Author: tille Date: 2011-02-03 22:05:22 +0000 (Thu, 03 Feb 2011) New Revision: 5879
Added: trunk/packages/mrbayes/trunk/debian/README.source trunk/packages/mrbayes/trunk/debian/mb-mpi.1 trunk/packages/mrbayes/trunk/debian/mrbayes-mpi.README.Debian trunk/packages/mrbayes/trunk/debian/mrbayes-mpi.install trunk/packages/mrbayes/trunk/debian/mrbayes-mpi.manpages trunk/packages/mrbayes/trunk/debian/mrbayes.README.Debian trunk/packages/mrbayes/trunk/debian/mrbayes.install trunk/packages/mrbayes/trunk/debian/mrbayes.manpages trunk/packages/mrbayes/trunk/debian/patches/ trunk/packages/mrbayes/trunk/debian/patches/no_ncurses.patch trunk/packages/mrbayes/trunk/debian/patches/series Removed: trunk/packages/mrbayes/trunk/debian/README.Debian Modified: trunk/packages/mrbayes/trunk/debian/changelog trunk/packages/mrbayes/trunk/debian/control trunk/packages/mrbayes/trunk/debian/rules Log: Some polishing, dropped useless libncurses dependency, provide better docs for MPI package Deleted: trunk/packages/mrbayes/trunk/debian/README.Debian =================================================================== --- trunk/packages/mrbayes/trunk/debian/README.Debian 2011-02-03 16:03:01 UTC (rev 5878) +++ trunk/packages/mrbayes/trunk/debian/README.Debian 2011-02-03 22:05:22 UTC (rev 5879) @@ -1,10 +0,0 @@ -MrBayes for Debian ------------------- - -You can download the Manual for MrBayes as PDF from - http://mrbayes.sourceforge.net/mb3.1_manual.pdf - -The command reference can be downloaded here - http://mrbayes.sourceforge.net/commref_mb3.1.pdf - - -- Andreas Tille <ti...@debian.org> Sat, 10 Jul 2010 19:03:40 +0200 Added: trunk/packages/mrbayes/trunk/debian/README.source =================================================================== --- trunk/packages/mrbayes/trunk/debian/README.source (rev 0) +++ trunk/packages/mrbayes/trunk/debian/README.source 2011-02-03 22:05:22 UTC (rev 5879) @@ -0,0 +1,4 @@ +This packages uses the quilt patch system. Please read +/usr/share/doc/quilt/README.source for more information. + + -- Andreas Tille <ti...@debian.org> Thu, 03 Feb 2011 16:39:19 +0100 Modified: trunk/packages/mrbayes/trunk/debian/changelog =================================================================== --- trunk/packages/mrbayes/trunk/debian/changelog 2011-02-03 16:03:01 UTC (rev 5878) +++ trunk/packages/mrbayes/trunk/debian/changelog 2011-02-03 22:05:22 UTC (rev 5879) @@ -1,15 +1,8 @@ mrbayes (3.1.2-1) UNRELEASED; urgency=low - * ITP IS MISSING - * Adjustments for latest Debian policy. - - build dependencies - - Debian source code management with Debian Med - * Added mrbayes-mpi package - * Added mb-mpi binary - * Using debhelper - * Initial upload to Debian. + * Initial release in Debian (Closes: #611928) - -- Steffen Moeller <moel...@debian.org> Mon, 01 Nov 2010 01:32:14 +0100 + -- Andreas Tille <ti...@debian.org> Thu, 03 Feb 2011 22:23:31 +0100 mrbayes (3.1.2-0ubuntu1) feisty; urgency=low Modified: trunk/packages/mrbayes/trunk/debian/control =================================================================== --- trunk/packages/mrbayes/trunk/debian/control 2011-02-03 16:03:01 UTC (rev 5878) +++ trunk/packages/mrbayes/trunk/debian/control 2011-02-03 22:05:22 UTC (rev 5879) @@ -9,7 +9,7 @@ Pjotr Prins <pjotr.deb...@thebird.nl>, Andreas Tille <ti...