toolkit-ansible-role

Ansible role for RNA-Puzzles Toolkit. Contains ansible-container configuration and an example playbook.

Currently the role supports Ubuntu only. It was tested with Ubuntu Xenial.

Docker image

This Ansible role is used to create Docker images which are available in Docker Hub as rnapuzzles/toolkit. If you are here just to use RNA-Puzzles Toolkit, you can use that image directly:

docker pull rnapuzzles/toolkit
docker run --publish 8888:8888 --name toolkit rnapuzzles/toolkit

The Jupyter notebook with RNA-Puzzles Toolkit examples will be available in your browser at address http://localhost:8888. The default password is demo. To kill the running container, execute:

docker kill toolkit

To access RNA-Puzzles Toolkit directly, start Docker image within a shell:

docker run --interactive --tty rnapuzzles/toolkit /bin/bash

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How to build and use Docker container image with RNA-Puzzles Toolkit

The repository contains configuration for ansible-container which uses roles and docker-compose-like syntax to describe creation of container images using Ansible.

Step 1: Install ansible-container

virtualenv venv
source venv/bin/activate
git clone https://github.com/ansible/ansible-container.git
pip install -e ansible-container

Step 2: Build the image

cd toolkit-ansible-role
ansible-container build

Step 3: Run the container

docker run --publish 8888:8888 --name toolkit rna-puzzles-toolkit 

To kill the running container, execute:

docker kill toolkit

Step 4: Explore RNA-Puzzles Toolkit

Open http://localhost:8888 browser and use default demo password. Explore the various Jupyter notebooks which demonstrate capabilities of RNA-Puzzles Toolkit.

Step 5 (optional): Directly use RNA-Puzzles Toolkit

You may wish to override default command of running Jupyter notebooks and work with the RNA-Puzzles Toolkit directly. To do so, run Docker with a shell command:

docker run --interactive --tty rna-puzzles-toolkit /bin/bash

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How to install RNA-Puzzles Toolkit in the cloud

The steps below describe a process of installation of RNA-Puzzles Toolkit on a cloud host. The assumption is that the machine has Ubuntu installed with ubuntu user having sudo capabilities. Please change site.yml to suit the configuration for your own needs.

Step 1: Install Ansible

Install Ansible using your OS way of package management.

Step 2: Configure your host

Edit /etc/ansible/hosts and add group ubuntu with the IP of your cloud-enabled machine:

[ubuntu]
192.168.1.1

Step 3: Configure your host

For Ansible to work, you need to be able to connect via SSH in a password-less manner as ubuntu user. And you need to have Python installed on the machine. Make sure these requirements are met.

Step 4: Apply Ansible role to the host

cd toolkit-ansible-role
ansible-playbook site.yml