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#!/usr/bin/make -f
# -*- makefile -*-
# Uncomment this to turn on verbose mode.
#export DH_VERBOSE=1
export LC_ALL=C.UTF-8
JAVA_HOME=/usr/lib/jvm/default-java
%:
dh $@ --with javahelper
override_dh_auto_configure:
dh_auto_configure
sed -e 's/BJLIB/biojava4-forester/g' debian/build.xml > biojava-forester/build.xml
sed -e 's/BJLIB/biojava4-aa-prop/g' debian/build.xml > biojava-aa-prop/build.xml
sed -e 's/BJLIB/biojava4-core/g' debian/build.xml > biojava-core/build.xml
sed -e 's/BJLIB/biojava4-alignment/g' debian/build.xml > biojava-alignment/build.xml
sed -e 's/BJLIB/biojava4-genome/g' debian/build.xml > biojava-genome/build.xml
sed -e 's/BJLIB/biojava4-modfinder/g' debian/build.xml > biojava-modfinder/build.xml
sed -e 's/BJLIB/biojava4-phylo/g' debian/build.xml > biojava-phylo/build.xml
sed -e 's/BJLIB/biojava4-sequencing/g' debian/build.xml > biojava-sequencing/build.xml
sed -e 's/BJLIB/biojava4-protein-disorder/g' debian/build.xml > biojava-protein-disorder/build.xml
sed -e 's/BJLIB/biojava4-structure/g' debian/build.xml > biojava-structure/build.xml
sed -e 's/BJLIB/biojava4-ws/g' debian/build.xml > biojava-ws/build.xml
sed -e 's/BJLIB/biojava4-structure-gui/g' debian/build.xml > biojava-structure-gui/build.xml
sed -e 's/BJLIB/biojava4-ontology/g' debian/build.xml > biojava-ontology/build.xml
sed -e 's/BJLIB/biojava4-protein-comparison-tool/g' debian/build.xml > biojava-protein-comparison-tool/build.xml
sed -e 's/BJLIB/biojava4-survival/g' debian/build.xml > biojava-survival/build.xml
sed -e 's/BJLIB/biojava4-jcolorbrewer/g' debian/build.xml > biojava-jcolorbrewer/build.xml
override_dh_auto_build:
cd biojava-jcolorbrewer && ant jar
cd biojava-forester && ant jar
cd biojava-core && ant jar
cd biojava-phylo && ant jar
cd biojava-alignment && ant jar
cd biojava-aa-prop && ant jar
cd biojava-genome && ant jar
cd biojava-sequencing && ant jar
cd biojava-structure && ant jar
cd biojava-structure-gui && ant jar
cd biojava-modfinder && ant jar
cd biojava-ontology && ant jar
cd biojava-protein-disorder && ant jar
cd biojava-protein-comparison-tool && ant jar
cd biojava-ws && ant jar
cd biojava-survival && ant jar
# make doc
rm -rf biojavadoc
mkdir biojavadoc
cp -r biojava-*/src biojavadoc/
sed -e 's/BJLIB/biojava/g' debian/build.xml > biojavadoc/build.xml
cd biojavadoc && ant javadocs
# rm -rf biojavadoc
override_jh_installjavadoc:
jh_installjavadoc
rdfind -makesymlinks true -followsymlinks true \
/usr/share/doc/openjdk-11-jre-headless \
debian/libbiojava4-java-doc/usr/share/doc/libbiojava4-java/
ifeq ($(DH_VERBOSE),1)
cat results.txt || /bin/true; rm -f results.txt
endif
override_dh_auto_test:
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
echo '*********************************************************************************'
echo '* The following test is ignored since under certain circumstances it might fail *'
echo '* Please check the result! *'
echo '* More information can be found in the Debian BTS at *'
echo '* https://bugs.debian.org/843712 *'
echo '*********************************************************************************'
cd biojava-core && (ant test || true)
cd biojava-alignment && ant test
# Investigate test failure
cd biojava-aa-prop && ant test
# Skip, missing dependency junitx
#cd biojava-genome && ant test
cd biojava-phylo && ant test
# Native errors may cause issue on NFS...; skipping
cd biojava-sequencing && ant test
# Serialization failure in pbuilder mode
#cd biojava-modfinder && ant test
# Investigate test failure
#cd biojava-protein-disorder && ant test
# Requires remote access and tmp directory write access
#cd biojava-structure && ant test
cd biojava-structure-gui && ant test
cd biojava-ontology && ant test
endif
override_dh_clean:
dh_clean
rm -rf build
rm -rf dist
rm -rf javadoc
rm -rf test
rm -f biojava-*/build.xml
rm -rf biojavadoc
rm -rf doc
find . -name "*.class" -delete
rm -rf buildtest
get-orig-source:
debian/get-orig-source
|
