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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).

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 dependencies:

```
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::R...
```
Install the external dependances either from source or from your packaging system:
```
bedtools cd-hit blast mcl GNUparallel prank mafft fasttree
```

### 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.

### Running the tests
The test can be run with dzil from the top level directory:  

```
dzil test
```

### Versions of software we test against
* Perl 5.14, 5.26
* cdhit 4.6.8
* ncbi blast+ 2.6.0
* mcl 14-137
* bedtools 2.27.1
* 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
We currently do not have the resources to provide support for Roary. However, the community might be able to help you out if you report any issues about usage of the software to the [issues page](https://github.com/sanger-pathogens/Roary/issues).

## 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)