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#!/usr/bin/make -f
# -*- makefile -*-
# Uncomment this to turn on verbose mode.
#export DH_VERBOSE=1
JAVA_HOME=/usr/lib/jvm/default-java
%:
dh $@ --with javahelper
override_dh_auto_configure:
dh_auto_configure
sed -e 's/BJLIB/biojava3-forester/g' debian/build.xml > biojava3-forester/build.xml
sed -e 's/BJLIB/biojava3-aa-prop/g' debian/build.xml > biojava3-aa-prop/build.xml
sed -e 's/BJLIB/biojava3-core/g' debian/build.xml > biojava3-core/build.xml
sed -e 's/BJLIB/biojava3-alignment/g' debian/build.xml > biojava3-alignment/build.xml
sed -e 's/BJLIB/biojava3-genome/g' debian/build.xml > biojava3-genome/build.xml
sed -e 's/BJLIB/biojava3-modfinder/g' debian/build.xml > biojava3-modfinder/build.xml
sed -e 's/BJLIB/biojava3-phylo/g' debian/build.xml > biojava3-phylo/build.xml
sed -e 's/BJLIB/biojava3-sequencing/g' debian/build.xml > biojava3-sequencing/build.xml
sed -e 's/BJLIB/biojava3-protein-disorder/g' debian/build.xml > biojava3-protein-disorder/build.xml
sed -e 's/BJLIB/biojava3-structure/g' debian/build.xml > biojava3-structure/build.xml
sed -e 's/BJLIB/biojava3-ws/g' debian/build.xml > biojava3-ws/build.xml
sed -e 's/BJLIB/biojava3-structure-gui/g' debian/build.xml > biojava3-structure-gui/build.xml
override_dh_auto_build:
cd biojava3-forester && ant jar
cd biojava3-core && ant jar
cd biojava3-phylo && ant jar
cd biojava3-alignment && ant jar
cd biojava3-aa-prop && ant jar
cd biojava3-genome && ant jar
cd biojava3-sequencing && ant jar
cd biojava3-structure && ant jar
cd biojava3-structure-gui && ant jar
cd biojava3-modfinder && ant jar
cd biojava3-protein-disorder && ant jar
cd biojava3-ws && ant jar
# make doc
rm -rf biojavadoc
mkdir biojavadoc
cp -r biojava3-*/src biojavadoc/
sed -e 's/BJLIB/biojava/g' debian/build.xml > biojavadoc/build.xml
cd biojavadoc && ant javadocs
rm -rf biojavadoc
override_dh_auto_test:
cd biojava3-core && ant test
cd biojava3-alignment && ant test
cd biojava3-aa-prop && ant test
# Skip, missing dependency
#cd biojava3-genome && ant test
cd biojava3-phylo && ant test
# Native errors may cause issue on NFS...; skipping
#cd biojava3-sequencing && ant test
#cd biojava3-modfinder && ant test
cd biojava3-protein-disorder && ant test
# Requires remote access and tmp directory write access
#cd biojava3-structure && ant test
cd biojava3-structure-gui && ant test
#No test in biojava-ws available
#cd biojava3-ws && ant test
override_dh_clean:
dh_clean
rm -rf build
rm -rf dist
rm -rf javadoc
rm -rf test
rm -f biojava3-*/build.xml
rm -rf biojavadoc
rm -rf doc
get-orig-source:
debian/get-orig-source
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