[med-svn] [roary] 01/04: New upstream version 3.11.4+dfsg

[Sascha Steinbiss]

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satta pushed a commit to branch master
in repository roary.

commit af9817c6ca0b18b1b59026525697798a76a24330
Author: Sascha Steinbiss <satta at debian.org>
Date:   Sun Jan 21 23:46:06 2018 +0100

    New upstream version 3.11.4+dfsg
---
 README.md                          | 29 ++++++++---------------------
 dist.ini                           |  2 +-
 lib/Bio/Roary/CommandLine/Roary.pm | 21 ++++++++++++++-------
 3 files changed, 23 insertions(+), 29 deletions(-)

diff --git a/README.md b/README.md
index 823f49a..fb94f70 100644
--- a/README.md
+++ b/README.md
@@ -17,7 +17,6 @@ Theres are a number of dependancies required for Roary, with instructions specif
 * CentOS/RedHat
 * Bioconda - OSX/Linux
 * Galaxy
-* Homebrew/Linuxbrew - OSX/Linux
 * Guix - Linux
 * Virtual Machine - OSX/Linux/Windows
 * Docker - OSX/Linux/Windows/Cloud
@@ -40,10 +39,7 @@ 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.
-
-## CentOS/RedHat
-To install the dependancies, the easiest way is to install [LinuxBrew](http://brew.sh/linuxbrew/) using the steps for Fedora, then follow the steps below for installing Roary on LinuxBrew.
+Some of the software versions in apt are quite old so follow the instructions for Bioconda below.
 
 ## Bioconda - OSX/Linux
 Install conda. Then install bioconda and roary:
@@ -57,16 +53,7 @@ conda install roary
 ```
 
 ## Galaxy
-Roary is available from the Galaxy toolshed ( as is Prokka).
-
-## Homebrew/Linuxbrew - OSX/Linux
-Assuming you have [homebrew](http://brew.sh/) (OSX) or [linuxbrew](http://brew.sh/linuxbrew/) (Linux) setup and installed on your system:
-
-```
-brew tap homebrew/science
-brew install bedtools cd-hit blast mcl parallel prank mafft fasttree cpanm
-sudo cpanm -f Bio::Roary
-```
+Roary is available from the Galaxy toolshed ( as is Prokka ).
 
 ## GNU Guix
 Roary is included in [Guix](https://www.gnu.org/software/guix) and can be installed in the usual way:
@@ -122,14 +109,14 @@ bedtools cd-hit blast mcl GNUparallel prank mafft fasttree
 ```
 
 ## Ancient systems and versions of perl
-The code will not work with perl 5.8 or below (pre-modern perl). We no longer test against 5.10 (released 2007). If you're running a very old verison of Linux, you're also in trouble.
+The code will not work with perl 5.8 or below (pre-modern perl). We no longer test against 5.10 (released 2007) or 5.12 (released 2010). If you're running a very old verison of Linux, you're also in trouble.
 
 # Versions of software we test against
-* Perl 5.14, 5.16, 5.20, 5.24
-* cdhit 4.6.1
-* ncbi blast+ 2.4.0
+* Perl 5.14, 5.26
+* cdhit 4.6.8
+* ncbi blast+ 2.6.0
 * mcl 14-137
 * bedtools 2.27.1
-* prank 130410
-* GNU parallel 20130922, 20160722, 20150122
+* prank 140603
+* GNU parallel 20170822, 20160722
 * FastTree 2.1.9
diff --git a/dist.ini b/dist.ini
index 1839c8f..2f0cae1 100644
--- a/dist.ini
+++ b/dist.ini
@@ -3,7 +3,7 @@ author  = Andrew J. Page <ap13 at sanger.ac.uk>
 license = GPL_3
 copyright_holder = Wellcome Trust Sanger Institute
 copyright_year   = 2013
-version = 3.11.3
+version = 3.11.4
 main_module = lib/Bio/Roary.pm
 
 [MetaResources]
diff --git a/lib/Bio/Roary/CommandLine/Roary.pm b/lib/Bio/Roary/CommandLine/Roary.pm
index a98610c..78ce692 100644
--- a/lib/Bio/Roary/CommandLine/Roary.pm
+++ b/lib/Bio/Roary/CommandLine/Roary.pm
@@ -42,6 +42,7 @@ has 'cpus'                    => ( is => 'rw', isa => 'Int',  default => 1 );
 has 'output_multifasta_files' => ( is => 'rw', isa => 'Bool', default => 0 );
 has 'perc_identity'           => ( is => 'rw', isa => 'Num',  default => 95 );
 has 'dont_delete_files'       => ( is => 'rw', isa => 'Bool', default => 0 );
+has 'check_dependancies'      => ( is => 'rw', isa => 'Bool', default => 0 );
 has 'dont_create_rplots'      => ( is => 'rw', isa => 'Bool', default => 1 );
 has 'dont_run_qc'             => ( is => 'rw', isa => 'Bool', default => 0 );
 has 'dont_split_groups'       => ( is => 'rw', isa => 'Bool', default => 0 );
@@ -126,16 +127,22 @@ sub BUILD {
 		print $self->usage_text;
 		return;
 	}
+	
+    if ( defined($verbose) ) {
+        $self->verbose($verbose);
+        $self->logger->level(10000);
+    }
 
-    if ($check_dependancies) {
+	$self->check_dependancies($check_dependancies) if ( defined($check_dependancies) );
+    if ($self->check_dependancies) {
         my $check_tools = Bio::Roary::External::CheckTools->new();
         $check_tools->check_all_tools;
         $self->logger->error( "Roary version " . $self->_version() );
-    }
-
-    if ( defined($verbose) ) {
-        $self->verbose($verbose);
-        $self->logger->level(10000);
+		
+		if( @{ $self->args } < 1 )
+		{
+			return;
+		}
     }
 
     if ( @{ $self->args } < 2 ) {
@@ -260,7 +267,7 @@ sub _setup_output_directory {
 sub run {
     my ($self) = @_;
 
-	return if($self->version || $self->help);
+	return if($self->version || $self->help || ($self->check_dependancies && @{$self->fasta_files} < 1) );
 
     $self->_setup_output_directory;
 

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