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#!/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
# Putting util classes under src/tests so that tests find them.
cp -r src/testFixtures/java/org/broadinstitute/dropseqrna/utils src/tests/java/org/broadinstitute/dropseqrna
cp -r src/testFixtures/java/org/broadinstitute/dropseqrna/barnyard/DigitalExpressionTestUtil.java src/tests/java/org/broadinstitute/dropseqrna/barnyard
#Attempts to delete unexisting file
override_dh_auto_clean:
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
override_dh_clean:
dh_clean
rm -rf dist lib
# Removing .class files created during the build.
find . -name "*.class" -delete
# Removing classes from testFixtures we put under src/tests.
-rm -r src/tests/java/org/broadinstitute/dropseqrna/utils
-rm src/tests/java/org/broadinstitute/dropseqrna/barnyard/DigitalExpressionTestUtil.java
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