[med-svn] r17084 - in trunk/packages/babraham/fastqc/trunk/debian: . patches

[Olivier Sallou]

Author: osallou
Date: 2014-06-09 08:59:27 +0000 (Mon, 09 Jun 2014)
New Revision: 17084

Modified:
   trunk/packages/babraham/fastqc/trunk/debian/changelog
   trunk/packages/babraham/fastqc/trunk/debian/control
   trunk/packages/babraham/fastqc/trunk/debian/patches/fastqc.patch
   trunk/packages/babraham/fastqc/trunk/debian/patches/fix-help-call.patch
   trunk/packages/babraham/fastqc/trunk/debian/patches/series
Log:
update patches, can't build yet because requires a new dependency, see changelog

Modified: trunk/packages/babraham/fastqc/trunk/debian/changelog
===================================================================
--- trunk/packages/babraham/fastqc/trunk/debian/changelog	2014-06-09 08:42:21 UTC (rev 17083)
+++ trunk/packages/babraham/fastqc/trunk/debian/changelog	2014-06-09 08:59:27 UTC (rev 17084)
@@ -1,6 +1,8 @@
 fastqc (0.11.2+dfsg-1) UNRELEASED; urgency=medium
 
   * New upstream release 
+    ISSUES: requires additional library:
+       http://iharder.sourceforge.net/current/java/base64/
 
  -- Olivier Sallou <osallou at debian.org>  Mon, 09 Jun 2014 10:41:06 +0200
 

Modified: trunk/packages/babraham/fastqc/trunk/debian/control
===================================================================
--- trunk/packages/babraham/fastqc/trunk/debian/control	2014-06-09 08:42:21 UTC (rev 17083)
+++ trunk/packages/babraham/fastqc/trunk/debian/control	2014-06-09 08:59:27 UTC (rev 17084)
@@ -6,10 +6,10 @@
  Andreas Tille <tille at debian.org>,
  Olivier Sallou <osallou at debian.org>
 Build-Depends: debhelper (>= 9), javahelper, default-jdk, libsam-java, libjbzip2-java
-Standards-Version: 3.9.4
+Standards-Version: 3.9.5
 Homepage: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
-Vcs-Svn: http://svn.debian.org/debian-med/trunk/packages/babraham/fastqc/trunk/
-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/babraham/fastqc/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/babraham/fastqc/trunk/
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/babraham/fastqc/trunk/
 
 Package: fastqc
 Architecture: all

Modified: trunk/packages/babraham/fastqc/trunk/debian/patches/fastqc.patch
===================================================================
--- trunk/packages/babraham/fastqc/trunk/debian/patches/fastqc.patch	2014-06-09 08:42:21 UTC (rev 17083)
+++ trunk/packages/babraham/fastqc/trunk/debian/patches/fastqc.patch	2014-06-09 08:59:27 UTC (rev 17084)
@@ -3,24 +3,27 @@
 
 --- a/fastqc
 +++ b/fastqc
-@@ -17,12 +17,12 @@
+@@ -33,16 +33,15 @@
+ }
+ 
+ my $delimiter = ':';
++my $JavaClasspathExtraDir="/usr/share/java";
+ 
+ if ($^O =~ /Win/) {
  	$delimiter = ';';
  }
  
-+my $JavaClasspathExtraDir="/usr/share/java";
-+
  if ($ENV{CLASSPATH}) {
--	$ENV{CLASSPATH} .= "$delimiter$RealBin$delimiter$RealBin/sam-1.32.jar$delimiter$RealBin/jbzip2-0.9.jar";
+-	$ENV{CLASSPATH} .= "$delimiter$RealBin$delimiter$RealBin/sam-1.103.jar$delimiter$RealBin/jbzip2-0.9.jar";
 -}
 -else {
--	$ENV{CLASSPATH} = "$RealBin$delimiter$RealBin/sam-1.32.jar$delimiter$RealBin/jbzip2-0.9.jar";
+-	$ENV{CLASSPATH} = "$RealBin$delimiter$RealBin/sam-1.103.jar$delimiter$RealBin/jbzip2-0.9.jar";
 +	$ENV{CLASSPATH} .= "$delimiter";
++	$ENV{CLASSPATH} .= "$JavaClasspathExtraDir/sam.jar$delimiter$JavaClasspathExtraDir/jbzip2.jar:$RealBin/fastqc.jar";
  }
-+$ENV{CLASSPATH} .= "$JavaClasspathExtraDir/sam.jar$delimiter$JavaClasspathExtraDir/jbzip2.jar:$RealBin/fastqc.jar";
  
  my @java_args;
- my @files;
-@@ -177,10 +177,10 @@
+@@ -251,10 +250,10 @@
  
  
  if ($java_bin ne 'java') {
@@ -33,7 +36,7 @@
  }
  
  __DATA__
-@@ -273,4 +273,4 @@
+@@ -367,4 +366,4 @@
      Any bugs in fastqc should be reported either to simon.andrews at babraham.ac.uk
      or in www.bioinformatics.babraham.ac.uk/bugzilla/
                     

Modified: trunk/packages/babraham/fastqc/trunk/debian/patches/fix-help-call.patch
===================================================================
--- trunk/packages/babraham/fastqc/trunk/debian/patches/fix-help-call.patch	2014-06-09 08:42:21 UTC (rev 17083)
+++ trunk/packages/babraham/fastqc/trunk/debian/patches/fix-help-call.patch	2014-06-09 08:59:27 UTC (rev 17084)
@@ -8,11 +8,11 @@
 --- a/uk/ac/babraham/FastQC/FastQCMenuBar.java
 +++ b/uk/ac/babraham/FastQC/FastQCMenuBar.java
 @@ -132,7 +132,7 @@ public class FastQCMenuBar extends JMenu
- 		}
- 		else if (command.equals("help_contents")) {
- 			try {
--				new HelpDialog(application,new File(URLDecoder.decode(ClassLoader.getSystemResource("Help").getFile(),"UTF-8")));
-+				new HelpDialog(application,new File(URLDecoder.decode("/usr/share/fastqc/Help","UTF-8")));
- 			} 
- 			catch (UnsupportedEncodingException e1) {
- 				e1.printStackTrace();
+ 		}
+ 		else if (command.equals("help_contents")) {
+ 			try {
+-				new HelpDialog(application,new File(URLDecoder.decode(ClassLoader.getSystemResource("Help").getFile(),"UTF-8")));
++				new HelpDialog(application,new File(URLDecoder.decode("/usr/share/fastqc/Help","UTF-8")));
+ 			} 
+ 			catch (UnsupportedEncodingException e1) {
+ 				e1.printStackTrace();

Modified: trunk/packages/babraham/fastqc/trunk/debian/patches/series
===================================================================
--- trunk/packages/babraham/fastqc/trunk/debian/patches/series	2014-06-09 08:42:21 UTC (rev 17083)
+++ trunk/packages/babraham/fastqc/trunk/debian/patches/series	2014-06-09 08:59:27 UTC (rev 17084)
@@ -1,4 +1,3 @@
 Makefile.patch
 fastqc.patch
 fix-help-call.patch
-fix_icon_loading