Author: fxf-guest Date: 2009-11-11 12:21:39 +0000 (Wed, 11 Nov 2009) New Revision: 4328
Added: trunk/packages/beast-mcmc/trunk/debian/compat trunk/packages/beast-mcmc/trunk/debian/dirs trunk/packages/beast-mcmc/trunk/debian/menu trunk/packages/beast-mcmc/trunk/debian/patches/fix_paths.patch trunk/packages/beast-mcmc/trunk/debian/patches/native_flags.patch trunk/packages/beast-mcmc/trunk/debian/patches/series Modified: trunk/packages/beast-mcmc/trunk/debian/ trunk/packages/beast-mcmc/trunk/debian/control trunk/packages/beast-mcmc/trunk/debian/rules Log: Compilation and package generation completed Property changes on: trunk/packages/beast-mcmc/trunk/debian ___________________________________________________________________ Added: mergeWithUpstream + 1 Added: trunk/packages/beast-mcmc/trunk/debian/compat =================================================================== --- trunk/packages/beast-mcmc/trunk/debian/compat (rev 0) +++ trunk/packages/beast-mcmc/trunk/debian/compat 2009-11-11 12:21:39 UTC (rev 4328) @@ -0,0 +1 @@ +7 Modified: trunk/packages/beast-mcmc/trunk/debian/control =================================================================== --- trunk/packages/beast-mcmc/trunk/debian/control 2009-11-10 07:47:00 UTC (rev 4327) +++ trunk/packages/beast-mcmc/trunk/debian/control 2009-11-11 12:21:39 UTC (rev 4328) @@ -4,7 +4,7 @@ Maintainer: Debian Med Packaging Team <[email protected]> DM-Upload-Allowed: yes Uploaders: Felix Feyertag <[email protected]> -Build-Depends: debhelper (>= 7) +Build-Depends: debhelper (>= 7), cdbs, openjdk-6-jdk, ant, ant-optional, libgcj10-dev Standards-Version: 3.8.0 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/beast-mcmc/trunk/?rev=0&sc=0 Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/beast-mcmc/trunk/ Added: trunk/packages/beast-mcmc/trunk/debian/dirs =================================================================== --- trunk/packages/beast-mcmc/trunk/debian/dirs (rev 0) +++ trunk/packages/beast-mcmc/trunk/debian/dirs 2009-11-11 12:21:39 UTC (rev 4328) @@ -0,0 +1,9 @@ +usr/bin +usr/share/applications +usr/share/java +usr/share/beast-mcmc +usr/share/beast-mcmc/lib/ +usr/share/beast-mcmc/doc/ +usr/share/beast-mcmc/examples/ +usr/share/menu +usr/share/pixmaps Added: trunk/packages/beast-mcmc/trunk/debian/menu =================================================================== --- trunk/packages/beast-mcmc/trunk/debian/menu (rev 0) +++ trunk/packages/beast-mcmc/trunk/debian/menu 2009-11-11 12:21:39 UTC (rev 4328) @@ -0,0 +1,8 @@ +?package(beast-mcmc):\ +needs="X11"\ +section="Applications/Science/Biology"\ +title="BEAST"\ +command="/usr/bin/beast-mcmc"\ +icon="/usr/share/pixmaps/beast.png" \ +hints="Phylogenetic inference"\ +longtitle="BEAST: Bayesian MCMC phylogenetic inference" Added: trunk/packages/beast-mcmc/trunk/debian/patches/fix_paths.patch =================================================================== --- trunk/packages/beast-mcmc/trunk/debian/patches/fix_paths.patch (rev 0) +++ trunk/packages/beast-mcmc/trunk/debian/patches/fix_paths.patch 2009-11-11 12:21:39 UTC (rev 4328) @@ -0,0 +1,50 @@ +--- beast-mcmc-1.5.2+svnr2377.orig/scripts/beast ++++ beast-mcmc-1.5.2+svnr2377/scripts/beast +@@ -22,6 +22,6 @@ + cd "$saveddir" + fi + +-BEAST_LIB=$BEAST/lib ++BEAST_LIB=/usr/share/beast-mcmc/lib + java -Xms64m -Xmx256m -Djava.library.path=$BEAST_LIB -jar $BEAST_LIB/beast.jar $* + +--- beast-mcmc-1.5.2+svnr2377.orig/scripts/beauti ++++ beast-mcmc-1.5.2+svnr2377/scripts/beauti +@@ -22,6 +22,6 @@ + cd "$saveddir" + fi + +-BEAST_LIB=$BEAST/lib ++BEAST_LIB=/usr/share/beast-mcmc/lib + java -Xms64m -Xmx256m -Djava.library.path=$BEAST_LIB -jar $BEAST_LIB/beauti.jar $* + +--- beast-mcmc-1.5.2+svnr2377.orig/scripts/loganalyser ++++ beast-mcmc-1.5.2+svnr2377/scripts/loganalyser +@@ -22,6 +22,6 @@ + cd "$saveddir" + fi + +-BEAST_LIB=$BEAST/lib ++BEAST_LIB=/usr/share/beast-mcmc/lib + java -Xms64m -Xmx256m -Djava.library.path=$BEAST_LIB -cp $BEAST_LIB/beast.jar dr.app.tools.LogAnalyser $* + +--- beast-mcmc-1.5.2+svnr2377.orig/scripts/logcombiner ++++ beast-mcmc-1.5.2+svnr2377/scripts/logcombiner +@@ -22,6 +22,6 @@ + cd "$saveddir" + fi + +-BEAST_LIB=$BEAST/lib ++BEAST_LIB=/usr/share/beast-mcmc/lib + java -Xms64m -Xmx128m -Djava.library.path=$BEAST_LIB -cp $BEAST_LIB/beast.jar dr.app.tools.LogCombiner $* + +--- beast-mcmc-1.5.2+svnr2377.orig/scripts/treeannotator ++++ beast-mcmc-1.5.2+svnr2377/scripts/treeannotator +@@ -22,6 +22,6 @@ + cd "$saveddir" + fi + +-BEAST_LIB=$BEAST/lib ++BEAST_LIB=/usr/share/beast-mcmc/lib + java -Xms64m -Xmx256m -Djava.library.path=$BEAST_LIB -cp $BEAST_LIB/beast.jar dr.app.tools.TreeAnnotator $* + Added: trunk/packages/beast-mcmc/trunk/debian/patches/native_flags.patch =================================================================== --- trunk/packages/beast-mcmc/trunk/debian/patches/native_flags.patch (rev 0) +++ trunk/packages/beast-mcmc/trunk/debian/patches/native_flags.patch 2009-11-11 12:21:39 UTC (rev 4328) @@ -0,0 +1,10 @@ +--- beast-mcmc-1.5.2+svnr2377.orig/native/Makefile ++++ beast-mcmc-1.5.2+svnr2377/native/Makefile +@@ -36,6 +36,6 @@ + -output lib$(OUTNAME).jnilib + + linux : +- gcc -c -O4 $(OPTIONS) $(LINUX_INCLUDES) -c $(INNAME) -std=c99 -DSTATE_COUNT=$(STATE_COUNT) -o lib$(OUTNAME).o ++ gcc -fPIC -c -O4 $(OPTIONS) $(LINUX_INCLUDES) -c $(INNAME) -std=c99 -DSTATE_COUNT=$(STATE_COUNT) -o lib$(OUTNAME).o + ld -$(LINUX_LINK) -o lib$(OUTNAME).so lib$(OUTNAME).o + Added: trunk/packages/beast-mcmc/trunk/debian/patches/series =================================================================== --- trunk/packages/beast-mcmc/trunk/debian/patches/series (rev 0) +++ trunk/packages/beast-mcmc/trunk/debian/patches/series 2009-11-11 12:21:39 UTC (rev 4328) @@ -0,0 +1,2 @@ +native_flags.patch +fix_paths.patch Modified: trunk/packages/beast-mcmc/trunk/debian/rules =================================================================== --- trunk/packages/beast-mcmc/trunk/debian/rules 2009-11-10 07:47:00 UTC (rev 4327) +++ trunk/packages/beast-mcmc/trunk/debian/rules 2009-11-11 12:21:39 UTC (rev 4328) @@ -1,10 +1,30 @@ #!