From: cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Sat, 9 Nov 2013 05:39:28 +0000 (+0000)
Subject: inprogress
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=f848d1835cc927b551aed4f8bcbe70bf81d12627;p=jalview.git

inprogress
---

diff --git a/forester/ruby/evoruby/exe/run_phylo_pipeline_x.rb b/forester/ruby/evoruby/exe/run_phylo_pipeline_x.rb
index 7a30ef5..0117b6a 100644
--- a/forester/ruby/evoruby/exe/run_phylo_pipeline_x.rb
+++ b/forester/ruby/evoruby/exe/run_phylo_pipeline_x.rb
@@ -68,6 +68,7 @@ module Evoruby
 
         hmm_name = ""
         id_norm = false
+        orig_input = input
 
         if input.downcase.end_with?( "_ni.fasta" )
           hmm_name = input[ 0 .. input.length - 10 ]
@@ -109,7 +110,7 @@ module Evoruby
         if id_norm
           FileUtils.mv "#{hmm_name}_ni.fasta", "#{hmm_name}/#{hmm_name}_ni.fasta"
           FileUtils.mv "#{hmm_name}.nim", "#{hmm_name}/#{hmm_name}.nim"
-          FileUtils.cp input, "#{hmm_name}/#{input}"
+          FileUtils.cp orig_input, "#{hmm_name}/#{orig_input}"
         end
 
       end