# $Id: phylogenies_decorator.rb,v 1.34 2010/12/13 19:00:11 cmzmasek Exp $
#
# Environment variable FORESTER_HOME needs to point to the appropriate
# $Id: phylogenies_decorator.rb,v 1.34 2010/12/13 19:00:11 cmzmasek Exp $
#
# Environment variable FORESTER_HOME needs to point to the appropriate
# -mdn is a hidden expert option to rename e.g. "6_ORYLA3" to "6_[3]_ORYLA"
#DECORATOR_OPTIONS_SEQ_NAMES = '-sn -r=1'
#DECORATOR_OPTIONS_DOMAINS = '-r=1'
# -mdn is a hidden expert option to rename e.g. "6_ORYLA3" to "6_[3]_ORYLA"
#DECORATOR_OPTIONS_SEQ_NAMES = '-sn -r=1'
#DECORATOR_OPTIONS_DOMAINS = '-r=1'
cmd = decorator + ' ' + DECORATOR_OPTIONS_DOMAINS + ' ' +
'-f=d ' + phylogeny_file + ' ' +
domains_mapfile_name + ' ' + my_outfile
cmd = decorator + ' ' + DECORATOR_OPTIONS_DOMAINS + ' ' +
'-f=d ' + phylogeny_file + ' ' +
domains_mapfile_name + ' ' + my_outfile