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8 changes: 7 additions & 1 deletion .travis.yml
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Expand Up @@ -23,4 +23,10 @@ env:
- PARALLEL_VERSION=20170822
install:
- "source ./install_dependencies.sh"
script: "ROARY_FULL_TESTS=1 dzil test"
before_script:
- cpanm --quiet --notest Dist::Zilla::App::Command::cover
- cpanm --quiet --notest --skip-satisfied Devel::Cover::Report::Codecov
script:
- ROARY_FULL_TESTS=1 dzil test
after_success:
- dzil cover -test -report codecov
154 changes: 120 additions & 34 deletions README.md
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@@ -1,47 +1,77 @@
# Roary the pan genome pipeline
For instructions on how to use the software, the input format and output formats, please see [the Roary website](http://sanger-pathogens.github.io/Roary).

[![Build Status](https://travis-ci.org/sanger-pathogens/Roary.svg?branch=master)](https://travis-ci.org/sanger-pathogens/Roary)

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

[![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)
* [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 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.

## Citation
"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](http://dx.doi.org/10.1093/bioinformatics/btv421)
## Installation
Roary has the following dependencies:

# Installation
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
### 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/)

If the installation fails please contact your system administrator. If you encounter a bug please let us know by emailing roary@sanger.ac.uk .
### Optional dependencies
* [kraken](http://ccb.jhu.edu/software/kraken/MANUAL.html)

## Ubuntu/Debian
### Debian Testing
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-pathogens/Roary/issues) or email us at roary-help@sanger.ac.uk.

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

### Ubuntu 14.04/16.04
#### 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
#### Ubuntu 12.04
Some of the software versions in apt are quite old so follow the instructions for Bioconda below.

## Bioconda - OSX/Linux
### Bioconda - OSX/Linux
Install conda. Then install bioconda and roary:

```
Expand All @@ -52,23 +82,23 @@ conda config --add channels bioconda
conda install roary
```

## Galaxy
Roary is available from the Galaxy toolshed ( as is Prokka ).
### Galaxy
Roary is available from the Galaxy toolshed (as is Prokka).

## GNU Guix
### 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
### 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'.

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.

## Docker - OSX/Linux/Windows/Cloud
### Docker - OSX/Linux/Windows/Cloud
We have a docker container which gets automatically built from the latest version of Roary in Debian Med. To install it:

```
Expand All @@ -80,7 +110,7 @@ To use it you would use a command such as this (substituting in your directories
docker run --rm -it -v /home/ubuntu/data:/data sangerpathogens/roary roary -f /data /data/*.gff
```

## Installing from source (advanced Linux users only)
### 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).

Expand Down Expand Up @@ -108,10 +138,10 @@ Install the external dependances either from source or from your packaging syste
bedtools cd-hit blast mcl GNUparallel prank mafft fasttree
```

## Ancient systems and versions of perl
### 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) 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
### Versions of software we test against
* Perl 5.14, 5.26
* cdhit 4.6.8
* ncbi blast+ 2.6.0
Expand All @@ -120,3 +150,59 @@ The code will not work with perl 5.8 or below (pre-modern perl). We no longer te
* prank 140603
* GNU parallel 20170822, 20160722
* FastTree 2.1.9

## Usage
```
Usage: roary [options] *.gff
Options: -p INT number of threads [1]
-o STR clusters output filename [clustered_proteins]
-f STR output directory [.]
-e create a multiFASTA alignment of core genes using PRANK
-n fast core gene alignment with MAFFT, use with -e
-i minimum percentage identity for blastp [95]
-cd FLOAT percentage of isolates a gene must be in to be core [99]
-qc generate QC report with Kraken
-k STR path to Kraken database for QC, use with -qc
-a check dependancies and print versions
-b STR blastp executable [blastp]
-c STR mcl executable [mcl]
-d STR mcxdeblast executable [mcxdeblast]
-g INT maximum number of clusters [50000]
-m STR makeblastdb executable [makeblastdb]
-r create R plots, requires R and ggplot2
-s dont split paralogs
-t INT translation table [11]
-ap allow paralogs in core alignment
-z dont delete intermediate files
-v verbose output to STDOUT
-w print version and exit
-y add gene inference information to spreadsheet, doesnt work with -e
-iv STR Change the MCL inflation value [1.5]
-h this help message
Example: Quickly generate a core gene alignment using 8 threads
roary -e --mafft -p 8 *.gff
For further info see: http://sanger-pathogens.github.io/Roary/
```
For further instructions on how to use the software, the input format and output formats, please see [the Roary website](http://sanger-pathogens.github.io/Roary).

## License
Roary is free software, licensed under [GPLv3](https://github.com/sanger-pathogens/Roary/blob/master/GPL-LICENSE).

## Feedback/Issues
Please report any issues to the [issues page](https://github.com/sanger-pathogens/Roary/issues) or email roary-help@sanger.ac.uk.

## Citation
If you use this software please cite:

"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](http://dx.doi.org/10.1093/bioinformatics/btv421)

## Further Information
For more information on this software see:
* [The Roary website](http://sanger-pathogens.github.io/Roary)
* [The Jupyter notebook tutorial](https://github.com/sanger-pathogens/pathogen-informatics-training)

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