#!/usr/bin/make -f

export JAVA_HOME=/usr/lib/jvm/default-java
export CLASSPATH=/usr/share/java/htsjdk.jar

%:
	dh $@ --with javahelper

override_jh_build:
	# This ugly thing below because jh_build search .java files in .pc folder so FTBFS...
	rm -rf $(CURDIR)/.pc/
	jh_build --javacopts="-source 1.8" --javadoc-opts="-source 1.8" --main="main.Main" beagle.jar $(CURDIR)

override_dh_install:
	dh_install beagle.jar /usr/share/beagle/

override_dh_installman:
	dh_installman debian/beagle.1

override_dh_installchangelogs:
	dh_installchangelogs debian/upstream.docs/release_notes

override_dh_link:
	dh_link /usr/share/beagle/beagle.jar usr/bin/beagle

get-orig-source:
	uscan --verbose --force-download --repack --compress xz
	# mv beagle_22Feb16.8ef+dfsg.orig.tar.xz beagle_4.1~160222-8ef+dfsg.orig.tar.xz
	# wget https://faculty.washington.edu/browning/beagle/beagle_4.1_09Feb16.pdf
	# wget https://faculty.washington.edu/browning/beagle/release_notes
	# wget https://faculty.washington.edu/browning/beagle/run.beagle.22Feb16.8ef.example
	# wget http://faculty.washington.edu/browning/beagle/test.22Feb16.8ef.vcf.gz

