[med-svn] r5899 - trunk/packages/beast-mcmc/trunk/debian
Andreas Tille
tille at alioth.debian.org
Sat Feb 5 07:17:57 UTC 2011
Author: tille
Date: 2011-02-05 07:17:51 +0000 (Sat, 05 Feb 2011)
New Revision: 5899
Added:
trunk/packages/beast-mcmc/trunk/debian/beast-doc.install
trunk/packages/beast-mcmc/trunk/debian/beast-mcmc-lib.install
trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.install
trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.manpages
Modified:
trunk/packages/beast-mcmc/trunk/debian/control
trunk/packages/beast-mcmc/trunk/debian/copyright
trunk/packages/beast-mcmc/trunk/debian/rules
Log:
Split up into three binary packages: Main beast-mcmc (arch=all), beast-doc and beast-mcmc-lib (arch=any) to keep thy byte-load of arch-any packages low; moved to non-free because there are several JAR files without source and we can not sort this out for the moment; debian/rules with short dh statement; make use of debian/<pkg>.{install,manpages} files
Added: trunk/packages/beast-mcmc/trunk/debian/beast-doc.install
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/beast-doc.install (rev 0)
+++ trunk/packages/beast-mcmc/trunk/debian/beast-doc.install 2011-02-05 07:17:51 UTC (rev 5899)
@@ -0,0 +1,3 @@
+doc/*.pdf usr/share/doc/beast-mcmc
+#doc/Virus\ Practical\ Tex/*.pdf usr/share/doc/beast-mcmc
+examples/release/*.xml usr/share/doc/beast-mcmc/examples
Added: trunk/packages/beast-mcmc/trunk/debian/beast-mcmc-lib.install
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/beast-mcmc-lib.install (rev 0)
+++ trunk/packages/beast-mcmc/trunk/debian/beast-mcmc-lib.install 2011-02-05 07:17:51 UTC (rev 5899)
@@ -0,0 +1 @@
+native/*.so usr/lib
Added: trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.install
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.install (rev 0)
+++ trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.install 2011-02-05 07:17:51 UTC (rev 5899)
@@ -0,0 +1,4 @@
+release/Linux/scripts/* usr/bin
+release/common/icons/beast.png usr/share/pixmaps
+lib/*.jar usr/share/beast-mcmc/lib
+build/dist/*.jar usr/share/beast-mcmc/lib
Added: trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.manpages
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.manpages (rev 0)
+++ trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.manpages 2011-02-05 07:17:51 UTC (rev 5899)
@@ -0,0 +1 @@
+debian/*.1
Modified: trunk/packages/beast-mcmc/trunk/debian/control
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/control 2011-02-04 22:21:30 UTC (rev 5898)
+++ trunk/packages/beast-mcmc/trunk/debian/control 2011-02-05 07:17:51 UTC (rev 5899)
@@ -1,5 +1,5 @@
Source: beast-mcmc
-Section: science
+Section: non-free/science
Priority: optional
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
DM-Upload-Allowed: yes
@@ -13,9 +13,10 @@
Homepage: http://beast.bio.ed.ac.uk/
Package: beast-mcmc
-Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}
-Description: Bayesian MCMC phylogenetic inference
+Architecture: all
+Depends: ${shlibs:Depends}, ${misc:Depends}, beast-mcmc-lib
+Suggests: beast-doc
+Description: Bayesian MCMC phylogenetic inference
BEAST is a cross-platform program for Bayesian MCMC analysis of molecular
sequences. It is entirely orientated towards rooted, time-measured
phylogenies inferred using strict or relaxed molecular clock models. It
@@ -29,3 +30,37 @@
When publishing results using this software please cite:
Drummond AJ, Rambaut A (2007) "BEAST: Bayesian evolutionary analysis by
sampling trees." BMC Evolutionary Biology 7:214
+
+Package: beast-mcmc-lib
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Suggests: beast-doc
+Description: Bayesian MCMC phylogenetic inference
+ BEAST is a cross-platform program for Bayesian MCMC analysis of molecular
+ sequences. It is entirely orientated towards rooted, time-measured
+ phylogenies inferred using strict or relaxed molecular clock models. It
+ can be used as a method of reconstructing phylogenies but is also a
+ framework for testing evolutionary hypotheses without conditioning on a
+ single tree topology. BEAST uses MCMC to average over tree space, so that
+ each tree is weighted proportional to its posterior probability. Included
+ is a simple to use user-interface program for setting up standard
+ analyses and a suit of programs for analysing the results.
+ .
+ This package contains an architecture dependant library.
+
+Package: beast-doc
+Architecture: all
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Enhances: beast-mcmc
+Description: Bayesian MCMC phylogenetic inference - documentation
+ BEAST is a cross-platform program for Bayesian MCMC analysis of molecular
+ sequences. It is entirely orientated towards rooted, time-measured
+ phylogenies inferred using strict or relaxed molecular clock models. It
+ can be used as a method of reconstructing phylogenies but is also a
+ framework for testing evolutionary hypotheses without conditioning on a
+ single tree topology. BEAST uses MCMC to average over tree space, so that
+ each tree is weighted proportional to its posterior probability. Included
+ is a simple to use user-interface program for setting up standard
+ analyses and a suit of programs for analysing the results.
+ .
+ This package contains the documentation and example data.
Modified: trunk/packages/beast-mcmc/trunk/debian/copyright
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/copyright 2011-02-04 22:21:30 UTC (rev 5898)
+++ trunk/packages/beast-mcmc/trunk/debian/copyright 2011-02-05 07:17:51 UTC (rev 5899)
@@ -44,4 +44,7 @@
in the source distribution available at
http://jakarta.apache.org/commons/math/
+The package has to be regarded as non-free as long as it ships with binary
+jar files which come without source.
