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

[Andreas Tille]

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 .
>  
> 
> 
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-- 
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