debian/changelog

+proalign (0.603-4) UNRELEASED; urgency=medium
+
+  * Drop unneeded get-orig-source target
+  * Use jh_build
+  * debhelper 11
+  * Point Vcs fields to salsa.debian.org
+  * Standards-Version: 4.2.1
+
+ -- Andreas Tille <tille@debian.org>  Tue, 23 Oct 2018 17:28:44 +0200
+
 proalign (0.603-3) unstable; urgency=medium
 
   * Moved packaging from SVN to Git

debian/compat

-10
+11

debian/control

@@ -4,11 +4,12 @@ Uploaders: Andreas Tille <tille@debian.org>,
            Thorsten Alteholz <debian@alteholz.de>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 10),
+Build-Depends: debhelper (>= 11~),
+               javahelper,
                default-jdk
-Standards-Version: 4.1.1
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/proalign.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/proalign.git
+Standards-Version: 4.2.1
+Vcs-Browser: https://salsa.debian.org/med-team/proalign
+Vcs-Git: https://salsa.debian.org/med-team/proalign.git
 Homepage: http://ueg.ulb.ac.be/ProAlign/
 
 Package: proalign

debian/manifest.txt

-Manifest-version: 1.0
-Main-Class: proalign.ProAlign
-

debian/proalign.install

 debian/scripts/proalign usr/bin
-build/ProAlign.jar usr/share/proalign
+proalign.jar	usr/share/proalign
 

debian/rules

@@ -6,12 +6,4 @@
 	dh $@
 
 override_dh_auto_build:
-	mkdir -p build
-	javac -d ./build *.java
-	(cd build; jar cmvf ../debian/manifest.txt ProAlign.jar *)
-	#(cd build; jar cmvf ../debian/manifest.txt ProAlign.jar proalign/ProAlign.class proalign/OutFile.class)
-
-get-orig-source:
-	mkdir -p ../tarballs
-	uscan --verbose --force-download --destdir=../tarballs
-
+	jh_build --main=proalign.ProAlign proalign.jar .

debian/scripts/proalign

@@ -9,13 +9,11 @@ else
 fi
 
 if [ -x /usr/share/proalign ]; then
-        if [ -r /usr/share/proalign/ProAlign.jar  ]; then 
-                #cd /usr/share/proalign && $java -jar ProAlign.jar
-                $java -jar /usr/share/proalign/ProAlign.jar $PARA
+        if [ -r /usr/share/proalign/proalign.jar  ]; then 
+                $java -jar /usr/share/proalign/proalign.jar $PARA
         else 
-                echo "Could not find /usr/share/proalign/ProAlign.jar"
+                echo "Could not find /usr/share/proalign/proalign.jar"
         fi
 else 
         echo "Could not find /usr/share/proalign directory."
 fi
-

debian/tests/control_

+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr

debian/tests/run-unit-test

+#!/bin/bash
+
+echo "TODO: find sample data prim.fas and prim.tre"
+echo "see http://ueg.ulb.ac.be/ProAlign/main.html#command"
+exit 1
+
+set -e
+
+pkg=proalign
+
+if [ "$AUTOPKGTEST_TMP" = "" ] ; then
+  AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
+  trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
+fi
+
+cp -a /usr/share/doc/${pkg}/examples/* $AUTOPKGTEST_TMP
+
+cd $AUTOPKGTEST_TMP
+
+proalign -nogui -seqfile=prim.fas -treefile=prim.tre -outfile=prim.pir -outformat=pir