inprogress

[jalview.git] / forester / ruby / evoruby / exe / run_phylo_pipeline_x.rb

diff --git a/forester/ruby/evoruby/exe/run_phylo_pipeline_x.rb b/forester/ruby/evoruby/exe/run_phylo_pipeline_x.rb
index e07a620..8745f32 100644 (file)
--- a/forester/ruby/evoruby/exe/run_phylo_pipeline_x.rb
+++ b/forester/ruby/evoruby/exe/run_phylo_pipeline_x.rb
@@ -135,12 +135,12 @@ module Evoruby
 
 
         dsx_output = "#{hmm_name}/#{hmm_name}__#{hmm_name}__ee#{e_value_exp.to_s}_#{length}"
-        unless File.exist? dsx_output
+        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}"
           run_command( cmd )
         else
-          puts "e. dsx output already exists: " + dsx_output
+          puts "e. dsx output already exists: " + dsx_output + ".fasta"
         end
         puts
 
@@ -163,14 +163,14 @@ module Evoruby
         run_1 = false
         run_100 = false
 
-        unless File.exist? "#{msa_dir}/#{dsx_output}"
+        unless File.exist? "#{msa_dir}/#{hmm_name}__#{hmm_name}__ee#{e_value_exp.to_s}_#{length}"
           run_1 = true
-          FileUtils.cp "#{dsx_output}.fasta", "#{msa_dir}/#{dsx_output}"
+          FileUtils.cp "#{dsx_output}.fasta", "#{msa_dir}/#{hmm_name}__#{hmm_name}__ee#{e_value_exp.to_s}_#{length}"
         end
 
-        unless File.exist? "#{msa_100_dir}/#{dsx_output}"
+        unless File.exist? "#{msa_100_dir}/#{hmm_name}__#{hmm_name}__ee#{e_value_exp.to_s}_#{length}"
           run_100 = true
-          FileUtils.cp "#{dsx_output}.fasta", "#{msa_100_dir}/#{dsx_output}"
+          FileUtils.cp "#{dsx_output}.fasta", "#{msa_100_dir}/#{hmm_name}__#{hmm_name}__ee#{e_value_exp.to_s}_#{length}"
         end
 
         if File.exist?( TEMPLATE_FILE )
@@ -181,7 +181,7 @@ module Evoruby
             FileUtils.cp TEMPLATE_FILE, msa_100_dir
           end
 
-          if LAUNCH_ANALYSIS
+          if LAUNCH_ANALYSIS && ( run_1 || run_100 )
             puts "f. analysis:"
             if run_1
               Dir.chdir msa_dir