@debian.org> Standards-Version: 3.9.1 -Build-Depends: debhelper (>= 7), libncurses-dev, libreadline-dev, mpi-default-dev, quilt +Build-Depends: debhelper (>= 7.1), libreadline-dev, mpi-default-dev, quilt (>=0.47) Homepage: http://mrbayes.csit.fsu.edu/ Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/mrbayes/trunk/?rev=0&sc=0 Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/mrbayes/trunk/ @@ -18,7 +18,7 @@ Package: mrbayes Architecture: any Depends: ${shlibs:Depends}, bash (>=3.1), ${misc:Depends} -Description: A program for the Bayesian estimation of phylogeny +Description: Bayesian Inference of Phylogeny Bayesian inference of phylogeny is based upon a quantity called the posterior probability distribution of trees, which is the probability of a tree conditioned on the observations. The conditioning is accomplished using @@ -31,7 +31,7 @@ Architecture: any Depends: ${shlibs:Depends}, bash (>=3.1), ${misc:Depends} Suggests: mpi-default -Description: A program for the Bayesian estimation of phylogeny - mpi version +Description: Bayesian Inference of Phylogeny - mpi version Bayesian inference of phylogeny is based upon a quantity called the posterior probability distribution of trees, which is the probability of a tree conditioned on the observations. The conditioning is accomplished using Added: trunk/packages/mrbayes/trunk/debian/mb-mpi.1 =================================================================== --- trunk/packages/mrbayes/trunk/debian/mb-mpi.1 (rev 0) +++ trunk/packages/mrbayes/trunk/debian/mb-mpi.1 2011-02-03 22:05:22 UTC (rev 5879) @@ -0,0 +1,11 @@ +.TH mrbayes "1" "Nov 2006" "mrbayes 3.1.2" "User Commands" +.SH NAME +mb-mpi \- A program for the Bayesian estimation (parallel version) +.SH SYNOPSIS +.B mb-mpi [OPTION]... [FILE]... +.SH DESCRIPTION +A program for the Bayesian estimation of phylogeny Bayesian inference of phylogeny +.SH OPTIONS +.B \-i +interactive mode + Added: trunk/packages/mrbayes/trunk/debian/mrbayes-mpi.README.Debian =================================================================== --- trunk/packages/mrbayes/trunk/debian/mrbayes-mpi.README.Debian (rev 0) +++ trunk/packages/mrbayes/trunk/debian/mrbayes-mpi.README.Debian 2011-02-03 22:05:22 UTC (rev 5879) @@ -0,0 +1,12 @@ +MrBayes for Debian +------------------ + +This is the MPI version of MrBayes. + +You can download the Manual for MrBayes as PDF from + http://mrbayes.sourceforge.net/mb3.1_manual.pdf + +The command reference can be downloaded here + http://mrbayes.sourceforge.net/commref_mb3.1.pdf + + -- Andreas Tille <ti...@debian.org> Thu, 03 Feb 2011 22:23:31 +0100 Added: trunk/packages/mrbayes/trunk/debian/mrbayes-mpi.install =================================================================== --- trunk/packages/mrbayes/trunk/debian/mrbayes-mpi.install (rev 0) +++ trunk/packages/mrbayes/trunk/debian/mrbayes-mpi.install 2011-02-03 22:05:22 UTC (rev 5879) @@ -0,0 +1 @@ +mb-mpi usr/bin Added: trunk/packages/mrbayes/trunk/debian/mrbayes-mpi.manpages =================================================================== --- trunk/packages/mrbayes/trunk/debian/mrbayes-mpi.manpages (rev 0) +++ trunk/packages/mrbayes/trunk/debian/mrbayes-mpi.manpages 2011-02-03 22:05:22 UTC (rev 5879) @@ -0,0 +1 @@ +debian/mb-mpi.1 Added: trunk/packages/mrbayes/trunk/debian/mrbayes.README.Debian =================================================================== --- trunk/packages/mrbayes/trunk/debian/mrbayes.README.Debian (rev 0) +++ trunk/packages/mrbayes/trunk/debian/mrbayes.README.Debian 2011-02-03 22:05:22 UTC (rev 5879) @@ -0,0 +1,10 @@ +MrBayes for Debian +------------------ + +You can download the Manual for MrBayes as PDF from + http://mrbayes.sourceforge.net/mb3.1_manual.pdf + +The command reference can be downloaded here + http://mrbayes.sourceforge.net/commref_mb3.1.pdf + + -- Andreas Tille <ti...