From ad4933fe7b5f82385d27b0c9e8979952d46e15db Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Fri, 3 Apr 2015 01:02:52 +0000 Subject: [PATCH] in progress --- .../evoruby/lib/evo/tool/phylogenies_decorator.rb | 40 ++++++++++---------- 1 file changed, 20 insertions(+), 20 deletions(-) diff --git a/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb b/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb index c8803e4..46926ca 100644 --- a/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb +++ b/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb @@ -199,25 +199,25 @@ module Evoruby Util.fatal_error( PRG_NAME, 'failed to read from [#{seqs_file_name }]: ' + $! ) end - cmd = decorator + - ' -t -p -f=m ' + phylogeny_file + ' ' + - seqs_file_name + ' ' + TMP_FILE_1 - puts cmd - begin - execute_cmd( cmd, log ) - rescue Error - Util.fatal_error( PRG_NAME, 'error: ' + $! ) - end - - cmd = decorator + ' ' + DECORATOR_OPTIONS_DOMAINS + ' ' + - '-f=d ' + TMP_FILE_1 + ' ' + - domains_mapfile_name + ' ' +TMP_FILE_2 - puts cmd - begin - execute_cmd( cmd, log ) - rescue Error - Util.fatal_error( PRG_NAME, 'error: ' + $! ) - end +# cmd = decorator + +# ' -t -p -f=m ' + phylogeny_file + ' ' + +# seqs_file_name + ' ' + TMP_FILE_1 +# puts cmd +# begin +# execute_cmd( cmd, log ) +# rescue Error +# Util.fatal_error( PRG_NAME, 'error: ' + $! ) +# end +# +# cmd = decorator + ' ' + DECORATOR_OPTIONS_DOMAINS + ' ' + +# '-f=d ' + TMP_FILE_1 + ' ' + +# domains_mapfile_name + ' ' +TMP_FILE_2 +# puts cmd +# begin +# execute_cmd( cmd, log ) +# rescue Error +# Util.fatal_error( PRG_NAME, 'error: ' + $! ) +# end cmd = decorator + ' ' + DECORATOR_OPTIONS_SEQ_NAMES + ' ' + '-f=n ' + TMP_FILE_2 + ' ' + @@ -243,7 +243,7 @@ module Evoruby end # def run def execute_cmd( cmd, log ) - log << 'excuting ' + cmd + NL + log << 'executing ' + cmd + NL IO.popen( cmd , 'r+' ) do | pipe | pipe.close_write log << pipe.read + NL + NL -- 1.7.10.2