Author: moeller Date: 2010-11-01 00:45:33 +0000 (Mon, 01 Nov 2010) New Revision: 5401
Added: trunk/packages/mrbayes/ trunk/packages/mrbayes/trunk/ trunk/packages/mrbayes/trunk/debian/ trunk/packages/mrbayes/trunk/debian/README.Debian trunk/packages/mrbayes/trunk/debian/changelog trunk/packages/mrbayes/trunk/debian/control trunk/packages/mrbayes/trunk/debian/copyright trunk/packages/mrbayes/trunk/debian/patches/ trunk/packages/mrbayes/trunk/debian/patches/fix_Makefile_clean.patch trunk/packages/mrbayes/trunk/debian/patches/misc/ trunk/packages/mrbayes/trunk/debian/patches/misc/makefile_clean_binary.diff trunk/packages/mrbayes/trunk/debian/patches/misc/man1.diff trunk/packages/mrbayes/trunk/debian/patches/series trunk/packages/mrbayes/trunk/debian/rules trunk/packages/mrbayes/trunk/debian/source/ trunk/packages/mrbayes/trunk/debian/source/format Log: Initial upload of Ubuntu's MrBayes with some yet untested patches towards a version with MPI.. Added: trunk/packages/mrbayes/trunk/debian/README.Debian =================================================================== --- trunk/packages/mrbayes/trunk/debian/README.Debian (rev 0) +++ trunk/packages/mrbayes/trunk/debian/README.Debian 2010-11-01 00:45:33 UTC (rev 5401) @@ -0,0 +1,11 @@ +MrBayes for Debian +================== + +The packages was originally made available for Ubuntu. It +was adopted for Debian by Dominique to help a tutorial +by Pjotr. + +We have a particular interest in MPI and as such branched +that effort into a second package of the same source tree. + +-- Steffen Moeller <[email protected]> Mon, 01 Nov 2010 01:31:10 +0100 Added: trunk/packages/mrbayes/trunk/debian/changelog =================================================================== --- trunk/packages/mrbayes/trunk/debian/changelog (rev 0) +++ trunk/packages/mrbayes/trunk/debian/changelog 2010-11-01 00:45:33 UTC (rev 5401) @@ -0,0 +1,17 @@ +mrbayes (3.1.2-1) unstable; urgency=low + + * Adjustments for latest Debian policy. + - build dependencies + - Debian source code management with Debian Med + * Added -mpi package + * Initial upload to Debian. + + -- Steffen Moeller <[email protected]> Mon, 01 Nov 2010 01:32:14 +0100 + +mrbayes (3.1.2-0ubuntu1) feisty; urgency=low + + * Initial release. + * Patch applied: misc/makefile_clean_binary.diff + * Patch applied: misc/man1.diff + + -- Fernando Ribeiro <[email protected]> Thu, 9 Nov 2006 02:37:20 -0200 Added: trunk/packages/mrbayes/trunk/debian/control =================================================================== --- trunk/packages/mrbayes/trunk/debian/control (rev 0) +++ trunk/packages/mrbayes/trunk/debian/control 2010-11-01 00:45:33 UTC (rev 5401) @@ -0,0 +1,35 @@ +Source: mrbayes +Section: math +Priority: optional +Maintainer: Fernando Ribeiro <[email protected]> +Uploaders: Steffen Moeller <[email protected]>, Dominique Belhachemi <[email protected]>, Pjotr Prins <[email protected]> +Standards-Version: 3.9.1 +Build-Depends: libncurses-dev, libreadline-dev +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/ + + +Package: mrbayes +Architecture: any +Depends: ${shlibs:Depends}, bash (>=3.1) +Description: A program for the Bayesian estimation 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 + Bayes's theorem. The posterior probability distribution of trees is + impossible to calculate analytically; instead, MrBayes uses a simulation + technique called Markov chain Monte Carlo (or MCMC) to approximate the + posterior probabilities of trees. + +Package: mrbayes-mpi +Architecture: any +Depends: ${shlibs:Depends}, bash (>=3.1) +Description: A program for the Bayesian estimation 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 + Bayes's theorem. The posterior probability distribution of trees is + impossible to calculate analytically; instead, MrBayes uses a simulation + technique called Markov chain Monte Carlo (or MCMC) to approximate the + posterior probabilities of trees. Added: trunk/packages/mrbayes/trunk/debian/copyright =================================================================== --- trunk/packages/mrbayes/trunk/debian/copyright (rev 0) +++ trunk/packages/mrbayes/trunk/debian/copyright 2010-11-01 00:45:33 UTC (rev 5401) @@ -0,0 +1,26 @@ +This package was debianized by Fernando Ribeiro <[email protected]> on +Thu, 09 Nov 2006 02:14:52 -0200. + +It was downloaded from http://mrbayes.csit.fsu.edu/download.php + +Upstream Author: John Huelsenbeck <[email protected]> + Fredrik Ronquist <[email protected]> + Bred Larget + Paul van der Mark + Donald Simon + +Copyright: + +Copyright 2002-2005 John Huelsenbeck <[email protected]> + Fredrik Ronquist <[email protected]> + + +License: + +This program is free software; you can redistribute it and/or modify it +under