Mercurial > repos > davidvanzessen > vidjil_with_browser

comparison vidjil.sh @ 6:7346cd210a43 draft

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Uploaded
author davidvanzessen
date Thu, 12 Feb 2015 09:54:07 -0500
parents fe4001bdf8d4
children e55dfd9a8c00
comparison
equal deleted inserted replaced
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;