debian/bin/pilon

+#! /bin/sh
+set -e
+
+# export JAVA_HOME=/usr/lib/jvm/default-java
+export JAVA_CMD=java
+
+# Include the wrappers utility script
+. /usr/lib/java-wrappers/java-wrappers.sh
+
+run_java -Xms128M -Xmx1G -jar /usr/share/java/pilon.jar "$@"

debian/control

@@ -5,7 +5,7 @@ Section: science
 Priority: optional
 Build-Depends: debhelper (>= 11~),
                scala,
-               libscala-pickling-java
+               libhtsjdk-java
 Standards-Version: 4.1.4
 Vcs-Browser: https://salsa.debian.org/med-team/pilon
 Vcs-Git: https://salsa.debian.org/med-team/pilon.git
@@ -15,6 +15,8 @@ Package: pilon
 Architecture: all
 Depends: ${misc:Depends},
          libhtsjdk-java
+Conflicts: pilon-non-free
+Replaces: pilon-non-free
 Description: automated genome assembly improvement and variant detection tool
  Pilon is a software tool which can be used to:
   * Automatically improve draft assemblies

debian/install

+pilon*.jar	usr/share/java
+debian/bin	usr

debian/rules

@@ -5,3 +5,6 @@ export LC_ALL=C.UTF-8
 
 %:
 	dh $@
+
+override_dh_auto_build:
+	scalac -classpath /usr/share/java/htsjdk.jar -d pilon.jar src/main/scala/org/broadinstitute/pilon/*