#!/usr/bin/make -f

# DH_VERBOSE := 1
export LC_ALL=C.UTF-8

include /usr/share/dpkg/default.mk

# for hardening you might like to uncomment this:
# export DEB_BUILD_MAINT_OPTIONS=hardening=+all

JAVA_HOME  := /usr/lib/jvm/default-java

%:
	dh $@ --with javahelper

override_dh_auto_configure:
	dh_auto_configure
	mkdir -p lib/test
	ln -s /usr/share/java/commons-collections4.jar lib/commons-collections4.jar
	ln -s /usr/share/java/biojava6-alignment.jar lib/biojava6-alignment.jar
	ln -s /usr/share/java/biojava6-core.jar lib/biojava6-core.jar
	ln -s /usr/share/java/commons-io.jar lib/commons-io.jar
	ln -s /usr/share/java/commons-lang.jar lib/commons-lang.jar
	ln -s /usr/share/java/commons-math3.jar lib/commons-math3.jar
	ln -s /usr/share/java/htsjdk.jar lib/htsjdk.jar
	ln -s /usr/share/java/la4j.jar lib/la4j.jar
	ln -s /usr/share/java/picard.jar lib/picard.jar
	ln -s /usr/share/java/snakeyaml.jar lib/snakeyaml.jar

	ln -s /usr/share/java/testng.jar lib/test/testng.jar
	ln -s /usr/share/java/junit4.jar lib/test/junit.jar

override_dh_auto_clean:
	rm -Rf lib

override_dh_fixperms:
	dh_fixperms
	find debian/drop-seq-testdata/usr/share -type f -exec chmod -x \{\} \;

# Invoking dh_installman with --language=C to get "traditional" manpages
# although the files we put in /usr/bin end with ".sh".
override_dh_installman:
	dh_installman --language=C