Package: fastqc / 0.11.8+dfsg-2

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From: Steffen Moeller <moeller@debian.org>
Subject: Ensure proper CLASSPATH according to location of Debian JARs

Index: fastqc/fastqc
===================================================================
--- fastqc.orig/fastqc
+++ fastqc/fastqc
@@ -33,16 +33,15 @@ if (-e "$RealBin/uk/ac/babraham/FastQC/F
 }
 
 my $delimiter = ':';
+my $JavaClasspathExtraDir="/usr/share/java";
 
 if ($^O =~ /Win/) {
 	$delimiter = ';';
 }
 
 if ($ENV{CLASSPATH}) {
-	$ENV{CLASSPATH} .= "$delimiter$RealBin$delimiter$RealBin/sam-1.103.jar$delimiter$RealBin/jbzip2-0.9.jar$delimiter$RealBin/cisd-jhdf5.jar";
-}
-else {
-	$ENV{CLASSPATH} = "$RealBin$delimiter$RealBin/sam-1.103.jar$delimiter$RealBin/jbzip2-0.9.jar$delimiter$RealBin/cisd-jhdf5.jar";
+	$ENV{CLASSPATH} .= "$delimiter";
+	$ENV{CLASSPATH} .= "$JavaClasspathExtraDir/commons-math3.jar$delimiter$JavaClasspathExtraDir/htsjdk.jar$delimiter$JavaClasspathExtraDir/jbzip2.jar:$RealBin/fastqc.jar";
 }
 
 my @java_args;
@@ -277,10 +276,10 @@ if (@files or $version or $help) {
 
 
 if ($java_bin ne 'java') {
-	system $java_bin,@java_args, "uk.ac.babraham.FastQC.FastQCApplication", @files;
+	system $java_bin,@java_args,"-cp","/usr/share/java/fastqc.jar:$JavaClasspathExtraDir/commons-math3.jar$delimiter$JavaClasspathExtraDir/htsjdk.jar$delimiter$JavaClasspathExtraDir/jbzip2.jar","uk.ac.babraham.FastQC.FastQCApplication", @files;
 }
 else {
-	exec $java_bin,@java_args, "uk.ac.babraham.FastQC.FastQCApplication", @files;
+	exec $java_bin,@java_args,"-cp","/usr/share/java/fastqc.jar:$JavaClasspathExtraDir/commons-math3.jar$delimiter$JavaClasspathExtraDir/htsjdk.jar$delimiter$JavaClasspathExtraDir/jbzip2.jar","uk.ac.babraham.FastQC.FastQCApplication", @files;
 }
 
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