Before you do anything, please have a look at the [Gubbins webpage](http://sanger-pathogens.github.io/gubbins/).

# Installation
There are a few ways to install Gubbins and its dependencies. The simpliest way is using conda.

* OSX/Linux - Bioconda
* Linux - Ubuntu Xenial (16.04) & Debian (unstable)
* OSX/Linux/Cloud/Windows - Docker
* OSX/Linux - from source
* OSX/Linux/Windows - Virtual Machine

## OSX/Linux - conda
Install conda and enable the bioconda channels.

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

## Linux - Ubuntu Xenial (16.04) & Debian (unstable)
Gubbins has been packaged by the Debian Med team and is trivial to install using apt.

    sudo apt-get install gubbins

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

    docker pull sangerpathogens/gubbins

To use it you would use a command such as this:

    docker run --rm -it -v <local_dir>:<remote_dir> sangerpathogens/gubbins run_gubbins -p <remote_dir>/<prefix> [<options>] <remote_dir>/<alignment_file>

The flag `-v` synchronizes a directory on the host machine (here denoted as `<local_dir>`) with a directory in the Docker container (here denoted as `<remote_dir>`).
`<remote_dir>` does not need to exist in the container before the run, a common choice is `/data`.
Note that both `<local_dir>` and `<remote_dir>` must be absolute paths.

The input alignment file must be present in `<local_dir>` (or in one of its subdirectories).
In order to retrieve the files produced by Gubbins, run the program with option `-p`; 
the argument of this option must consist of `<remote_dir>`, followed by an arbitrary identifier (here denoted as `<prefix>`).


## OSX/Linux - from source
This is the most difficult method and is only suitable for someone with advanced computing skills. Please consider using Conda instead.

Install the dependencies and include them in your `PATH`:
* [FastTree](http://www.microbesonline.org/fasttree/#Install) ( >=2.1.4 )
* [RAxML](https://github.com/stamatak/standard-RAxML) ( >=8.0 )
* Python modules: Biopython (> 1.59), DendroPy (>=4.0), Reportlab, nose, pillow
* Standard build environment tools (e.g. python3, pip3, make, autoconf, libtool, gcc, check, etc...)

Clone or download the source code from GitHub and run the following commands to install Gubbins:
```
autoreconf -i
./configure [--prefix=$PREFIX]
make
[sudo] make install
cd python
[sudo] python3 setup.py install
```
Use `sudo` to install Gubbins system-wide. If you don't have the permissions, run `configure` with a prefix to install Gubbins in your home directory.

## OSX/Linux/Windows - Virtual Machine
Roary wont run natively on Windows but we have created a virtual machine which has all of the software setup, 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 your trying to do bioinformatics on Windows, your not going to get very far and you should seriously consider upgrading to Linux.