Merge pull request #173 from andrewjpage/dont_create_core_tree

revert core tree generation
sanger-pathogens · Sep 2, 2015 · ba978ac · ba978ac
2 parents 8c5fb3b + a05923c
commit ba978ac
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Showing 3 changed files with 1 addition and 10 deletions.
diff --git a/dist.ini b/dist.ini
@@ -1,5 +1,5 @@
 name    = Bio-Roary
-version = 3.2.5
+version = 3.2.6
 author  = Andrew J. Page <ap13@sanger.ac.uk>
 license = GPL_3
 copyright_holder = Wellcome Trust Sanger Institute

diff --git a/lib/Bio/Roary/CommandLine/RoaryPostAnalysis.pm b/lib/Bio/Roary/CommandLine/RoaryPostAnalysis.pm
@@ -149,13 +149,6 @@ sub run {
       );
       $seg->run();
 
-      my $core_tree = Bio::Roary::External::Fasttree->new(
-	          input_file => 'core_gene_alignment.aln',
-	          verbose    => $self->verbose,
-	          logger     => $self->logger
-	      );
-	  $core_tree->run();
-
       # Cleanup intermediate multifasta files
       if($self->dont_delete_files == 0)
       {

diff --git a/t/Bio/Roary/CommandLine/Roary.t b/t/Bio/Roary/CommandLine/Roary.t
@@ -129,8 +129,6 @@ SKIP:
     mock_execute_script_and_check_output( $script_name, \%scripts_and_expected_files );
 
     ok( -e 'core_gene_alignment.aln', 'Core gene alignment exists' );
-	ok( -e 'core_gene_alignment.aln.newick', 'core gene newick tree exists');
-
 }
 
 SKIP: