From: cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Tue, 12 Nov 2013 00:16:56 +0000 (+0000)
Subject: inprogress
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=9ad4eb52d172607313ea119d7a33992258632b95;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 8d0a27d..b13581a 100644
--- a/forester/ruby/evoruby/exe/run_phylo_pipeline_x.rb
+++ b/forester/ruby/evoruby/exe/run_phylo_pipeline_x.rb
@@ -131,10 +131,10 @@ module Evoruby
           if LAUNCH_ANALYSIS
             puts "f. analysis:"
             Dir.chdir "#{hmm_name}/msa/"
-            run_command "#{PF} -s"
+            run_command "#{PF} -b=1 -s"
             Dir.chdir "../.."
             Dir.chdir "#{hmm_name}/msa100/"
-            run_command "#{PF} -s"
+            run_command "#{PF} -b=100 -s"
             Dir.chdir "../.."
             puts
           end