From fa082c051977930bd571e1c66918a771dd877c32 Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Tue, 14 Jan 2014 00:40:18 +0000 Subject: [PATCH] inprogress --- .../evoruby/lib/evo/tool/phylogenies_decorator.rb | 18 +++++++++++++++--- 1 file changed, 15 insertions(+), 3 deletions(-) diff --git a/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb b/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb index 6d50174..a6ba133 100644 --- a/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb +++ b/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb @@ -203,19 +203,31 @@ module Evoruby ' -p -f=m ' + phylogeny_file + ' ' + seqs_file_name + ' ' + TMP_FILE_1 puts cmd - execute_cmd( cmd, log ) + 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 - execute_cmd( cmd, log ) + 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 + ' ' + ids_mapfile_name + ' ' + outfile puts cmd - execute_cmd( cmd, log ) + begin + execute_cmd( cmd, log ) + rescue Error + Util.fatal_error( PRG_NAME, 'error: ' + $! ) + end File.delete( TMP_FILE_1 ) File.delete( TMP_FILE_2 ) -- 1.7.10.2