[med-svn] r8951 - in trunk/packages/mrbayes/trunk/debian: . patches

[Timothy Booth]

Author: tbooth-guest
Date: 2011-12-14 13:10:59 +0000 (Wed, 14 Dec 2011)
New Revision: 8951

Removed:
   trunk/packages/mrbayes/trunk/debian/patches/series
Modified:
   trunk/packages/mrbayes/trunk/debian/changelog
   trunk/packages/mrbayes/trunk/debian/control
   trunk/packages/mrbayes/trunk/debian/mb-mpi
   trunk/packages/mrbayes/trunk/debian/rules
Log:
Improved build for MrBayes 3.2.0 with Beagle


Modified: trunk/packages/mrbayes/trunk/debian/changelog
===================================================================
--- trunk/packages/mrbayes/trunk/debian/changelog	2011-12-14 13:06:03 UTC (rev 8950)
+++ trunk/packages/mrbayes/trunk/debian/changelog	2011-12-14 13:10:59 UTC (rev 8951)
@@ -1,3 +1,11 @@
+mrbayes (3.2.0-2) lucid; urgency=low
+
+  * A couple of build fixes
+  * Add dependencies on autotools
+  * Now builds against Beagle library so CUDA should be possible
+
+ -- Tim Booth <tbooth at ceh.ac.uk>  Wed, 14 Dec 2011 13:05:36 +0000
+
 mrbayes (3.2.0-1) lucid; urgency=low
 
   * Rebuild of new 3.2.0 release.  Pjotr mentioned having a package for

Modified: trunk/packages/mrbayes/trunk/debian/control
===================================================================
--- trunk/packages/mrbayes/trunk/debian/control	2011-12-14 13:06:03 UTC (rev 8950)
+++ trunk/packages/mrbayes/trunk/debian/control	2011-12-14 13:10:59 UTC (rev 8951)
@@ -9,7 +9,7 @@
  Pjotr Prins <pjotr.debian at thebird.nl>,
  Andreas Tille <tille at debian.org>
 Standards-Version: 3.9.2
-Build-Depends: debhelper (>= 8), libreadline-dev, mpi-default-dev, quilt (>=0.47)
+Build-Depends: debhelper (>= 8), libreadline-dev, mpi-default-dev, quilt (>=0.47), libhmsbeagle-dev, autoconf (>= 2.65), automake (>= 1:1.11)
 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/
@@ -17,7 +17,7 @@
 
 Package: mrbayes
 Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}
+Depends: ${shlibs:Depends}, ${misc:Depends}, libhmsbeagle1
 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 

Modified: trunk/packages/mrbayes/trunk/debian/mb-mpi
===================================================================
--- trunk/packages/mrbayes/trunk/debian/mb-mpi	2011-12-14 13:06:03 UTC (rev 8950)
+++ trunk/packages/mrbayes/trunk/debian/mb-mpi	2011-12-14 13:10:59 UTC (rev 8951)
@@ -1,3 +1,6 @@
 #!/bin/sh
-# PATH="/usr/lib/mrbayes-mpi:$PATH"
-orterun /usr/lib/mrbayes-mpi/mb-mpi "$@"
+# To use more than one processor set MPI_OPTIONS - eg.
+#
+# export MPI_OPTIONS="-np 4"
+
+exec mpirun `echo $MPI_OPTIONS` /usr/lib/mrbayes-mpi/mb-mpi "$@"

Deleted: trunk/packages/mrbayes/trunk/debian/patches/series
===================================================================
Modified: trunk/packages/mrbayes/trunk/debian/rules
===================================================================
--- trunk/packages/mrbayes/trunk/debian/rules	2011-12-14 13:06:03 UTC (rev 8950)
+++ trunk/packages/mrbayes/trunk/debian/rules	2011-12-14 13:10:59 UTC (rev 8951)
@@ -11,11 +11,13 @@
 
 override_dh_auto_configure:
 	#Configure for MPI at first
-	dh_auto_configure -- --with-beagle=no --enable-mpi=yes --enable-debug=yes
+	( cd src ; autoconf )
+	dh_auto_configure -- --with-beagle=/usr --enable-mpi=yes --enable-debug=yes
 
 override_dh_auto_clean:
 	( cd src ; $(MAKE) -f Makefile.in distclean )
-	rm -f mb mb-mpi
+	rm -f src/configure
+	rm -f mb mb-mpi src/mb
 
 override_dh_auto_build:
 	# build mb-mpi (from initial config)
@@ -23,7 +25,7 @@
 	mv src/mb ./mb-mpi
 	# Now - build mb
 	( cd src ; make clean )
-	dh_auto_configure -- --with-beagle=no --enable-mpi=no --enable-debug=yes
+	dh_auto_configure -- --with-beagle=/usr --enable-mpi=no --enable-debug=yes
 	LIBS="-Wl,--as-needed" dh_auto_build
 	mv src/mb .