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#!/usr/bin/make -f
# -*- makefile -*-
# debian/rules file for beast-mcmc
# Andreas Tille <tille@debian.org>
# GPL
#export DH_VERBOSE=1
export LC_ALL=C.UTF-8
export DEB_BUILD_MAINT_OPTIONS=hardening=+all
JAVA_HOME := /usr/lib/jvm/default-java
DEBJAR := /usr/share/java
CLASS_PATH := /usr/share/ant/lib/ant.jar:/usr/share/ant/lib/ant-launcher.jar:/usr/share/ant/lib/ant-nodeps.jar:/usr/share/ant/lib/ant-junit.jar:$(JAVA_HOME)/lib/tools.jar:$(DEBJAR)/beagle.jar:$(DEBJAR)/mpj.jar:$(DEBJAR)/org.boehn.kmlframework.jar:$(DEBJAR)/itext1-1.4.jar:$(DEBJAR)/junit4.jar:$(DEBJAR)/figtree.jar:lib/colt.jar:$(DEBJAR)/options.jar:$(DEBJAR)/mtj.jar:$(DEBJAR)/jam.jar:$(DEBJAR)/jdom1.jar:$(DEBJAR)/jebl.jar:$(DEBJAR)/commons-math.jar:$(DEBJAR)/EJML.jar:$(DEBJAR)/jlapack-lapack.jar:/usr/lib/R/site-library/rJava/jri/JRI.jar
# to run the test suite
JAVA := $(JAVA_HOME)/bin/java
ANT_HOME := /usr/share/ant
ANT_BIN := $(ANT_HOME)/bin/ant
ANT_ARGS := -Dcompile.debug=true -Dcompile.optimize=true
%:
dh $@ --with javahelper
override_dh_auto_clean:
rm -f native/*\.o native/*\.so native/*\.so\.*
ifeq ($(HASTEXDOC),yes)
for cleantex in \
Practical_BEAST \
BookSection \
Practical_BEAST \
Yule \
SerialSampleCoalescent \
BEAST14_Manual \
; do \
find doc -not -name "*.tex" -a -not -name "*.bib" -and -name "$${cleantex}.*" -exec rm -f \{\} \; ; \
done
endif
ant clean
CFLAGS:=$(shell dpkg-buildflags --get CFLAGS)
LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS)
PDFLATEX:=pdflatex -interaction=batchmode
override_dh_auto_build:
# CLASSPATH=$(CLASS_PATH)
mkdir -p lib
ant build
# FIXME: There is no such file build_tracer.xml any more
# ant -buildfile build_tracer.xml dist
# native/compileNativeLinux.sh does not create dynamic libraries
cd native ; $(MAKE) -f Makefile.linux JAVA_HOME=$(JAVA_HOME)
# gcc $(CFLAGS) $(LDFLAGS) -Wall -funroll-loops -ffast-math -fstrict-aliasing -c -I/usr/lib/jvm/default-java/include/ NucleotideLikelihoodCore.c -o libNucleotideLikelihoodCore.o ; \
# gcc -shared -Wl,-soname,libNucleotideLikelihoodCore.so.0 -o libNucleotideLikelihoodCore.so.0 libNucleotideLikelihoodCore.o -lc ; \
# gcc $(CFLAGS) $(LDFLAGS) -Wall -funroll-loops -ffast-math -fstrict-aliasing -c -I/usr/lib/jvm/default-java/include/ AminoAcidLikelihoodCore.c -o libAminoAcidLikelihoodCore.o ; \
# gcc -shared -Wl,-soname,libAminoAcidLikelihoodCore.so.0 -o libAminoAcidLikelihoodCore.so libAminoAcidLikelihoodCore.o -lc
ifeq ($(HASTEXDOC),yes)
#
# Build extra LaTeX documentation
#
cd doc/BookSection; $(PDFLATEX) BookSection.tex; $(PDFLATEX) BookSection.tex
cd doc/tutorial/Virus_Practical*; $(PDFLATEX) Practical_BEAST.tex; $(PDFLATEX) Practical_BEAST.tex
cd doc; $(PDFLATEX) Yule.tex; $(PDFLATEX) Yule.tex
cd doc; $(PDFLATEX) SerialSampleCoalescent.tex; $(PDFLATEX) SerialSampleCoalescent.tex
cd doc; $(PDFLATEX) BEAST14_Manual.tex; $(PDFLATEX) BEAST14_Manual.tex
endif
override_dh_auto_test:
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
#####################################################################
## Run test suite ##
## -------------- ##
## While this test suite runs quite a bit of time (about 30min) it ##
## is recommended to be run at least once per new version upload ##
#####################################################################
#
# $(JAVA) -classpath $(CLASS_PATH) -Dant.home=$(ANT_HOME) org.apache.tools.ant.Main $(ANT_ARGS) -buildfile build.xml junit
endif
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