mafft/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 mafft-6.706-without-extensions
  17 mkdir -p usr
  18 tar -zxf mafft-6.706-without-extensions-src.tgz
  19 cd mafft-6.706-without-extensions/core
  20 make clean
  21 sed -i -e "s|PREFIX = /usr/local|PREFIX = $p/usr|g" Makefile
  22 make -j $procs CFLAGS="$CFLAGS"
  23 make install
  24 cp -f $p/mafft-6.706-without-extensions/scripts/mafft $p/usr
  25 bunzip2 $p/pyruvate_decarboxylase.fasta.bz2 -c > $p/usr/pyruvate_decarboxylase.fasta
  26 cd $p/usr
  27 before=`date +%s.%N`
  28 ./mafft --localpair --maxiterate 10000 pyruvate_decarboxylase.fasta 1>/dev/null 2>&1
  29 after=`date +%s.%N`
  30 echo "mafft run time: `echo "$after - $before" | bc`" > $p/log
  31 cd $p; rm -rf usr mafft-6.706-without-extensions