From: cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Fri, 28 Sep 2012 01:57:51 +0000 (+0000)
Subject: in progress
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=649c47b17bfa0e31a3c773d54da4edbee60bfb8b;p=jalview.git

in progress
---

diff --git a/forester/ruby/evoruby/exe/run_phylo_pipeline.rb b/forester/ruby/evoruby/exe/run_phylo_pipeline.rb
index e144552..045faaf 100755
--- a/forester/ruby/evoruby/exe/run_phylo_pipeline.rb
+++ b/forester/ruby/evoruby/exe/run_phylo_pipeline.rb
@@ -31,8 +31,8 @@ module Evoruby
 
       input       = ARGV[ 0 ]
       hmm         = ARGV[ 1 ]
-      length      = ARGV[ 2 ]
-      e_value_exp = ARGV[ 3 ]
+      length      = ARGV[ 2 ].to_i
+      e_value_exp = ARGV[ 3 ].to_i
       do_domain_combination_analysis = true
 
       if e_value_exp < 0
@@ -48,7 +48,7 @@ module Evoruby
       elsif input.downcase.end_with?( ".fsa" )
         base_name = input[ 0 .. input.length - 5 ]
       else
-         base_name = input
+        base_name = input
       end
 
       if do_domain_combination_analysis