From: cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Tue, 14 Jan 2014 00:40:18 +0000 (+0000)
Subject: inprogress
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=fa082c051977930bd571e1c66918a771dd877c32;p=jalview.git

inprogress
---

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 )