the terms of the GNU General Public License as published by the +Free Software Foundation; either version 2, or (at your option) any +later version. + +On Debian systems, the complete text of the GNU General Public License +can be found in the file `/usr/share/common-licenses/GPL'. Added: trunk/packages/mrbayes/trunk/debian/patches/fix_Makefile_clean.patch =================================================================== --- trunk/packages/mrbayes/trunk/debian/patches/fix_Makefile_clean.patch (rev 0) +++ trunk/packages/mrbayes/trunk/debian/patches/fix_Makefile_clean.patch 2010-11-01 00:45:33 UTC (rev 5401) @@ -0,0 +1,12 @@ +Index: mrbayes-3.1.2/Makefile +=================================================================== +--- mrbayes-3.1.2.orig/Makefile 2010-11-01 01:38:20.624266148 +0100 ++++ mrbayes-3.1.2/Makefile 2010-11-01 01:39:17.808266148 +0100 +@@ -88,6 +88,7 @@ + + clean: + rm -f *.o ++ rm -f $(PROGS) + + showdep: + @$(CC) -MM bayes.c command.c mbmath.c mcmc.c model.c plot.c sump.c sumt.c Added: trunk/packages/mrbayes/trunk/debian/patches/misc/makefile_clean_binary.diff =================================================================== --- trunk/packages/mrbayes/trunk/debian/patches/misc/makefile_clean_binary.diff (rev 0) +++ trunk/packages/mrbayes/trunk/debian/patches/misc/makefile_clean_binary.diff 2010-11-01 00:45:33 UTC (rev 5401) @@ -0,0 +1,10 @@ +--- Makefile-old 2006-11-16 02:29:23.000000000 -0200 ++++ Makefile 2006-11-16 02:29:51.000000000 -0200 +@@ -88,6 +88,7 @@ + + clean: + rm -f *.o ++ rm $(PROGS) + + showdep: + @$(CC) -MM bayes.c command.c mbmath.c mcmc.c model.c plot.c sump.c sumt.c Added: trunk/packages/mrbayes/trunk/debian/patches/misc/man1.diff =================================================================== --- trunk/packages/mrbayes/trunk/debian/patches/misc/man1.diff (rev 0) +++ trunk/packages/mrbayes/trunk/debian/patches/misc/man1.diff 2010-11-01 00:45:33 UTC (rev 5401) @@ -0,0 +1,14 @@ +diff -uNr mrbayes-3.1.2-old/doc/man/man1/mb.1 mrbayes-3.1.2-patch/doc/man/man1/mb.1 +--- mrbayes-3.1.2-old/doc/man/man1/mb.1 1969-12-31 21:00:00.000000000 -0300 ++++ mrbayes-3.1.2-patch/doc/man/man1/mb.1 2006-11-16 02:19:06.000000000 -0200 +@@ -0,0 +1,10 @@ ++.TH mrbayes "1" "Nov 2006" "mrbayes 3.1.2" "User Commands" ++.SH NAME ++mb \- A program for the Bayesian estimation ++.SH SYNOPSIS ++.B mb [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/patches/series =================================================================== --- trunk/packages/mrbayes/trunk/debian/patches/series (rev 0) +++ trunk/packages/mrbayes/trunk/debian/patches/series 2010-11-01 00:45:33 UTC (rev 5401) @@ -0,0 +1,3 @@ +fix_Makefile_clean.patch +misc/makefile_clean_binary.diff -p0 +misc/man1.diff -p1 Added: trunk/packages/mrbayes/trunk/debian/rules =================================================================== --- trunk/packages/mrbayes/trunk/debian/rules (rev 0) +++ trunk/packages/mrbayes/trunk/debian/rules 2010-11-01 00:45:33 UTC (rev 5401) @@ -0,0 +1,56 @@ +#!/usr/bin/make -f + +package = mrbayes +docdir = debian/tmp/usr/share/doc/$(package) +mandir = debian/tmp/usr/share/man + +build: + $(checkdir) + quilt push -a || test $$? = 2 + MPI=yes $(MAKE) + mv mb mb-mpi + $(MAKE) clean + MPI=no $(MAKE) + touch build + +clean: + $(checkdir) + -$(MAKE) -i clean + ln -sf debian/patches + quilt pop -a || test $$? = 2 + rm -f build + rm -rf *~ .pc debian/tmp debian/*~ debian/files* debian/substvars patches + +binary-indep: checkroot build + $(checkdir) + +binary-arch: checkroot build + $(checkdir) + rm -rf debian/tmp + install -d debian/tmp/DEBIAN $(docdir) $(mandir) debian/tmp/usr/bin + install -s -m 755 mb debian/tmp/usr/bin + install -s -m 755 mb-mpi debian/tmp/usr/bin + cp -a debian/copyright $(docdir) + cp -a debian/changelog $(docdir)/changelog.Debian + cp -a doc/man/man1 $(mandir) + cd $(docdir) && gzip -9 changelog.Debian + dpkg-shlibdeps debian/tmp/usr/bin/mb + dpkg-shlibdeps debian/tmp/usr/bin/mb-mpi + dpkg-gencontrol -isp + gzip -r9 debian/tmp/usr/share/man + chown -R root:root debian/tmp + chmod -R u+w,go=rX debian/tmp + chmod u=rwx,go=rx debian/tmp/usr/bin/mb + dpkg --build debian/tmp .. + +define checkdir + test -f mb.c -a -f debian/rules +endef + +binary: binary-indep binary-arch + +checkroot: + $(checkdir) + test $$(id -u) = 0 + +.PHONY: clean binary binary-arch binary-indep checkroot Added: trunk/packages/mrbayes/trunk/debian/source/format =================================================================== --- trunk/packages/mrbayes/trunk/debian/source/format (rev 0) +++ trunk/packages/mrbayes/trunk/debian/source/format 2010-11-01 00:45:33 UTC (rev 5401) @@ -0,0 +1 @@ +3.0 (quilt) _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
