[med-svn] [roary] 01/04: New upstream version 3.7.0+dfsg

[Sascha Steinbiss]

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satta pushed a commit to branch master
in repository roary.

commit 9a2720ff72a2640f4048be43b5ff1df1ee4e757c
Author: Sascha Steinbiss <satta at debian.org>
Date:   Sat Sep 24 20:34:54 2016 +0000

    New upstream version 3.7.0+dfsg
---
 README.md                           |  7 +++++++
 dist.ini                            | 10 +++++++++-
 lib/Bio/Roary/AssemblyStatistics.pm |  2 +-
 lib/Bio/Roary/ReformatInputGFFs.pm  |  2 +-
 4 files changed, 18 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index c873c98..5003ec2 100644
--- a/README.md
+++ b/README.md
@@ -51,6 +51,13 @@ brew install bedtools cd-hit blast mcl parallel prank mafft fasttree cpanm
 sudo cpanm -f Bio::Roary
 ```
 
+##GNU Guix
+Roary is not included in version in [Guix](https://www.gnu.org/software/guix) 0.11.0 so `guix pull` is currently required before installation.
+```
+guix pull
+guix package --install roary
+```
+
 ##Virtual Machine - OSX/Linux/Windows
 Roary wont run natively on Windows but we have created virtual machine which has all of the software setup, including Prokka, along with the test datasets from the paper. It is based on [Bio-Linux 8](http://environmentalomics.org/bio-linux/).  You need to first install [VirtualBox](https://www.virtualbox.org/), then load the virtual machine, using the 'File -> Import Appliance' menu option. The root password is 'manager'.
 
diff --git a/dist.ini b/dist.ini
index 41391bf..37708e3 100644
--- a/dist.ini
+++ b/dist.ini
@@ -1,5 +1,5 @@
 name    = Bio-Roary
-version = 3.6.8
+version = 3.7.0
 author  = Andrew J. Page <ap13 at sanger.ac.uk>
 license = GPL_3
 copyright_holder = Wellcome Trust Sanger Institute
@@ -16,7 +16,15 @@ repository.type = git
 [PruneCruft]
 [ExtraTests]
 [AutoPrereqs]
+
+[FileFinder::ByName / BinNotR]
+dir = bin
+skip = .*\.R$
+
 [PodWeaver]
+finder = :InstallModules
+finder = BinNotR
+
 [PkgVersion]
 
 [Prereqs]
diff --git a/lib/Bio/Roary/AssemblyStatistics.pm b/lib/Bio/Roary/AssemblyStatistics.pm
index ccda667..8c13088 100644
--- a/lib/Bio/Roary/AssemblyStatistics.pm
+++ b/lib/Bio/Roary/AssemblyStatistics.pm
@@ -39,7 +39,7 @@ sub BUILD {
 sub _build_logger
 {
     my ($self) = @_;
-    Log::Log4perl->easy_init(level => $ERROR);
+    Log::Log4perl->easy_init( $ERROR );
     my $logger = get_logger();
     return $logger;
 }
diff --git a/lib/Bio/Roary/ReformatInputGFFs.pm b/lib/Bio/Roary/ReformatInputGFFs.pm
index 86289ca..0ae52ce 100644
--- a/lib/Bio/Roary/ReformatInputGFFs.pm
+++ b/lib/Bio/Roary/ReformatInputGFFs.pm
@@ -33,7 +33,7 @@ has 'fixed_gff_files' => ( is => 'rw', isa => 'ArrayRef', default => sub { [] }
 
 sub _build_logger {
     my ($self) = @_;
-    Log::Log4perl->easy_init( level => $ERROR );
+    Log::Log4perl->easy_init( $ERROR );
     my $logger = get_logger();
     return $logger;
 }

-- 
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