDir |
| 13 | 15 |
| 14 unzip $dir/browser.zip -d $outputDir/ > $outputDir/unziplog.log | 16 unzip $dir/browser.zip -d $outputDir/ > $outputDir/unziplog.log |
| 15 | 17 |
| 16 mkdir $outputDir/out | 18 mkdir $outputDir/data |
| 17 | 19 |
| 18 if [[ "$database" == "download" ]] ; then | 20 if [[ "$database" == "download" ]] ; then |
| 19 echo "Downloading up to date database from IMGT..." | 21 echo "Downloading up to date database from IMGT..." |
| 20 mkdir $outputDir/tmp | 22 mkdir $outputDir/tmp |
| 21 mkdir $outputDir/tmp/germline | 23 mkdir $outputDir/tmp/germline |
| 26 ./get-germline 2>&1 | 28 ./get-germline 2>&1 |
| 27 cd $outputDir/tmp | 29 cd $outputDir/tmp |
| 28 else | 30 else |
| 29 cd $dir | 31 cd $dir |
| 30 fi | 32 fi |
| 31 ./vidjil $inputFile -y all -r ${limit_reads} -% ${limit_ratio} -b data -o $outputDir | |
| 32 | 33 |
| 33 | 34 |
| 35 inputFiles=$(echo "$inputFile" | tr "| " "\n") | |
| 36 files_for_config="" | |
| 37 last_file="" | |
| 38 for id_file in $inputFiles | |
| 39 do | |
| 40 tmp=($(echo "${id_file}" | tr ";" "\n")) | |
| 41 id=${tmp[0]} | |
| 42 file=${tmp[1]} | |
| 43 | |
| 44 ./vidjil -G germline/$germline -y all -r ${limit_reads} -% ${limit_ratio} -b $id -o $outputDir/data $file | |
| 45 | |
| 46 if [[ "$files_for_config" != "" ]] ; then | |
| 47 files_for_config="${files_for_config}," | |
| 48 fi | |
| 49 files_for_config="${files_for_config}'${id}.vidjil'" | |
| 50 last_file="${id}.vidjil" | |
| 51 done | |
| 34 | 52 |
| 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 | 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>" > $outputFile |
| 36 | 54 |
| 37 cd "$outputDir" | 55 echo -e \ |
| 56 "var config = {\n" \ | |
| 57 " 'file_menu' : {\n" \ | |
| 58 " 'path' : 'data/',\n" \ | |
| 59 " 'file' : [\n" \ | |
| 60 " ${files_for_config}\n" \ | |
| 61 " ]\n" \ | |
| 62 " },\n" \ | |
| 63 " 'autoload' : 'data/${last_file}'\n" \ | |
| 64 "}" > $outputDir/js/conf.js; |