COMBAT-TB Workbench

The COMBAT-TB Workbench is an IRIDA based, module workbench for M. tuberculosis bioinformatics. It is designed to be easily deployed on a single server.

Up and running

Prerequisites

• docker
• docker-compose

Specs

This setup was tested on a VM with the following specs.

• 32G RAM
• 4 vCPU
• 250G Disk

Using docker-compose

Assumption :

• You have docker and docker-compose installed on destination instance/VM.

NOTE:

You can use scripts to install docker and deploy this stack.

Connect to the server where you want to install the Workbench:

ssh [email protected]

git clone https://github.com/COMBAT-TB/irida-galaxy-deploy.git ; cd irida-galaxy-deploy

Install tools needed by workflows

The 'new style' irida-plugin-builder bundles a tools.yaml with each pipeline in the pipeline jar file. The TB Sample Report and TB Phylogeny pipelines are built using this builder and for each release a pipeline is published on the corresponding Github repositories.

This repository includes a script update_plugins_and_tools.py (a Python3 script) that can download these plugins and configure the collection of tools to be installed into Galaxy. This tool takes as input a list of workflows to download (see workflows.txt) and optionally some extra Galaxy tools not mentioned in the workflows (see extra-galaxy-tools.yml). Here is a typical run of this tool:

./update_plugins_and_tools.py --extra_tools_file extra-galaxy-tools.yml workflows.txt

This should be run before the docker-compose up command and whenever workflows are updated or new ones added. It will require rebuilding the Docker containers i.e. docker-compose up --build -d. The update_plugins_and_tools.py script also has an option --remove_old_workflows that will delete all workflows in the workflow directory before downloading new ones. This should be used when new versions of workflows are downloaded.

Start the Workbench

For the first time you start the Workbench

docker-compose up --build -d

To shut down the Workbench (again from the same directory where the Workbench code is installed):

docker-compose down

To start the Workbench again:

docker-compose up -d

NOTE:

This will take a couple of minutes.. ⌚ ☕

Upon completion, point your browser to:

• REMOTE.SERVER:8080/irida/ to access IRIDA
• REMOTE.SERVER:9090 to access Galaxy

The default administrator username and password are:

• admin:password1 for IRIDA
• admin:admin for Galaxy

Deploying to OpenStack

Please see openstack-terraform to deploy to OpenStack using Terraform.