v 1.04

[jalview.git] / forester / ruby / evoruby / exe / run_phylo_pipeline_x.rb

diff --git a/forester/ruby/evoruby/exe/run_phylo_pipeline_x.rb b/forester/ruby/evoruby/exe/run_phylo_pipeline_x.rb
index 2836f02..1711880 100644 (file)
--- a/forester/ruby/evoruby/exe/run_phylo_pipeline_x.rb
+++ b/forester/ruby/evoruby/exe/run_phylo_pipeline_x.rb
@@ -15,7 +15,7 @@ module Evoruby
 
   class RunPhyloPipeline
 
-    LAUNCH_ANALYSIS = true
+    LAUNCH_ANALYSIS = false
     HOME          = "/home/czmasek/"
     FORESTER_RUBY = "#{HOME}SOFTWARE/FORESTER/DEV/forester/forester/ruby/evoruby/exe/"
     PFAM          = "#{HOME}DATA/PFAM/PFAM270X/"
@@ -58,6 +58,8 @@ module Evoruby
 
       input_files = Dir.entries(".").select { |f| !File.directory?( f ) && f.downcase.end_with?( ".fasta" ) }
 
+      input_files.sort!
+
       puts "Input files:"
       input_files.each do | input |
         puts input
@@ -91,7 +93,7 @@ module Evoruby
             unless File.exist? input
               error "expected to already exist: " + input
             end
-            puts "a. identifier normalization already done:" + input
+            puts "a. identifier normalization already done: " + input
           end
         else
           error "illegal name: " + input