[med-svn] [fastqc] 02/03: Build-Depends: libhtsjdk-java | libsam-java and try to enable htsjdk.jar in Build system

[Andreas Tille]

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tille pushed a commit to branch master
in repository fastqc.

commit bc56edf6bbb417fb2950e10cdeb11309e9d26ed9
Author: Andreas Tille <tille at debian.org>
Date:   Thu Jan 14 14:42:24 2016 +0100

    Build-Depends: libhtsjdk-java | libsam-java and try to enable htsjdk.jar in Build system
---
 debian/changelog               | 7 +++++++
 debian/control                 | 2 +-
 debian/patches/build_xml.patch | 5 +++--
 3 files changed, 11 insertions(+), 3 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index ac6153b..4e849b8 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+fastqc (0.11.4+dfsg-3) UNRELEASED; urgency=medium
+
+  * Build-Depends: libhtsjdk-java | libsam-java and try to enable
+    htsjdk.jar in Build system
+
+ -- Andreas Tille <tille at debian.org>  Thu, 14 Jan 2016 13:50:56 +0100
+
 fastqc (0.11.4+dfsg-2) unstable; urgency=medium
 
   * Add explicit Depends: default-jre | java7-runtime
diff --git a/debian/control b/debian/control
index 4dbe450..cb73c48 100644
--- a/debian/control
+++ b/debian/control
@@ -9,7 +9,7 @@ Build-Depends: debhelper (>= 9),
                javahelper,
                default-jdk,
                ant,
-               libsam-java,
+               libhtsjdk-java | libsam-java,
                libjbzip2-java,
                libcommons-math3-java,
                libsis-jhdf5-java
diff --git a/debian/patches/build_xml.patch b/debian/patches/build_xml.patch
index 193c6f2..627a5d5 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 +11,10 @@
+@@ -11,9 +11,11 @@
      <property name="source" value="1.5"/>
      <path id="FastQC.classpath">
          <pathelement location="bin"/>
@@ -14,12 +14,13 @@ Description: Use Debian packaged JARs
 -        <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 +35,7 @@
+@@ -34,6 +36,7 @@
          <echo message="${ant.project.name}: ${ant.file}"/>
          <javac debug="true" debuglevel="${debuglevel}" destdir="bin" includeantruntime="false" source="${source}" target="${target}">
              <src path="."/>

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