+
This package was debianized by Felix Feyertag <felix.feyertag at googlemail.com>.
Modified: trunk/packages/beast-mcmc/trunk/debian/rules
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/rules 2011-02-04 22:21:30 UTC (rev 5898)
+++ trunk/packages/beast-mcmc/trunk/debian/rules 2011-02-05 07:17:51 UTC (rev 5899)
@@ -3,10 +3,8 @@
#export DH_VERBOSE=1
-include /usr/share/quilt/quilt.make
-
-
PACKAGE = beast-mcmc
+DOCPACKAGE = beast-doc
SRC_VERSION := $(shell dpkg-parsechangelog | sed -ne 's/^Version: \(\([0-9]\+\):\)\?\(.*\)-.*/\3/p')
SVN_REVISION := $(shell echo $(SRC_VERSION) | awk -F"+" '{ print $$2 }' | sed 's/svn//' )
TARBALL = $(PACKAGE)_$(SRC_VERSION).orig.tar.gz
@@ -17,92 +15,39 @@
ANT_BIN := $(ANT_HOME)/bin/ant
ANT_ARGS := -Dcompile.debug=true -Dcompile.optimize=true
-orig_tar = ${CURDIR}/../${TARBARLL}
-DEBIAN_DIR := "${CURDIR}/$(shell echo ${MAKEFILE_LIST} | awk '{print $$1}' | xargs dirname )"
-SRC_TEMP_DIR := get-orig-source.tmp
+%:
+ dh $@
+override_dh_auto_clean:
+ rm -f build-stamp configure-stamp
+ #$(JAVA) -classpath $(CLASS_PATH) -Dant.home=$(ANT_HOME) org.apache.tools.ant.Main $(ANT_ARGS) -buildfile build.xml clean
+ rm -f native/*\.o
+override_dh_auto_build:
+ $(JAVA) -classpath $(CLASS_PATH) -Dant.home=$(ANT_HOME) org.apache.tools.ant.Main $(ANT_ARGS) -buildfile build.xml build
+ cd native && /bin/sh compileNativeLinux.sh
+ ##
+ ## 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
+
+override_dh_install:
+ dh_install
+ # dh_install seems to fail in moving this fail for whatever reason
+ cp -a doc/Virus\ Practical\ Tex/*.pdf $(CURDIR)/debian/$(DOCPACKAGE)/usr/share/doc/beast-mcmc
+ # rename beast to beast-mcmc
+ mv $(CURDIR)/release/Linux/scripts/beast $(CURDIR)/release/Linux/scripts/beast-mcmc
+
get-orig-source:
rm -rf get-orig-source $(TARBALL)
mkdir get-orig-source
svn export -r $(SVN_REVISION) http://beast-mcmc.googlecode.com/svn/trunk/ \
get-orig-source/$(PACKAGE)-$(SRC_VERSION).orig
- GZIP=--best tar czf $(TARBALL) -C get-orig-source $(PACKAGE)-$(SRC_VERSION).orig
+ GZIP="--best --no-name" tar czf $(TARBALL) -C get-orig-source $(PACKAGE)-$(SRC_VERSION).orig
rm -rf get-orig-source
rm -rf ../tarballs/
mkdir ../tarballs/
mv $(TARBALL) ../tarballs/
-
-clean:
- dh_testdir
- dh_testroot
- rm -f build-stamp configure-stamp
- ## Add here commands to clean up after the build process.
- #$(JAVA) -classpath $(CLASS_PATH) -Dant.home=$(ANT_HOME) org.apache.tools.ant.Main $(ANT_ARGS) -buildfile build.xml clean
- rm -f native/*\.o
- dh_clean
-
-configure: configure-stamp
-
-configure-stamp:
- dh_testdir
- # Add here commands to configure the package.
- 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.xml build
- cd native && /bin/sh compileNativeLinux.sh
- touch build-stamp
-
-binary-indep: build-indep install
- dh_testdir
- dh_testroot
-
-test:
- dh_testdir
- $(JAVA) -classpath $(CLASS_PATH) -Dant.home=$(ANT_HOME) org.apache.tools.ant.Main $(ANT_ARGS) -buildfile build.xml junit
-
-binary-arch: build install
- dh binary-arch
-
-binary: binary-arch
-
-install: build
- dh_testdir
- dh_testroot
- dh_clean -k
- dh_installdirs
- dh_installman debian/beast-mcmc.1 debian/beauti.1
- dh_installdocs
- dh_installchangelogs
- dh_link
- dh_strip
- dh_compress
- dh_fixperms
- dh_installdeb
- dh_perl
- dh_shlibdeps
- dh_gencontrol
- dh_md5sums
- #dh_builddeb
- mv $(CURDIR)/release/Linux/scripts/beast $(CURDIR)/release/Linux/scripts/beast-mcmc
- install $(CURDIR)/release/Linux/scripts/beast-mcmc $(CURDIR)/debian/beast-mcmc/usr/bin/
- install $(CURDIR)/release/Linux/scripts/beauti $(CURDIR)/debian/beast-mcmc/usr/bin/
- install $(CURDIR)/release/Linux/scripts/loganalyser $(CURDIR)/debian/beast-mcmc/usr/bin/
- install $(CURDIR)/release/Linux/scripts/logcombiner $(CURDIR)/debian/beast-mcmc/usr/bin/
- install $(CURDIR)/release/Linux/scripts/treeannotator $(CURDIR)/debian/beast-mcmc/usr/bin/
- install $(CURDIR)/release/Linux/scripts/treestat $(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 -m 664 $(CURDIR)/examples/release/*\.xml $(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
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