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 <[email protected]> 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 <[email protected]>, Olivier Sallou <[email protected]> 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 [email protected] 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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
