[med-svn] r4328 - in trunk/packages/beast-mcmc/trunk/debian: . patches
Felix Feyertag
fxf-guest at alioth.debian.org
Wed Nov 11 12:21:40 UTC 2009
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 <debian-med-packaging at lists.alioth.debian.org>
DM-Upload-Allowed: yes
Uploaders: Felix Feyertag <felix.feyertag at googlemail.com>
-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
More information about the debian-med-commit
mailing list