From: cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Sat, 9 Nov 2013 04:22:29 +0000 (+0000)
Subject: inprogress
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=fb99cf2ca63c175f1f3155e32db17792f95ab6f4;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 fb351c2..05507b9 100644
--- a/forester/ruby/evoruby/exe/run_phylo_pipeline_x.rb
+++ b/forester/ruby/evoruby/exe/run_phylo_pipeline_x.rb
@@ -22,7 +22,7 @@ module Evoruby
     TAP       = "/home/czmasek/SOFTWARE/FORESTER/DEV/forester/forester/ruby/evoruby/exe/tap.rb"
 
     def run
-      unless ARGV.length >= 4 && ARGV.length <= 6
+      unless ARGV.length >= 2 && ARGV.length <= 4
         error "arguments are:  <min-length> " +
          "<neg E-value exponent for domain extraction> [E-value for hmmscan, default is 10] [hmmscan option, default is --nobias, --max for no heuristics]"
       end
@@ -58,11 +58,13 @@ module Evoruby
       end
       puts
 
-      counter = 0
+      counter = 1
       input_files.each do | input |
 
         puts counter.to_s + "/" +  input_files.size.to_s + " " + input + ": "
         
+        counter += 1
+        
         hmm_name = ""
 
         if input.downcase.end_with?( "_ni.fasta" )