view release on metacpan or  search on metacpan

README.md  view on Meta::CPAN

# Roary - The pan genome pipeline
Takes annotated assemblies in GFF3 format and calculates the pan genome.

PLEASE NOTE: we currently do not have the resources to provide support for Roary, so please do not expect a reply if you flag any issue.

[![Unmaintained](http://unmaintained.tech/badge.svg)](http://unmaintained.tech/)  
[![Build Status](https://travis-ci.org/sanger-pathogens/Roary.svg?branch=master)](https://travis-ci.org/sanger-pathogens/Roary)   
[![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-brightgreen.svg)](https://github.com/sanger-pathogens/roary/blob/master/GPL-LICENSE)   
[![status](https://img.shields.io/badge/Bioinformatics-10.1093-brightgreen.svg)](https://academic.oup.com/bioinformatics/article/31/22/3691/240757)  
[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg)](http://bioconda.github.io/recipes/roary/README.html)  
[![Container ready](https://img.shields.io/badge/container-ready-brightgreen.svg)](https://quay.io/repository/biocontainers/roary)  
[![Docker Build Status](https://img.shields.io/docker/build/sangerpathogens/roary.svg)](https://hub.docker.com/r/sangerpathogens/roary)  
[![Docker Pulls](https://img.shields.io/docker/pulls/sangerpathogens/roary.svg)](https://hub.docker.com/r/sangerpathogens/roary)  
[![codecov](https://codecov.io/gh/sanger-pathogens/roary/branch/master/graph/badge.svg)](https://codecov.io/gh/sanger-pathogens/roary)

## Contents
  * [Introduction](#introduction)
  * [Installation](#installation)
    * [Required dependencies](#required-dependencies)
    * [Optional dependencies](#optional-dependencies)
    * [Ubuntu/Debian](#ubuntudebian)
      * [Debian Testing](#debian-testing)
      * [Ubuntu 14\.04/16\.04](#ubuntu-14041604)
      * [Ubuntu 12\.04](#ubuntu-1204)
    * [Bioconda \- OSX/Linux](#bioconda---osxlinux)
    * [Galaxy](#galaxy)
    * [GNU Guix](#gnu-guix)
    * [Virtual Machine \- OSX/Linux/Windows](#virtual-machine---osxlinuxwindows)
    * [Docker \- OSX/Linux/Windows/Cloud](#docker---osxlinuxwindowscloud)
    * [Installing from source (advanced Linux users only)](#installing-from-source-advanced-linux-users-only)
    * [Ancient systems and versions of perl](#ancient-systems-and-versions-of-perl)
    * [Running the tests](#running-the-tests)
    * [Versions of software we test against](#versions-of-software-we-test-against)
  * [Usage](#usage)
  * [License](#license)
  * [Feedback/Issues](#feedbackissues)
  * [Citation](#citation)
  * [Further Information](#further-information)

## Introduction
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 whic...

## Installation
Roary has the following dependencies:

### Required dependencies
* [bedtools](https://bedtools.readthedocs.io/en/latest/)
* [cd-hit](http://weizhongli-lab.org/cd-hit/)
* [ncbi-blast+](https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download)
* [mcl](https://micans.org/mcl/)
* [parallel](https://www.gnu.org/software/parallel/)
* [prank](http://wasabiapp.org/software/prank/)
* [mafft](https://mafft.cbrc.jp/alignment/software/)
* [fasttree](http://www.microbesonline.org/fasttree/)

### Optional dependencies
* [kraken](http://ccb.jhu.edu/software/kraken/MANUAL.html)

There are a number of ways to install Roary and details are provided below. If you encounter an issue when installing Roary please contact your local system administrator. If you encounter a bug please log it [here](https://github.com/sanger-pathogen...

### Ubuntu/Debian
#### Debian Testing
```
sudo apt-get install roary
```

#### Ubuntu 14.04/16.04
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
```

#### Ubuntu 12.04
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:

```
conda config --add channels r
conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda
conda install roary
```

### Galaxy
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:
```
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 ne...

ftp://ftp.sanger.ac.uk/pub/pathogens/pathogens-vm/pathogens-vm.latest.ova