From: cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Fri, 28 Sep 2012 01:24:34 +0000 (+0000)
Subject: in progress
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=4efe5abda9af7f075953aa056d6530fe4f4c17db;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 a36f56a..d09655f 100755
--- a/forester/ruby/evoruby/exe/run_phylo_pipeline.rb
+++ b/forester/ruby/evoruby/exe/run_phylo_pipeline.rb
@@ -27,11 +27,13 @@ module Evoruby
 
     def run
       unless ARGV.length == 4
+        puts
         puts "arguments are: [inputfile].fasta [hmm-name] [min-length] [neg e-value exponent]"
+        puts
         exit
       end
 
-      pfam      = "/home/czmasek/DATA/PFAM/PFAM260/"
+      pfam      = "/home/czmasek/DATA/PFAM/PFAM260X/"
       hmmscan   = "/home/czmasek/SOFTWARE/HMMER/hmmer-3.0/src/hmmscan"
       hmmsearch = "/home/czmasek/SOFTWARE/HMMER/hmmer-3.0/src/hmmsearch"
       hsp       = "/home/czmasek/SOFTWARE/FORESTER/DEV/forester/forester/ruby/evoruby/exe/hsp.rb"