[med-svn] [roary] 01/05: New upstream version 3.7.1+dfsg

[Andreas Tille]

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tille pushed a commit to branch master
in repository roary.

commit 8b85bf79e3de895839b63064f0d68eb616ae3e5a
Author: Andreas Tille <tille at debian.org>
Date:   Thu Jan 19 08:30:27 2017 +0100

    New upstream version 3.7.1+dfsg
---
 Dockerfile                      |  7 +------
 README.md                       | 16 +++++++++++++++-
 lib/Bio/Roary/AnnotateGroups.pm |  4 ++--
 3 files changed, 18 insertions(+), 9 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index d6bc8f2..e63498e 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -11,9 +11,4 @@ MAINTAINER ap13 at sanger.ac.uk
 #
 # Pull in packages from testing
 #
-RUN apt-get update -qq
-
-#
-# Install Roary
-#
-RUN apt-get install roary
+RUN apt-get update -qq && apt-get install -y roary
diff --git a/README.md b/README.md
index 5003ec2..7e9e0bf 100644
--- a/README.md
+++ b/README.md
@@ -16,8 +16,10 @@ Theres are a number of dependancies required for Roary, with instructions specif
 * Ubuntu/Debian
 * CentOS/RedHat
 * Homebrew/Linuxbrew - OSX/Linux
-* Installing from source - OSX/Linux
+* Guix - Linux
 * Virtual Machine - OSX/Linux/Windows
+* Docker
+* Installing from source - OSX/Linux
 
 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 .
 
@@ -65,6 +67,18 @@ ftp://ftp.sanger.ac.uk/pub/pathogens/pathogens-vm/pathogens-vm.latest.ova
 
 More importantly though, if your trying to do bioinformatics on Windows, your not going to get very far and you should seriously consider upgrading to Linux.
 
+##Docker
+We have a docker container which gets automatically built from the latest version of Roary in Debian Med. To install it:
+
+```
+docker pull sangerpathogens/roary
+```
+
+To use it you would use a command such as this (substituting in your directories), where your GFF files are assumed to be stored in /home/ubuntu/data:
+```
+docker run --rm -it -v /home/ubuntu/data:/data sangerpathogens/roary roary -f /data /data/*.gff
+```
+
 ##Installing from source (advanced Linux users only)
 As a last resort you can install everything from source. This is for users with advanced Linux skills and we do not provide any support with this method since you have the skills to figure things out.
 Download the latest software from (https://github.com/sanger-pathogens/Roary/tarball/master).
diff --git a/lib/Bio/Roary/AnnotateGroups.pm b/lib/Bio/Roary/AnnotateGroups.pm
index 2c02b1a..32fa201 100644
--- a/lib/Bio/Roary/AnnotateGroups.pm
+++ b/lib/Bio/Roary/AnnotateGroups.pm
@@ -1,10 +1,10 @@
 package Bio::Roary::AnnotateGroups;
 
-# ABSTRACT: Take in a group file and assosiated GFF files for the isolates and update the group name to the gene name
+# ABSTRACT: Take in a group file and associated GFF files for the isolates and update the group name to the gene name
 
 =head1 SYNOPSIS
 
-Take in a group file and assosiated GFF files for the isolates and update the group name to the gene name
+Take in a group file and associated GFF files for the isolates and update the group name to the gene name
    use Bio::Roary::AnnotateGroups;
    
    my $obj = Bio::Roary::AnnotateGroups->new(

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