# HG changeset patch
# User davidvanzessen
# Date 1423752847 18000
# Node ID 7346cd210a4308fb7e99c0503c2b39667e73a838
# Parent b94a4ec63d12fe7e6c2f029a7ef3b9abd1157fcc
Uploaded
diff -r b94a4ec63d12 -r 7346cd210a43 browser.zip
Binary file browser.zip has changed
diff -r b94a4ec63d12 -r 7346cd210a43 vidjil
Binary file vidjil has changed
diff -r b94a4ec63d12 -r 7346cd210a43 vidjil.sh
--- 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 "Tip: Open it in a new tab (middle mouse button or right mouse button -> 'open in new tab' on the link above)" > $outputFile
-cd "$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;
diff -r b94a4ec63d12 -r 7346cd210a43 vidjil.xml
--- a/vidjil.xml Tue Dec 09 04:14:03 2014 -0500
+++ b/vidjil.xml Thu Feb 12 09:54:07 2015 -0500
@@ -1,19 +1,40 @@
- vidjil.sh $in_file $out_file $out_file.files_path $database $limit_reads $limit_ratio
+ vidjil.sh "
+#for $i, $f in enumerate($in_files)
+${f.id};${f.in_file}|
+#end for
+" $out_file $out_file.files_path $database $limit_reads $limit_ratio $selection $germline
-
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A Galaxy wrapper for Vidijl and the Vidjil browser for analysis and visualization of **FASTA** and **FASTQ** files.