mrbayes/go.sh

   1 #!/bin/bash -x
   2
   3 # Copyright (C) 2011 Sebastian Pop <sebpop@gmail.com>.
   4 # This program is free software; you can redistribute it and/or modify
   5 # it under the terms of the GNU General Public License as published by
   6 # the Free Software Foundation; either version 3 of the License, or
   7 # (at your option) any later version.
   8 #
   9 # This program is distributed in the hope that it will be useful,
  10 # but WITHOUT ANY WARRANTY; without even the implied warranty of
  11 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  12 # GNU General Public License for more details.  A copy of this license
  13 # can be downloaded from http://www.gnu.org/copyleft/gpl.html
  14
  15 p=`pwd`
  16 rm -rf usr mpich2-1.0.8p1 mrbayes-3.1.2
  17 mkdir -p usr
  18 tar -zxf mpich2-1.0.8p1.tar.gz
  19 tar -zxf mrbayes-3.1.2.tar.gz
  20 cd $p/mpich2-1.0.8p1/
  21 ./configure --prefix=$p/usr --enable-fast=all --with-pm=gforker --disable-option-checking
  22 if ! make -j $procs; then
  23     make
  24 fi
  25 make install
  26 cd $p/mrbayes-3.1.2/
  27 sed -i -e "s/MPI ?= no/MPI ?= yes/g" Makefile
  28 sed -i -e "s/USEREADLINE ?= yes/USEREADLINE ?= no/g" Makefile
  29 sed -i -e "s/define WIN_VERSION/define UNIX_VERSION/g" mb.h
  30 make -j $procs PATH=$p/usr/bin/:$PATH CFLAGS="$CFLAGS" ARCHITECTURE=unix
  31 cat>job.nex<<EOT
  32 begin mrbayes;
  33    set autoclose=yes nowarn=yes;
  34    execute primates.nex;
  35    lset nst=6 rates=invgamma;
  36    mcmc ngen=30000 samplefreq=10;
  37    sump burnin=250;
  38    sumt burnin=250;
  39 end;
  40 EOT
  41 before=`date +%s.%N`
  42 $p/usr/bin/mpiexec -np $procs ./mb job.nex 1>/dev/null 2>&1
  43 after=`date +%s.%N`
  44 echo "mrbayes run time: `echo "$after - $before" | bc`" > $p/log
  45 cd $p; rm -rf usr mpich2-1.0.8p1 mrbayes-3.1.2