Skip to content

Latest commit

 

History

History
84 lines (51 loc) · 3.2 KB

README.md

File metadata and controls

84 lines (51 loc) · 3.2 KB
Raw

INNUENDO Platform Docker-Compose version

Codacy Badge Documentation Status

INNUENDO Platform made easy!

This repository provides a series of dockerfiles, configuration files and a docker-compose file to launch the INNUENDO Platform without the requirement of installing every component individually.

Requirements

  • Docker
  • Docker-compose

Installation

Check the documentation on how to install the required dependencies.

Usage

# Get the repository source code
get clone https://github.com/bfrgoncalves/INNUENDO_docker.git

# Enter the repository directory
cd INNUENDO_docker

# Run the docker-compose application
docker-compose up

# Access the application at http://localhost

The last command will pull all the required images first then it will launch all the Docker containers. They will will communicate between each other by a docker network that is built by default with docker-compose.

Downloading legacy data and building profile databases

The application provides a script to download all the required files to perform comparisons with some already publicly available strains. This is made through the download of the following data available here:

  • chewBBACA schemas
  • Legacy strain metadata (for each species)
  • Legacy strain profiles (for each species)
  • Serotyping files
  • Prodigal training files

These data will be available under ./inputs and will be mapped to the docker containers running the application.

The script also build the required files for a rapid comparison between profiles using fast-mlst and populates the mlst_database.

To run the script, type the following command:


# Enter repository directory
cd <innuendo_docker_directory>/build_files

# Run script to get legacy input files
./get_inputs.sh

These steps might take up to 1h depending on the available internet connection and the host machine.

Loading data from a predefined backup

We offer an option to load a predefined set of protocols and workflows, together with test projects and strains. Currently, this option is only available for machines with above 8 cpus and 8gb of RAM. This is due to the backup expecting at least those resources for at least one of the predefined protocols.

To load the predefined data, do the following:


# Enter the build_files directory
cd <innuendo_docker_directory>/build_files

# Run the script to load the data
./init_8cpu_components.sh

NOTE: The above script will delete ALL data available in the AllegroGraph database and INNUENDO general database. It will then replaced by the predefined data.

More information about the software can be found at the documentation.