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 0727eb7..795aba7 100644 (file)
--- a/forester/ruby/evoruby/exe/run_phylo_pipeline_x.rb
+++ b/forester/ruby/evoruby/exe/run_phylo_pipeline_x.rb
@@ -135,7 +135,7 @@ module Evoruby
 
 
         dsx_output = "#{hmm_name}/#{hmm_name}__#{hmm_name}__ee#{e_value_exp.to_s}_#{length}"
-        unless File.exist? d2f_output
+        unless File.exist? dsx_output
           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 )
@@ -160,21 +160,39 @@ module Evoruby
           Dir.mkdir( msa_100_dir )
         end
 
-        FileUtils.cp "#{dsx_output}.fasta", "#{msa_dir}/#{dsx_output}"
-        FileUtils.cp "#{dsx_output}.fasta", "#{msa_100_dir}/#{dsx_output}"
+        run_1 = false
+        run_100 = false
+
+        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}/#{hmm_name}__#{hmm_name}__ee#{e_value_exp.to_s}_#{length}"
+        end
+
+        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}/#{hmm_name}__#{hmm_name}__ee#{e_value_exp.to_s}_#{length}"
+        end
 
         if File.exist?( TEMPLATE_FILE )
-          FileUtils.cp TEMPLATE_FILE, msa_dir
-          FileUtils.cp TEMPLATE_FILE, msa_100_dir
+          if run_1
+            FileUtils.cp TEMPLATE_FILE, msa_dir
+          end
+          if run_100
+            FileUtils.cp TEMPLATE_FILE, msa_100_dir
+          end
 
           if LAUNCH_ANALYSIS
             puts "f. analysis:"
-            Dir.chdir msa_dir
-            run_command "#{PF} -b=1 -s"
-            Dir.chdir "../.."
-            Dir.chdir msa_100_dir
-            run_command "#{PF} -b=100 -s"
-            Dir.chdir "../.."
+            if run_1
+              Dir.chdir msa_dir
+              run_command "#{PF} -b=1 -s"
+              Dir.chdir "../.."
+            end
+            if run_100
+              Dir.chdir msa_100_dir
+              run_command "#{PF} -b=100 -s"
+              Dir.chdir "../.."
+            end
             puts
           end
         end