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 <[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 08:59:27 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 <[email protected]>, Andreas Tille <[email protected]>, Olivier Sallou <[email protected]> -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 <[email protected]> +License: Public Domain + Files: * Copyright: Simon Adrews <[email protected]> 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; _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
