[med-svn] [fastqc] 02/03: It seems there is no chance to keep libsam-java usable (for instance for backports)

[Andreas Tille]

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 <tille at debian.org>
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