[med-svn] [fastqc] 02/03: Refresh patches

[Andreas Tille]

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tille pushed a commit to branch master
in repository fastqc.

commit 7989bfb56848f8dc82773f3d975458eb48867727
Author: Andreas Tille <tille at debian.org>
Date:   Sun May 3 08:45:50 2015 +0200

    Refresh patches
---
 debian/patches/Makefile.patch   |  4 +---
 debian/patches/fastqc.patch     | 12 +++++------
 debian/patches/fix_icon_loading | 44 -----------------------------------------
 3 files changed, 7 insertions(+), 53 deletions(-)

diff --git a/debian/patches/Makefile.patch b/debian/patches/Makefile.patch
index 87eb01d..69b00f4 100644
--- a/debian/patches/Makefile.patch
+++ b/debian/patches/Makefile.patch
@@ -1,10 +1,8 @@
 From: Steffen Moeller <moeller at debian.org>
 Subject: Simplyfy installation by creating a Makefile
 
-Index: FastQC/Makefile
-===================================================================
 --- /dev/null
-+++ FastQC/Makefile
++++ b/Makefile
 @@ -0,0 +1,21 @@
 +
 +all: fastqc.jar
diff --git a/debian/patches/fastqc.patch b/debian/patches/fastqc.patch
index 94e16cf..78a13f2 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 @@
+@@ -33,16 +33,15 @@ if (-e "$RealBin/uk/ac/babraham/FastQC/F
  }
  
  my $delimiter = ':';
@@ -14,16 +14,16 @@ Subject: Ensure proper CLASSPATH according to location of Debian JARs
  }
  
  if ($ENV{CLASSPATH}) {
--	$ENV{CLASSPATH} .= "$delimiter$RealBin$delimiter$RealBin/sam-1.103.jar$delimiter$RealBin/jbzip2-0.9.jar";
+-	$ENV{CLASSPATH} .= "$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";
+-	$ENV{CLASSPATH} = "$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/sam.jar$delimiter$JavaClasspathExtraDir/jbzip2.jar:$RealBin/fastqc.jar";
  }
  
  my @java_args;
-@@ -251,10 +250,10 @@
+@@ -260,10 +259,10 @@ if (@files or $version or $help) {
  
  
  if ($java_bin ne 'java') {
@@ -36,10 +36,10 @@ Subject: Ensure proper CLASSPATH according to location of Debian JARs
  }
  
  __DATA__
-@@ -367,4 +366,4 @@
+@@ -381,4 +380,4 @@ BUGS
      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
-+
++    
diff --git a/debian/patches/fix_icon_loading b/debian/patches/fix_icon_loading
deleted file mode 100644
index c1162b8..0000000
--- a/debian/patches/fix_icon_loading
+++ /dev/null
@@ -1,44 +0,0 @@
-Subject: issue when loading resources
-Description: in Debian, templates and other resources are not embedded in Jar file.
- This is a problem when app tries to access the resources.
- This patch provides the path in Debian hierarcy to find resources.
-Author: Olivier Sallou <osallou at debian.org>
-Last-Updated: 2013-06-05
-Forwarded: no
---- a/uk/ac/babraham/FastQC/Report/HTMLReportArchive.java
-+++ b/uk/ac/babraham/FastQC/Report/HTMLReportArchive.java
-@@ -167,12 +167,12 @@
- 		data.append("\n");
- 		
- 		// Add in the icon files for pass/fail/warn
--		File templatesDir = new File(URLDecoder.decode(ClassLoader.getSystemResource("Templates/Icons").getFile(),"UTF-8"));
-+		File templatesDir = new File("/usr/share/fastqc/Templates/Icons");
- 		String [] names = templatesDir.list();
- 		for (int n=0;n<names.length;n++) {
- 			if (names[n].toLowerCase().endsWith(".png") || names[n].toLowerCase().endsWith(".jpg") || names[n].toLowerCase().endsWith(".jpeg")) {
- 				zip.putNextEntry(new ZipEntry(folderName()+"/Icons/"+names[n]));
--				FileInputStream fileIn = new FileInputStream(new File(URLDecoder.decode(ClassLoader.getSystemResource("Templates/Icons/"+names[n]).getFile(),"UTF-8")));
-+				FileInputStream fileIn = new FileInputStream(new File("/usr/share/fastqc/Templates/Icons/"+names[n]));
- 				int len;
- 				while ((len = fileIn.read(buffer)) > 0) { 
- 					zip.write(buffer, 0, len); 
-@@ -235,7 +235,7 @@
- 	
- 	private void addTemplate (String filename, String date) throws IOException {
- 		
--		BufferedReader br = new BufferedReader(new FileReader(new File(URLDecoder.decode(ClassLoader.getSystemResource("Templates/header_template.html").getFile(),"UTF-8"))));
-+		BufferedReader br = new BufferedReader(new FileReader(new File("/usr/share/fastqc/Templates/header_template.html")));
- 		String line;
- 		while ((line = br.readLine())!=null) {
- 			
---- a/uk/ac/babraham/FastQC/Sequence/Contaminant/ContaminentFinder.java
-+++ b/uk/ac/babraham/FastQC/Sequence/Contaminant/ContaminentFinder.java
-@@ -60,7 +60,7 @@
- 		
- 		try {
- 			
--			File contaminantFile = new File (URLDecoder.decode(ClassLoader.getSystemResource("Contaminants/contaminant_list.txt").getFile(),"UTF-8"));
-+			File contaminantFile = new File ("/usr/share/fastqc/Contaminants/contaminant_list.txt");
- 			
- 			if (System.getProperty("fastqc.contaminant_file") != null && System.getProperty("fastqc.contaminant_file").length()>0) {
- 				contaminantFile = new File(System.getProperty("fastqc.contaminant_file"));

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