X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fruby%2Fevoruby%2Fexe%2Frun_phylo_pipeline.rb;h=d09655f457d8f52bcc5c2a5b8849dadf988f923c;hb=4efe5abda9af7f075953aa056d6530fe4f4c17db;hp=a36f56ac5b5c457fa6569fbdaecb0d872d1de5b1;hpb=93b9f80ae6a390a4cf014e9262c1e4a2f7ff24db;p=jalview.git

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"