This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository fastqc.
commit 86c199c3dcd540b95d48ba7c0cdcac3263f0bc27 Author: Andreas Tille <[email protected]> Date: Thu Jan 14 15:15:19 2016 +0100 It seems there is no chance to keep libsam-java usable (for instance for backports) --- debian/control | 2 +- debian/patches/build_xml.patch | 5 ++--- debian/patches/fastqc.patch | 2 +- 3 files changed, 4 insertions(+), 5 deletions(-) diff --git a/debian/control b/debian/control index cb73c48..f84d7cb 100644 --- a/debian/control +++ b/debian/control @@ -9,7 +9,7 @@ Build-Depends: debhelper (>= 9), javahelper, default-jdk, ant, - libhtsjdk-java | libsam-java, + libhtsjdk-java, libjbzip2-java, libcommons-math3-java, libsis-jhdf5-java diff --git a/debian/patches/build_xml.patch b/debian/patches/build_xml.patch index 627a5d5..c1b97e9 100644 --- a/debian/patches/build_xml.patch +++ b/debian/patches/build_xml.patch @@ -5,7 +5,7 @@ Description: Use Debian packaged JARs --- a/build.xml +++ b/build.xml -@@ -11,9 +11,11 @@ +@@ -11,9 +11,10 @@ <property name="source" value="1.5"/> <path id="FastQC.classpath"> <pathelement location="bin"/> @@ -13,14 +13,13 @@ Description: Use Debian packaged JARs - <pathelement location="sam-1.103.jar"/> - <pathelement location="cisd-jhdf5.jar"/> + <pathelement location="/usr/share/java/jbzip2.jar"/> -+ <pathelement location="/usr/share/java/sam.jar"/> + <pathelement location="/usr/share/java/htsjdk.jar"/> + <pathelement location="/usr/share/java/sis-jhdf5.jar"/> + <pathelement location="/usr/share/java/commons-math3.jar"/> </path> <target name="init"> <mkdir dir="bin"/> -@@ -34,6 +36,7 @@ +@@ -34,6 +35,7 @@ <echo message="${ant.project.name}: ${ant.file}"/> <javac debug="true" debuglevel="${debuglevel}" destdir="bin" includeantruntime="false" source="${source}" target="${target}"> <src path="."/> diff --git a/debian/patches/fastqc.patch b/debian/patches/fastqc.patch index 88f366c..dbfc2ff 100644 --- a/debian/patches/fastqc.patch +++ b/debian/patches/fastqc.patch @@ -19,7 +19,7 @@ Subject: Ensure proper CLASSPATH according to location of Debian JARs -else { - $ENV{CLASSPATH} = "$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"; ++ $ENV{CLASSPATH} .= "$JavaClasspathExtraDir/commons-math3.jar$delimiter$JavaClasspathExtraDir/htsjdk.jar$delimiter$JavaClasspathExtraDir/jbzip2.jar:$RealBin/fastqc.jar"; } my @java_args; -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/fastqc.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
