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#!/usr/bin/make -f
export DH_VERBOSE=1
export DH_OPTIONS
export ANT_HOME=/usr/share/ant
export JAVA_HOME=$(readlink -f /usr/bin/javac | sed "s:/bin/javac::")
%:
dh $@ --buildsystem=gradle --with javahelper,jh_maven_repo_helper
override_dh_link:
rm -f debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/jquery/external/jquery/jquery.js
dh_link
override_dh_auto_build:
@echo 'blhc: ignore-line-regexp: .*gradle.*ScriptTransformer.*'
dh_auto_build -- jar javadoc
override_dh_auto_test:
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
# ensure the .jar can be executed
/usr/bin/java -XX:ParallelGCThreads=1 -Xmx4G -Xss16M -Djava.io.tmpdir=/tmp -jar `find . -name "picard*.jar" BamIndexStats|head -n 1` -h > /dev/null
# Tests do not work with locales with a different decimal separator
# (for example ',')
env LC_ALL=C \
dh_auto_build -- test
endif
override_dh_clean:
dh_clean
# also remove bai files that are left after tests
# find testdata -iname "*.bai" -exec rm {} \; # This needs to be more fine grained since testdata/picard/indices/index_test_b.bam.bai needs to stay!
$(RM) debian/bd-temp-substvars
$(RM) debian/bd.substvars
override_dh_gencontrol:
cat debian/control \
| sed -e '/^Build-.*Depends:/,/^[^[:space:]#]/{s/^Build-.*Depends:/ /;p};d' \
| grep '^[[:space:]]' \
| tr ',' '\n' \
> debian/bd-temp-substvars
echo -n "bd:libhtsjdk-java=" > debian/bd.substvars
grep 'libhtsjdk-java ' debian/bd-temp-substvars \
| tr "\n" "," \
| sed -e 's/[[:space:]]\+/ /g;s/,$$/\n/' \
>> debian/bd.substvars
echo -n "bd:libguava-java=" >> debian/bd.substvars
grep 'libguava-java ' debian/bd-temp-substvars \
| tr "\n" "," \
| sed -e 's/[[:space:]]\+/ /g;s/,$$/\n/' \
>> debian/bd.substvars
dh_gencontrol -O--buildsystem=gradle -- -Tdebian/bd.substvars
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