A packer.io configuration for building out Galaxy (http://galaxyproject.org/) tool development environments.
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README.md

planemo-machine

A set of packer and ansible configuration files and scripts used to build Ubuntu environment for Galaxy tool development.

Build Status

Setup

This project makes use of git submodules and before you build any planemo machines, you'll need to initialize them:

make init

This will simply execute the following command git submodule init && git submodule update.

Example Uses

  • Build and register Vagrant box (named planemo).

make vagrant

  • Build a virtualbox OVA for this vagrant box.

make virtualbox

The virtualbox OVA unlink the other variants will include a graphical environment (Xubuntu) tailored for development (auto logins to the ubuntu user, configured with tools such as Komodo).

  • Build a modified variant of the recipes with a Dockerfile directly (skipping packer). Skipping packer makes it easier to iterate on and applicable for tools like Docker Hub, the cost is some amount of duplication between the Dockerfile in this directory and provision.yml.

make docker

To override the Docker command to use sudo for instance do

make docker DOCKER_COMMAND='sudo docker'

  • Build docker image using development Dockerfile (dev.Dockerfile). This Dockefile is broken out into more steps and will result in a much larger final container but can be quicker to develop against since the individual steps are checkmarked.

make docker-dev

  • Build Docker image (using packer directly).

make docker-via-packer

The VM version of this build process will enable Docker by default - but when building a Docker image we disable this so the developer doesn't need to configure docker-in-docker functionality.

packer build -var 'gce_project_id=<PROJECT_ID>' --only googlecompute packer.json

  • Build Amazon Web Services AMI (untested).

packer build -var 'ami_access_key=<AWS ACCESS KEY>' -var 'ami_secret_key=<AWS SECRET KEY>' --only googlecompute packer.json

How it works

The file packer.json contains a description of steps to execute to provision a box - broken out by where it is being provisioned (Docker, AWS,GCE, etc...). The main step is the ansible provisioning step preceeded immediately by the execution of the setup_ansible.sh script. These steps are executed for all platforms. To get to that point however, the RAW image needs to be configured - basically an Ubuntu 14.04 machine needs to be created with a password-less sudoing user (defaulting to ubuntu but overridable using -var 'username=XXX' argument to packer - see for instance vagrant_create_box.sh script which overrides this to be ubuntu).

The Ansible roles used to provision the box are found in roles and the ansible playbook used to specify and configure them is provision.yml. Overview of the roles:

  • galaxyprojectdotorg.cloudmanimage A subset of the CloudMan image role, hopefully this can be refactored an trimmed down so this project and CloudMan can share the same base (via Ansible Galaxy or gitsubmodules).

  • galaxyprojectdotorg.cloudmandatabase The database role from CloudMan (maybe with added defaults that should be backported). Used to create postgres database.

  • galaxyprojectdotorg.galaxy Nate's Galaxy image - clones Galaxy, fetches eggs, sets up static configuration, etc...

  • galaxyprojectdotorg.galaxyextras New role created by extracting and generalizing stuff in Bjoern's Galaxy stable. Sets up Slurm, Proftp, Supervisor, uwsgi, nginx.

  • galaxyprojectdotorg.devbox New role created explicitly for allocating a development box. Install linuxbrew, planemo, and a codebox IDE.

  • galaxyprojectdotorg.trackster, smola.java - these are modified roles from CloudMan that work but seem less important for the devbox. They are commented out in provision.yml but should be added back in once things stabilize to unify CloudMan and this project.

Ideas and code borrowed from various places