[Bio-linux-dev] MrBayes and OpenMPI

[Tony Travis]

Hi, Tim.

I've created an OpenMPI version of bio-linux-mrbayes-multi:

Bye,

   Tony.

> aptitude download bio-linux-mrbayes-multi
> dpkg-unpack bio-linux-mrbayes-multi_3.1.2-1_amd64.deb
> cd bio-linux-mrbayes-multi_3.1.2-1_amd64/usr/local/bioinf/mrbayes/mrbayes-multi-3.1.2
> make
> cd ../../../DEBIAN
> vim control # see patch below
> cd ../..
> mv -i bio-linux-mrbayes-multi_3.1.2-1_amd64 bio-linux-mrbayes-multi_3.1.2-2_amd64
> dpkg-repack bio-linux-mrbayes-multi_3.1.2-2_amd64

You can download the deb at:

> http://bioinformatics.rri.sari.ac.uk/download/bio-linux-mrbayes-multi_3.1.2-2_amd64.deb

Patch to remove mpich2 dependency:

--- bio-linux-mrbayes-multi_3.1.2-1_amd64/DEBIAN/control	2010-03-23 
16:00:24.000000000 +0000
+++ bio-linux-mrbayes-multi_3.1.2-2_amd64/DEBIAN/control	2011-06-09 
15:24:59.403563781 +0100
@@ -1,11 +1,11 @@
  Package: bio-linux-mrbayes-multi
-Version: 3.1.2-1
+Version: 3.1.2-2
  Section: science
  Priority: optional
-Depends: bio-linux-base-directories (>= 1.0-1), mpich2, libopenmpi-dev
+Depends: bio-linux-base-directories (>= 1.0-1), libopenmpi-dev
  Architecture: amd64
  Installed-Size: 7436
-Maintainer: Oliver Buckley <helpdesk at nebc.nox.ac.uk>
+Maintainer: Tony Travis <a.travis at abdn.ac.uk>
  Provides: bio-linux-mrbayes-multi
-Description: Multiprocessor version of MrBayes.
+Description: OpenMPI version of MrBayes.
   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. This version has been compiled 
to run on multiple processors.

Here are my easy-to-remember dpkg-unpack/dpkg-repack scripts:

#!/bin/sh
# @(#)dpkg-unpack  2007-07-12  A.J.Travis

#
# Unpack Debian package ready to rebuild
#
package=$1
extract=`basename $package .deb`
dpkg-deb -x ${package} ${extract}
dpkg-deb -e ${package} ${extract}/DEBIAN

#!/bin/sh
# @(#)dpkg-repack  2007-03-29  A.J.Travis

#
# Re-pack unpacked Debian package
#
package=$1
dpkg-deb -b ${package}

-- 
Dr. A.J.Travis, University of Aberdeen, Rowett Institute of Nutrition
and Health, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, Scotland, UK
tel +44(0)1224 712751, fax +44(0)1224 716687, http://www.rowett.ac.uk
mailto:a.travis at abdn.ac.uk, http://bioinformatics.rri.sari.ac.uk