[med-svn] r17085 - in trunk/packages/babraham/fastqc/trunk/debian: . patches

[Olivier Sallou]

Author: osallou
Date: 2014-06-09 09:39:05 +0000 (Mon, 09 Jun 2014)
New Revision: 17085

Modified:
   trunk/packages/babraham/fastqc/trunk/debian/changelog
   trunk/packages/babraham/fastqc/trunk/debian/control
   trunk/packages/babraham/fastqc/trunk/debian/copyright
   trunk/packages/babraham/fastqc/trunk/debian/patches/Makefile.patch
   trunk/packages/babraham/fastqc/trunk/debian/patches/fastqc.patch
Log:
remove apache commons math 3 extra included code and use Debian lib, update license before base64 embedded code

Modified: trunk/packages/babraham/fastqc/trunk/debian/changelog
===================================================================
--- trunk/packages/babraham/fastqc/trunk/debian/changelog	2014-06-09 08:59:27 UTC (rev 17084)
+++ trunk/packages/babraham/fastqc/trunk/debian/changelog	2014-06-09 09:39:05 UTC (rev 17085)
@@ -1,8 +1,6 @@
 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 08:59:27 UTC (rev 17084)
+++ trunk/packages/babraham/fastqc/trunk/debian/control	2014-06-09 09:39:05 UTC (rev 17085)
@@ -5,7 +5,7 @@
 Uploaders: Steffen Moeller <moeller at debian.org>,
  Andreas Tille <tille at debian.org>,
  Olivier Sallou <osallou at debian.org>
-Build-Depends: debhelper (>= 9), javahelper, default-jdk, libsam-java, libjbzip2-java
+Build-Depends: debhelper (>= 9), javahelper, default-jdk, libsam-java, libjbzip2-java, libcommons-math3-java
 Standards-Version: 3.9.5
 Homepage: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
 Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/babraham/fastqc/trunk/
@@ -13,7 +13,7 @@
 
 Package: fastqc
 Architecture: all
-Depends: ${shlibs:Depends}, ${misc:Depends}, ${java:Depends}, libsam-java, libjbzip2-java
+Depends: ${shlibs:Depends}, ${misc:Depends}, ${java:Depends}, libsam-java, libjbzip2-java, libcommons-math3-java
 Description: quality control for high throughput sequence data
  FastQC aims to provide a simple way to do some quality control checks on
  raw sequence data coming from high throughput sequencing pipelines. It

Modified: trunk/packages/babraham/fastqc/trunk/debian/copyright
===================================================================
--- trunk/packages/babraham/fastqc/trunk/debian/copyright	2014-06-09 08:59:27 UTC (rev 17084)
+++ trunk/packages/babraham/fastqc/trunk/debian/copyright	2014-06-09 09:39:05 UTC (rev 17085)
@@ -1,8 +1,14 @@
 Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: FastQC
 Source: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
-Files-Excluded: *.jar
+Files-Excluded:
+ *.jar
+ org
 
+Files: net/sourceforge/iharder/base64/*
+Copyright: Robert Harder <rob at iharder.net>
+License: Public Domain
+
 Files: *
 Copyright: Simon Adrews <simon.andrews at bbsrc.ac.uk>
 License: GPL-3.0+

Modified: trunk/packages/babraham/fastqc/trunk/debian/patches/Makefile.patch
===================================================================
--- trunk/packages/babraham/fastqc/trunk/debian/patches/Makefile.patch	2014-06-09 08:59:27 UTC (rev 17084)
+++ trunk/packages/babraham/fastqc/trunk/debian/patches/Makefile.patch	2014-06-09 09:39:05 UTC (rev 17085)
@@ -8,7 +8,7 @@
 +all: fastqc.jar
 +
 +fastqc.jar:
-+	javac -cp /usr/share/java/sam.jar:/usr/share/java/jbzip2.jar `find uk -name "*.java"`
++	javac -cp /usr/share/java/commons-math3.jar:/usr/share/java/sam.jar:/usr/share/java/jbzip2.jar `find uk -name "*.java"` `find net -name "*.java"`
 +	jar cf fastqc.jar `find uk -name "*.class" -o -name "*.png"`
 +
 +DESTDIR=
@@ -19,7 +19,7 @@
 +	chmod +x  $(DESTDIR)$(PREFIX)/bin/fastqc
 +	mkdir -p $(DESTDIR)$(PREFIX)/share/fastqc/
 +	cp -a fastqc.jar $(DESTDIR)$(PREFIX)/share/fastqc/
-+	cp -r Contaminants Templates Help $(DESTDIR)$(PREFIX)/share/fastqc/
++	cp -r Configuration Templates Help $(DESTDIR)$(PREFIX)/share/fastqc/
 +
 +clean:
 +	find . -name "*.jar" -o -name "*.class" | xargs -r rm

Modified: trunk/packages/babraham/fastqc/trunk/debian/patches/fastqc.patch
===================================================================
--- trunk/packages/babraham/fastqc/trunk/debian/patches/fastqc.patch	2014-06-09 08:59:27 UTC (rev 17084)
+++ trunk/packages/babraham/fastqc/trunk/debian/patches/fastqc.patch	2014-06-09 09:39:05 UTC (rev 17085)
@@ -19,7 +19,7 @@
 -else {
 -	$ENV{CLASSPATH} = "$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/commons-math3.jar$delimiter$JavaClasspathExtraDir/sam.jar$delimiter$JavaClasspathExtraDir/jbzip2.jar:$RealBin/fastqc.jar";
  }
  
  my @java_args;