@debian.org> Thu, 03 Feb 2011 22:23:31 +0100 Added: trunk/packages/mrbayes/trunk/debian/mrbayes.install =================================================================== --- trunk/packages/mrbayes/trunk/debian/mrbayes.install (rev 0) +++ trunk/packages/mrbayes/trunk/debian/mrbayes.install 2011-02-03 22:05:22 UTC (rev 5879) @@ -0,0 +1 @@ +mb usr/bin Added: trunk/packages/mrbayes/trunk/debian/mrbayes.manpages =================================================================== --- trunk/packages/mrbayes/trunk/debian/mrbayes.manpages (rev 0) +++ trunk/packages/mrbayes/trunk/debian/mrbayes.manpages 2011-02-03 22:05:22 UTC (rev 5879) @@ -0,0 +1 @@ +debian/mb.1 Added: trunk/packages/mrbayes/trunk/debian/patches/no_ncurses.patch =================================================================== --- trunk/packages/mrbayes/trunk/debian/patches/no_ncurses.patch (rev 0) +++ trunk/packages/mrbayes/trunk/debian/patches/no_ncurses.patch 2011-02-03 22:05:22 UTC (rev 5879) @@ -0,0 +1,15 @@ +Author: Andreas Tille <ti...@debian.org> +Date: Thu, 03 Feb 2011 16:39:19 +0100 +Description: There is no need to link against ncurses + +--- mrbayes-3.1.2.orig/Makefile ++++ mrbayes-3.1.2/Makefile +@@ -49,7 +49,7 @@ + + ifeq ($(strip $(USEREADLINE)),yes) + CFLAGS += -DUSE_READLINE +- LIBS += -lncurses -lreadline ++ LIBS += -lreadline + endif + + ifeq ($(strip $(MPI)),yes) Added: trunk/packages/mrbayes/trunk/debian/patches/series =================================================================== --- trunk/packages/mrbayes/trunk/debian/patches/series (rev 0) +++ trunk/packages/mrbayes/trunk/debian/patches/series 2011-02-03 22:05:22 UTC (rev 5879) @@ -0,0 +1 @@ +no_ncurses.patch Modified: trunk/packages/mrbayes/trunk/debian/rules =================================================================== --- trunk/packages/mrbayes/trunk/debian/rules 2011-02-03 16:03:01 UTC (rev 5878) +++ trunk/packages/mrbayes/trunk/debian/rules 2011-02-03 22:05:22 UTC (rev 5879) @@ -1,77 +1,27 @@ #!/usr/bin/make -f +# debian/rules for mrbayes +# Andreas Tille <ti...@debian.org> +# GPL -package = mrbayes +# Uncomment this to turn on verbose mode. +#export DH_VERBOSE=1 -include /usr/share/quilt/quilt.make +mpipkg=mrbayes-mpi +mpibin=mb-mpi -docdir = debian/$(package)/usr/share/doc/$(package) -mandir = debian/$(package)/usr/share/man +%: + dh $@ -export DH_VERBOSE=1 +override_dh_auto_clean: + $(MAKE) clean + rm -f mb mb-mpi -build: - dh_testdir - quilt push -a || test $$? = 2 - - # build mb-mpi +override_dh_auto_build: + # build mb-mpi MPI=yes $(MAKE) mv mb mb-mpi # build mb - $(MAKE) clean + # $(MAKE) clean # <-- seems to delete mb-mpi somehow + rm -f *.o MPI=no $(MAKE) - touch build - -clean: - dh_testdir - dh_testroot - [ ! -f Makefile ] || $(MAKE) clean - ln -sf debian/patches - quilt pop -a || test $$? = 2 - rm -f mb-mpi - rm -f build - rm -rf *~ .pc debian/$(package) debian/*~ debian/files* debian/substvars patches - dh_clean - -install-arch: - dh_testdir - dh_testroot - dh_prep - - install -d debian/$(package)/DEBIAN $(docdir) $(mandir) debian/$(package)/usr/bin - install -s -m 755 mb debian/$(package)/usr/bin - install -s -m 755 mb-mpi debian/$(package)/usr/bin - cp -a doc/man/man1 $(mandir) - - dh_install -pmrbayes usr/bin/mb usr/bin - dh_install -pmrbayes-mpi usr/bin/mb-mpi usr/bin - - -# Build architecture-independent files here. -binary-indep: -# We have nothing to do by default. - -# Build architecture-dependent files here. -binary-arch: install-arch - dh_testdir - dh_testroot - dh_installchangelogs - dh_installdocs - dh_lintian - dh_installexamples - dh_installman -# dh_install --sourcedir=$(CURDIR)/debian/tmp --list-missing - dh_link - dh_strip - dh_compress - dh_fixperms - dh_makeshlibs - dh_installdeb - dh_shlibdeps - dh_gencontrol - dh_md5sums - dh_builddeb - -binary: binary-indep binary-arch -.PHONY: build clean binary-indep binary-arch binary install configure - _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
