[med-svn] [fastqc] 03/05: make sure jar dependencies are found

[Sascha Steinbiss]

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satta pushed a commit to branch master
in repository fastqc.

commit 26b99988324a371a749f221e6c17ac0380b2d5ed
Author: Sascha Steinbiss <satta at debian.org>
Date:   Thu Dec 8 19:25:15 2016 +0000

    make sure jar dependencies are found
---
 debian/patches/fastqc.patch | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/debian/patches/fastqc.patch b/debian/patches/fastqc.patch
index dbfc2ff..123cb90 100644
--- a/debian/patches/fastqc.patch
+++ b/debian/patches/fastqc.patch
@@ -3,7 +3,7 @@ Subject: Ensure proper CLASSPATH according to location of Debian JARs
 
 --- a/fastqc
 +++ b/fastqc
-@@ -33,16 +33,15 @@ if (-e "$RealBin/uk/ac/babraham/FastQC/F
+@@ -33,16 +33,15 @@
  }
  
  my $delimiter = ':';
@@ -23,23 +23,22 @@ Subject: Ensure proper CLASSPATH according to location of Debian JARs
  }
  
  my @java_args;
-@@ -271,10 +270,10 @@ if (@files or $version or $help) {
+@@ -271,10 +270,10 @@
  
  
  if ($java_bin ne 'java') {
 -	system $java_bin, at java_args, "uk.ac.babraham.FastQC.FastQCApplication", @files;
-+	system $java_bin, at java_args,"-jar","/usr/share/java/fastqc.jar", @files;
++	system $java_bin, at java_args,"-cp","/usr/share/java/fastqc.jar:$JavaClasspathExtraDir/commons-math3.jar$delimiter$JavaClasspathExtraDir/htsjdk.jar$delimiter$JavaClasspathExtraDir/jbzip2.jar","uk.ac.babraham.FastQC.FastQCApplication", @files;
  }
  else {
 -	exec $java_bin, at java_args, "uk.ac.babraham.FastQC.FastQCApplication", @files;
-+	exec $java_bin, at java_args,"-jar","/usr/share/java/fastqc.jar", @files;
++	exec $java_bin, at java_args,"-cp","/usr/share/java/fastqc.jar:$JavaClasspathExtraDir/commons-math3.jar$delimiter$JavaClasspathExtraDir/htsjdk.jar$delimiter$JavaClasspathExtraDir/jbzip2.jar","uk.ac.babraham.FastQC.FastQCApplication", @files;
  }
  
  __DATA__
-@@ -392,4 +391,4 @@ BUGS
+@@ -392,4 +391,3 @@
      Any bugs in fastqc should be reported either to simon.andrews at babraham.ac.uk
      or in www.bioinformatics.babraham.ac.uk/bugzilla/
                     
 -    
 \ No newline at end of file
-+    

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