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

[Andreas Tille]

Hi Tim,

I just noticed your commit.  I'll check libhmsbeagle which is obviosely
needed and keep you updated.

Sorry for the noise

       Andreas.

On Wed, Dec 14, 2011 at 05:33:50PM +0100, Andreas Tille wrote:
> Hi Tim,
> 
> I vaguely remember some mail about mrbayes and beagle but I did not
> found something like this via Ggl on the mailing lists.  I just want to
> make sure that you are realising that currently in Debian is no such
> package libhmsbeagle-dev you can Build-Depend from.  If needed we need
> to package this first.
> 
> Kind regards
> 
>        Andreas.
> 
> PS: I guess you noticed that I prepared a solution for 
>       #651983: qiime: Recommends: not available 'cd-hit' package
>     by packaging cd-hit.  You might like to check out my work
>     and verify if this is helpful for qiime.
> 
> On Wed, Dec 14, 2011 at 01:11:00PM +0000, Timothy Booth wrote:
> > 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 .
> >  
> > 
> > 
> > _______________________________________________
> > debian-med-commit mailing list
> > debian-med-commit at lists.alioth.debian.org
> > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
> > 
> 
> -- 
> http://fam-tille.de
> 
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