Docker

To bypass the installation steps, we have provided a docker [image](https://stackoverflow.com/questions/23735149/what-is-the-difference-between-a-docker-image-and-a-container) for PhaME. To run PhaME from a docker image, follow these steps:

1. Install .. _Docker: https://docs.docker.com/install/

2. Download the latest PhaME image from [quay.io](https:quay.io/)

   $ docker pull quay.io/biocontainers/phame:1.0.3--0
   

3. Check if the image is correctly downloaded by running the provided test:

   $ docker run --rm quay.io/biocontainers/phame:1.0.3--0 phame -h
   $ docker run --rm quay.io/biocontainers/phame:1.0.3--0 phame -vcheck
   

4. Run your own data using docker. A step by step guide

   • Create a folder to mount onto your docker

   $ mkdir -p phame_analysis_folder
   

   • Create a refdir folder with complete genomes within phame_analysis_folder

     This folder will contain fasta files representing complete genomes.

     $ cd phame_analysis_folder
     $ mkdir -p refdir
     

     Copy or download genomes and their gff files (if needed) onto this folder.

   • Create a workdir folder within the phame_analysis_folder.

     This folder will have all the intermediate and final outputs of the analysis including input contigs and reference.

     $ mkdir -p workdir
     

   • Create a control file.

     All the inputs and parameters of a PhaME analysis is set in the control file. Using the provided template create a control file with apprpriate parameters and save it in the phame_analysis_foler.

   • Run the analysis using docker.

   $ docker run --rm -v $(pwd)/phame_analysis_folder:/data migun/phame src/phame /data/ecoli.ctl
   $ git clone https://github.com/mshakya/phame_examples.git
   $ docker run --rm -v $(pwd)/phame_examples:/data migun/phame-1 perl src/phame /data/ecoli/ecoli.ctl