[med-svn] r5401 - in trunk/packages: . mrbayes mrbayes/trunk mrbayes/trunk/debian mrbayes/trunk/debian/patches mrbayes/trunk/debian/patches/misc mrbayes/trunk/debian/source
Steffen Möller
moeller at alioth.debian.org
Mon Nov 1 00:45:37 UTC 2010
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+The packages was originally made available for Ubuntu.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 <moeller at debian.org> 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 <moeller at debian.org> 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 <fernando at staff.nerdgroup.org> 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 <fernando at staff.nerdgroup.org>
+Uploaders: Steffen Moeller <moeller at debian.org>, Dominique Belhachemi <domibel at debian.org>, Pjotr Prins <pjotr.debian at thebird.nl>
+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 <fernando at staff.nerdgroup.org> on
+Thu, 09 Nov 2006 02:14:52 -0200.
+
+It was downloaded from http://mrbayes.csit.fsu.edu/download.php
+
+Upstream Author: John Huelsenbeck <johnh at biomail.ucsd.edu>
+ Fredrik Ronquist <ronquist at csit.fsu.edu>
+ Bred Larget
+ Paul van der Mark
+ Donald Simon
+
+Copyright:
+
+Copyright 2002-2005 John Huelsenbeck <johnh at biomail.ucsd.edu>
+ Fredrik Ronquist <ronquist at csit.fsu.edu>
+
+
+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)
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