For instructions on how to use the software, the input format and output formats, please see the Roary website.
Roary is a high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka) and calculates the pan genome. Using a standard desktop PC, it can analyse datasets with thousands of samples, something which is computationally infeasible with existing methods, without compromising the quality of the results. 128 samples can be analysed in under 1 hour using 1 GB of RAM and a single processor. To perform this analysis using existing methods would take weeks and hundreds of GB of RAM.
"Roary: Rapid large-scale prokaryote pan genome analysis",
Andrew J. Page, Carla A. Cummins, Martin Hunt, Vanessa K. Wong, Sandra Reuter, Matthew T. G. Holden, Maria Fookes, Daniel Falush, Jacqueline A. Keane, Julian Parkhill,
Bioinformatics, (2015). doi: http://dx.doi.org/10.1093/bioinformatics/btv421
Roary: Rapid large-scale prokaryote pan genome analysis
Theres are a number of dependancies required for Roary, with instructions specific to the type of system you have:
- Ubuntu/Debian
- CentOS/RedHat
- Bioconda - OSX/Linux
- Galaxy
- Guix - Linux
- Virtual Machine - OSX/Linux/Windows
- Docker - OSX/Linux/Windows/Cloud
- 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@sanger.ac.uk .
sudo apt-get install roary
All the dependancies can be installed using apt and cpanm. Root permissions are required. Ubuntu 16.04 contains a package for Roary but it is frozen at v3.6.0.
sudo apt-get install bedtools cd-hit ncbi-blast+ mcl parallel cpanminus prank mafft fasttree
sudo cpanm -f Bio::Roary
Some of the software versions in apt are quite old so follow the instructions for Bioconda below.
Install conda. Then install bioconda and roary:
conda config --add channels r
conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda
conda install roary
Roary is available from the Galaxy toolshed ( as is Prokka ).
Roary is included in Guix and can be installed in the usual way:
guix package --install roary
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. You need to first install VirtualBox, then load the virtual machine, using the 'File -> Import Appliance' menu option. The root password is 'manager'.
ftp://ftp.sanger.ac.uk/pub/pathogens/pathogens-vm/pathogens-vm.latest.ova
More importantly though, if you're trying to do bioinformatics on Windows, you're not going to get very far and you should seriously consider upgrading to Linux.
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
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).
Choose somewhere to put it, for example in your home directory (no root access required):
cd $HOME
tar zxvf sanger-pathogens-Roary-xxxxxx.tar.gz
ls Roary-*
Add the following lines to your $HOME/.bashrc file, or to /etc/profile.d/roary.sh to make it available to all users:
export PATH=$PATH:$HOME/Roary-x.x.x/bin
export PERL5LIB=$PERL5LIB:$HOME/Roary-x.x.x/lib
Install the perl dependancies:
sudo cpanm Array::Utils Bio::Perl Exception::Class File::Basename File::Copy File::Find::Rule File::Grep File::Path File::Slurper File::Spec File::Temp File::Which FindBin Getopt::Long Graph Graph::Writer::Dot List::Util Log::Log4perl Moose Moose::Role Text::CSV PerlIO::utf8_strict
Install the external dependances either from source or from your packaging system:
bedtools cd-hit blast mcl GNUparallel prank mafft fasttree
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.
- Perl 5.14, 5.16, 5.20, 5.24
- cdhit 4.6.1
- ncbi blast+ 2.4.0
- mcl 14-137
- bedtools 2.27.1
- prank 130410
- GNU parallel 20130922, 20160722, 20150122
- FastTree 2.1.9