[med-svn] [roary] 01/03: Imported Upstream version 3.6.2+dfsg

[Sascha Steinbiss]

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sascha-guest pushed a commit to branch master
in repository roary.

commit 1c08513c5f1446b5c0f8fb6f0a2c376ba4fc877d
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date:   Tue May 10 21:29:59 2016 +0000

    Imported Upstream version 3.6.2+dfsg
---
 README.md                                   | 11 +++++++++--
 dist.ini                                    |  2 +-
 lib/Bio/Roary/CommandLine/Common.pm         |  4 ++--
 lib/Bio/Roary/ParallelAllAgainstAllBlast.pm | 10 ++++++++--
 4 files changed, 20 insertions(+), 7 deletions(-)

diff --git a/README.md b/README.md
index 6c3ece6..4d8d1a9 100644
--- a/README.md
+++ b/README.md
@@ -22,12 +22,19 @@ Theres are a number of dependancies required for Roary, with instructions specif
 If the installation fails please contact your system administrator. If you encounter a bug please let us know by emailing roary at sanger.ac.uk .
 
 ##Ubuntu/Debian
-All the dependancies can be installed using apt and cpanm (tested on Ubuntu 14.04). Root permissions are required.
+### Ubuntu 16.04
+
+```
+sudo apt-get install roary
+```
+
+###Ubuntu 14.04
+All the dependancies can be installed using apt and cpanm. Root permissions are required.
 
 ```
 sudo apt-get install bedtools cd-hit ncbi-blast+ mcl parallel cpanminus prank mafft fasttree
 sudo cpanm -f Bio::Roary
-```   
+```
 
 ###Ubuntu 12.04
 Some of the software versions in apt are quite old so follow the instructions for [LinuxBrew](http://brew.sh/linuxbrew/) below.
diff --git a/dist.ini b/dist.ini
index ee8e8a3..18fd998 100644
--- a/dist.ini
+++ b/dist.ini
@@ -1,5 +1,5 @@
 name    = Bio-Roary
-version = 3.6.1
+version = 3.6.2
 author  = Andrew J. Page <ap13 at sanger.ac.uk>
 license = GPL_3
 copyright_holder = Wellcome Trust Sanger Institute
diff --git a/lib/Bio/Roary/CommandLine/Common.pm b/lib/Bio/Roary/CommandLine/Common.pm
index 9db65f5..b391a21 100644
--- a/lib/Bio/Roary/CommandLine/Common.pm
+++ b/lib/Bio/Roary/CommandLine/Common.pm
@@ -19,7 +19,7 @@ has 'version'                 => ( is => 'rw', isa => 'Bool', default => 0 );
 sub _build_logger
 {
     my ($self) = @_;
-    Log::Log4perl->easy_init(level => $ERROR);
+    Log::Log4perl->easy_init($ERROR);
     my $logger = get_logger();
     return $logger;
 }
@@ -54,4 +54,4 @@ before 'run' => sub {
 };
 
 no Moose;
-1;
\ No newline at end of file
+1;
diff --git a/lib/Bio/Roary/ParallelAllAgainstAllBlast.pm b/lib/Bio/Roary/ParallelAllAgainstAllBlast.pm
index 17474b0..01c48c1 100644
--- a/lib/Bio/Roary/ParallelAllAgainstAllBlast.pm
+++ b/lib/Bio/Roary/ParallelAllAgainstAllBlast.pm
@@ -88,8 +88,14 @@ sub _combine_blast_results {
         Bio::Roary::Exceptions::FileNotFound->throw( error => "Cant find blast results: " . $output_file )
           unless ( -e $output_file );
     }
-    my $output_files_param = join( ' ', @{$output_files} );
-    system( "cat $output_files_param > " . $self->blast_results_file_name );
+    if ( -e $self->blast_results_file_name )
+    {
+        system( "rm " . $self->blast_results_file_name );
+    }
+    system( "touch " . $self->blast_results_file_name );
+    for my $output_file ( @{$output_files} ) {
+        system( "cat $output_file >> " . $self->blast_results_file_name );
+    }
     return 1;
 }
 

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