|
0
|
1 #!/bin/bash
|
|
6
|
2 set -e
|
|
0
|
3
|
|
|
4 inputFile=$1
|
|
7
|
5 id=$2
|
|
|
6 outputFile=$3
|
|
|
7 outputDir=$4
|
|
|
8 database=$5
|
|
|
9 limit_reads=$6
|
|
|
10 limit_ratio=$7
|
|
|
11 selection=$8
|
|
|
12 germline=$9
|
|
|
13 fastaFile=${10}
|
|
0
|
14
|
|
7
|
15 wd="$PWD"
|
|
0
|
16 dir="$(cd "$(dirname "$0")" && pwd)"
|
|
|
17 mkdir $outputDir
|
|
7
|
18 mkdir $outputDir/data
|
|
|
19 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
|
|
0
|
20
|
|
|
21 unzip $dir/browser.zip -d $outputDir/ > $outputDir/unziplog.log
|
|
|
22
|
|
|
23 if [[ "$database" == "download" ]] ; then
|
|
|
24 echo "Downloading up to date database from IMGT..."
|
|
|
25 mkdir $outputDir/tmp
|
|
|
26 mkdir $outputDir/tmp/germline
|
|
|
27 cp $dir/germline/get-germline $outputDir/tmp/germline
|
|
|
28 cp $dir/germline/split-from-imgt.py $outputDir/tmp/germline
|
|
|
29 cp $dir/vidjil $outputDir/tmp
|
|
|
30 cd $outputDir/tmp/germline
|
|
|
31 ./get-germline 2>&1
|
|
|
32 cd $outputDir/tmp
|
|
|
33 else
|
|
|
34 cd $dir
|
|
|
35 fi
|
|
|
36
|
|
7
|
37 ./vidjil -G germline/$germline -y all -r ${limit_reads} -% ${limit_ratio} -b $id -o $outputDir/data $inputFile
|
|
0
|
38
|
|
7
|
39 mv $outputDir/data/${id}.vdj.fa $fastaFile
|
|
0
|
40
|
|
6
|
41 echo -e \
|
|
|
42 "var config = {\n" \
|
|
7
|
43 " 'autoload' : 'data/${id}.vidjil'\n" \
|
|
6
|
44 "}" > $outputDir/js/conf.js;
|
|
7
|
45
|
