debian/changelog

@@ -2,7 +2,7 @@ jmodeltest (2.1.10+dfsg-7) UNRELEASED; urgency=medium
 
   * alter-sequence-alignment now has two JARs - add alter-lib.jar to manifest
     Closes: #906371
-  * Standards-Version: 4.2.0
+  * Standards-Version: 4.2.1
 
  -- Andreas Tille <tille@debian.org>  Tue, 21 Aug 2018 08:15:38 +0200
 

debian/control

@@ -17,7 +17,7 @@ Build-Depends: debhelper (>= 11~),
                texlive-latex-base,
                texlive-fonts-recommended,
                texlive-latex-recommended
-Standards-Version: 4.2.0
+Standards-Version: 4.2.1
 Vcs-Browser: https://salsa.debian.org/med-team/jmodeltest
 Vcs-Git: https://salsa.debian.org/med-team/jmodeltest.git
 Homepage: https://github.com//ddarriba/jmodeltest2

debian/patches/use_debian_packaged_jars.patch

@@ -16,7 +16,15 @@ Description: Use Debian packaged JARs
  	<property name="log.dir" location="${dist.dir}/log" />
  	<property name="manual.dir" location="manual" />
  	<property name="src.resources.dir" location="src/main/resources" />
-@@ -30,7 +30,6 @@
+@@ -21,6 +21,7 @@
+ 
+ 	<path id="lib.path">
+ 		<fileset refid="lib.jars" />
++                <fileset dir="/usr/share/java" includes="alter-lib.jar"/>
+ 	</path>
+ 
+ 	<!-- Stub install target.  Install should depend on the 'jar' target,
+@@ -30,7 +31,6 @@
  
  	<target name="compile" description="Compile code">
  		<mkdir dir="${build.dir}" />
@@ -24,3 +32,12 @@ Description: Use Debian packaged JARs
  		<property environment="env" />
  		<property name="java6.boot.classpath" value="${env.JAVA6_BOOTCLASSES}" />
  		<javac srcdir="${src.dir}" destdir="${build.dir}" includeAntRuntime="no" 
+--- a/Manifest
++++ b/Manifest
+@@ -1,5 +1,5 @@
+ Main-Class: es.uvigo.darwin.jmodeltest.ModelTest
+ Class-Path: lib/appframework-1.0.3.jar lib/mpj.
+- jar lib/pal.jar lib/alter.jar lib/swing-worker-1.1.jar.
++ jar lib/pal.jar lib/alter.jar lib/alter-lib.jar lib/swing-worker-1.1.jar.
+  jar lib/freemarker.jar lib/BrowserLauncher2-all-1_3.
+  jar lib/jfreechart-1.0.14.jar lib/jcommon-1.0.17.jar