/usr/bin/make -f # -*- makefile -*- + +#export DH_VERBOSE=1 + +#include /usr/share/cdbs/1/rules/debhelper.mk +#include /usr/share/cdbs/1/class/ant.mk +#include /usr/share/cdbs/1/rules/simple-patchsys.mk +include /usr/share/quilt/quilt.make + + PACKAGE = beast-mcmc SRC_VERSION := $(shell dpkg-parsechangelog | sed -ne 's/^Version: \(\([0-9]\+\):\)\?\(.*\)-.*/\3/p') SVN_REVISION := $(shell echo $(SRC_VERSION) | awk -F"+" '{ print $$2 }' | sed 's/svn//' ) TARBALL = $(PACKAGE)_$(SRC_VERSION).orig.tar.gz -.PHONY: get-orig-source + +JAVA := /usr/lib/jvm/java-6-openjdk/bin/java +CLASS_PATH := /usr/share/ant/lib/ant.jar:/usr/share/ant/lib/ant-launcher.jar:/usr/share/ant/lib/ant-nodeps.jar:/usr/share/ant/lib/ant-junit.jar:lib/beagle.jar:lib/commons-math-1.2.jar:lib/itext-1.4.5.jar:lib/jdom.jar:lib/JRI.jar:lib/libjri.jnilib:lib/mtj.jar:lib/colt.jar:lib/figtreepanel.jar:lib/jam.jar:lib/jebl.jar:lib/junit-4.4.jar:lib/mpj.jar:lib/options.jar:/usr/lib/jvm/java-6-openjdk//lib/tools.jar +ANT_HOME := /usr/share/ant +ANT_BIN := $(ANT_HOME)/bin/ant +ANT_ARGS := -Dcompile.debug=true -Dcompile.optimize=true + +orig_tar = ${CURDIR}/../${TARBARLL} +DEBIAN_DIR := "${CURDIR}/$(shell echo ${MAKEFILE_LIST} | awk '{print $$1}' | xargs dirname )" +SRC_TEMP_DIR := get-orig-source.tmp + + get-orig-source: rm -rf get-orig-source $(TARBALL) mkdir get-orig-source @@ -12,4 +32,93 @@ get-orig-source/$(PACKAGE)-$(SRC_VERSION).orig GZIP=--best tar czf $(TARBALL) -C get-orig-source $(PACKAGE)-$(SRC_VERSION).orig rm -rf get-orig-source - echo " "$(TARBALL)" created; move it to the right destination to build the package" + mv $(TARBALL) ../ + +clean: + dh_testdir + dh_testroot + rm -f build-stamp configure-stamp + ## Add here commands to clean up after the build process. + $(JAVA) -classpath $(CLASS_PATH) -Dant.home=$(ANT_HOME) org.apache.tools.ant.Main $(ANT_ARGS) -buildfile build_BEAST_MCMC.xml clean + rm -f native/*\.o + dh_clean + +configure: configure-stamp + +configure-stamp: + dh_testdir + # Add here commands to configure the package. + $(JAVA) -classpath $(CLASS_PATH) -Dant.home=$(ANT_HOME) org.apache.tools.ant.Main $(ANT_ARGS) -buildfile build_BEAST_MCMC.xml init + $(JAVA) -classpath $(CLASS_PATH) -Dant.home=$(ANT_HOME) org.apache.tools.ant.Main $(ANT_ARGS) -buildfile build_coalsim.xml init + $(JAVA) -classpath $(CLASS_PATH) -Dant.home=$(ANT_HOME) org.apache.tools.ant.Main $(ANT_ARGS) -buildfile build_pathogen.xml init + $(JAVA) -classpath $(CLASS_PATH) -Dant.home=$(ANT_HOME) org.apache.tools.ant.Main $(ANT_ARGS) -buildfile build_treestat.xml init + $(JAVA) -classpath $(CLASS_PATH) -Dant.home=$(ANT_HOME) org.apache.tools.ant.Main $(ANT_ARGS) -buildfile build_vcs.xml init + $(JAVA) -classpath $(CLASS_PATH) -Dant.home=$(ANT_HOME) org.apache.tools.ant.Main $(ANT_ARGS) -buildfile build.xml init + touch configure-stamp + +build: build-stamp + +build-stamp: patch + dh_testdir + $(JAVA) -classpath $(CLASS_PATH) -Dant.home=$(ANT_HOME) org.apache.tools.ant.Main $(ANT_ARGS) -buildfile build_BEAST_MCMC.xml compile-all dist_all_BEAST + $(JAVA) -classpath $(CLASS_PATH) -Dant.home=$(ANT_HOME) org.apache.tools.ant.Main $(ANT_ARGS) -buildfile build_coalsim.xml compile-all + $(JAVA) -classpath $(CLASS_PATH) -Dant.home=$(ANT_HOME) org.apache.tools.ant.Main $(ANT_ARGS) -buildfile build_pathogen.xml compile-all dist + $(JAVA) -classpath $(CLASS_PATH) -Dant.home=$(ANT_HOME) org.apache.tools.ant.Main $(ANT_ARGS) -buildfile build_treestat.xml compile-all + $(JAVA) -classpath $(CLASS_PATH) -Dant.home=$(ANT_HOME) org.apache.tools.ant.Main $(ANT_ARGS) -buildfile build_vcs.xml compile-all + $(JAVA) -classpath $(CLASS_PATH) -Dant.home=$(ANT_HOME) org.apache.tools.ant.Main $(ANT_ARGS) -buildfile build.xml build-project + cd native && make linux + touch build-stamp + +binary-indep: build-indep install + dh_testdir + dh_testroot + #dh_installdocs $(CURDIR)/debian/readme.html + dh_installdocs + dh_installman debian/mencal.1 + dh_installchangelogs + dh_link + dh_strip + dh_compress + dh_fixperms + dh_installdeb + dh_perl + dh_shlibdeps + dh_gencontrol + dh_md5sums + dh_builddeb + + + +test: + dh_testdir + $(JAVA) -classpath $(CLASS_PATH) -Dant.home=$(ANT_HOME) org.apache.tools.ant.Main $(ANT_ARGS) -buildfile build_BEAST_MCMC.xml junit + +binary-arch: build install + dh binary-arch + +binary: binary-arch +binary-indep: # does nothing + + + +install: build + dh_testdir + dh_testroot + dh_clean -k + dh_installdirs + install $(CURDIR)/scripts/beast $(CURDIR)/debian/beast-mcmc/usr/bin/ + install $(CURDIR)/scripts/beauti $(CURDIR)/debian/beast-mcmc/usr/bin/ + install $(CURDIR)/scripts/loganalyser $(CURDIR)/debian/beast-mcmc/usr/bin/ + install $(CURDIR)/scripts/logcombiner $(CURDIR)/debian/beast-mcmc/usr/bin/ + install $(CURDIR)/scripts/treeannotator $(CURDIR)/debian/beast-mcmc/usr/bin/ + install -m 664 $(CURDIR)/lib/*\.jar $(CURDIR)/debian/beast-mcmc/usr/share/beast-mcmc/lib + install -m 664 $(CURDIR)/build/dist/*\.jar $(CURDIR)/debian/beast-mcmc/usr/share/beast-mcmc/lib + install -m 664 $(CURDIR)/native/*\.so $(CURDIR)/debian/beast-mcmc/usr/share/beast-mcmc/lib + install -m 664 $(CURDIR)/release/common/icons/beast.png $(CURDIR)/debian/beast-mcmc/usr/share/pixmaps/ + install -m 664 $(CURDIR)/doc/*pdf $(CURDIR)/debian/beast-mcmc/usr/share/beast-mcmc/doc + install -m 664 $(CURDIR)/doc/Virus\ Practical\ Tex/*pdf $(CURDIR)/debian/beast-mcmc/usr/share/beast-mcmc/doc + install -d -m 664 $(CURDIR)/examples $(CURDIR)/debian/beast-mcmc/usr/share/beast-mcmc/examples + dh_desktop + dh_installmenu + +.PHONY: get-orig-source build build-indep binary-arch binary test install clean _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
