X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=forester%2Fruby%2Fevoruby%2Fexe%2Frun_phylo_pipeline_x.rb;h=1711880cd0d0307fe66270742ec70c4caff9e801;hb=c5518ace0749f79670bc0bbba517b400802b0902;hp=8745f32385d4c5311deb5a7b57637942ca8991d1;hpb=40a1d5df3180278f76e7a6a90dc2464060db9a90;p=jalview.git

diff --git a/forester/ruby/evoruby/exe/run_phylo_pipeline_x.rb b/forester/ruby/evoruby/exe/run_phylo_pipeline_x.rb
index 8745f32..1711880 100644
--- 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
@@ -133,8 +135,8 @@ module Evoruby
         end
         puts
 
-
-        dsx_output = "#{hmm_name}/#{hmm_name}__#{hmm_name}__ee#{e_value_exp.to_s}_#{length}"
+        dsx_output_base = "#{hmm_name}__#{hmm_name}__ee#{e_value_exp.to_s}_#{length}"
+        dsx_output = hmm_name +"/" + dsx_output_base
         unless File.exist? dsx_output + ".fasta"
           puts "e. dsx:"
           cmd = "#{DSX} -d -e=1e-#{e_value_exp.to_s} -l=#{length} #{hmm_name} #{hmmscan_output} #{input} #{dsx_output}"
@@ -163,14 +165,14 @@ module Evoruby
         run_1 = false
         run_100 = false
 
-        unless File.exist? "#{msa_dir}/#{hmm_name}__#{hmm_name}__ee#{e_value_exp.to_s}_#{length}"
+        unless File.exist? "#{msa_dir}/#{dsx_output_base}"
           run_1 = true
-          FileUtils.cp "#{dsx_output}.fasta", "#{msa_dir}/#{hmm_name}__#{hmm_name}__ee#{e_value_exp.to_s}_#{length}"
+          FileUtils.cp "#{dsx_output}.fasta", "#{msa_dir}/#{dsx_output_base}"
         end
 
-        unless File.exist? "#{msa_100_dir}/#{hmm_name}__#{hmm_name}__ee#{e_value_exp.to_s}_#{length}"
+        unless File.exist? "#{msa_100_dir}/#{dsx_output_base}"
           run_100 = true
-          FileUtils.cp "#{dsx_output}.fasta", "#{msa_100_dir}/#{hmm_name}__#{hmm_name}__ee#{e_value_exp.to_s}_#{length}"
+          FileUtils.cp "#{dsx_output}.fasta", "#{msa_100_dir}/#{dsx_output_base}"
         end
 
         if File.exist?( TEMPLATE_FILE )