Mercurial > repos > davidvanzessen > vidjil_with_browser

comparison vidjil.sh @ 7:e55dfd9a8c00 draft default tip

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author davidvanzessen
date Thu, 12 Feb 2015 10:47:15 -0500
parents 7346cd210a43
children
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6:7346cd210a43 7:e55dfd9a8c00
1 #!/bin/bash 1 #!/bin/bash
2 set -e 2 set -e
3 3
4 inputFile=$1 4 inputFile=$1
5 outputFile=$2 5 id=$2
6 outputDir=$3 6 outputFile=$3
7 database=$4 7 outputDir=$4
8 limit_reads=$5 8 database=$5
9 limit_ratio=$6 9 limit_reads=$6
10 selection=$7 10 limit_ratio=$7
11 germline=$8 11 selection=$8
12 germline=$9
13 fastaFile=${10}
12 14
15 wd="$PWD"
13 dir="$(cd "$(dirname "$0")" && pwd)" 16 dir="$(cd "$(dirname "$0")" && pwd)"
14 mkdir $outputDir 17 mkdir $outputDir
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
15 20
16 unzip $dir/browser.zip -d $outputDir/ > $outputDir/unziplog.log 21 unzip $dir/browser.zip -d $outputDir/ > $outputDir/unziplog.log
17
18 mkdir $outputDir/data
19 22
20 if [[ "$database" == "download" ]] ; then 23 if [[ "$database" == "download" ]] ; then
21 echo "Downloading up to date database from IMGT..." 24 echo "Downloading up to date database from IMGT..."
22 mkdir $outputDir/tmp 25 mkdir $outputDir/tmp
23 mkdir $outputDir/tmp/germline 26 mkdir $outputDir/tmp/germline
29 cd $outputDir/tmp 32 cd $outputDir/tmp
30 else 33 else
31 cd $dir 34 cd $dir
32 fi 35 fi
33 36
37 ./vidjil -G germline/$germline -y all -r ${limit_reads} -% ${limit_ratio} -b $id -o $outputDir/data $inputFile
34 38
35 inputFiles=$(echo "$inputFile" | tr "| " "\n") 39 mv $outputDir/data/${id}.vdj.fa $fastaFile
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
52
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>" > $outputFile
54 40
55 echo -e \ 41 echo -e \
56 "var config = {\n" \ 42 "var config = {\n" \
57 " 'file_menu' : {\n" \ 43 " 'autoload' : 'data/${id}.vidjil'\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; 44 "}" > $outputDir/js/conf.js;
45