https://github.com/galaxyproject/planemo-machine

A packer.io configuration for building out Galaxy (http://galaxyproject.org/) tool development environments.
https://github.com/galaxyproject/planemo-machine

docker-image planemo-machine usegalaxy virtualbox-ova

Last synced: about 1 year ago
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A packer.io configuration for building out Galaxy (http://galaxyproject.org/) tool development environments.

• Host: GitHub
• URL: https://github.com/galaxyproject/planemo-machine
• Owner: galaxyproject
• Created: 2015-01-16T03:30:12.000Z (over 11 years ago)
• Default Branch: master
• Last Pushed: 2020-12-29T03:40:00.000Z (over 5 years ago)
• Last Synced: 2024-04-09T21:49:25.655Z (about 2 years ago)
• Topics: docker-image, planemo-machine, usegalaxy, virtualbox-ova
• Language: HTML
• Size: 246 KB
• Stars: 10
• Watchers: 33
• Forks: 16
• Open Issues: 26
• Metadata Files:
  • Readme: README.md

Awesome Lists containing this project

• awesome-galaxy - Planemo Machine

README

          
planemo-machine

=====================

A set of [packer](http://packer.io) and

[ansible](http://www.ansible.com/) configuration files and scripts

used to build [Ubuntu](http://www.ubuntu.com/) environment for

[Galaxy](http://galaxyproject.org) tool development.

[![Build Status](https://travis-ci.org/galaxyproject/planemo-machine.svg?branch=master)](https://travis-ci.org/galaxyproject/planemo-machine)

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](http://xubuntu.org/)) tailored for development (auto logins to the ``ubuntu`` user, configured with tools such as [Komodo](http://komodoide.com/komodo-edit/)).

 * 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.

 * Build Google Compute Engine image (untested). Follow instructions on

     https://www.packer.io/docs/builders/googlecompute.html, you will

     need to download your account file to gce_account.json (or set a

     path with ``-var 'gce_account_file=/path/to/account.json'``)

``packer build -var 'gce_project_id=' --only googlecompute packer.json``

 * Build Amazon Web Services AMI (untested).

``packer build -var 'ami_access_key=' -var 'ami_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

-------------------------------------------

 * https://github.com/galaxyproject/cloudman-image-playbook

 * https://github.com/bgruening/docker-galaxy-stable

 * https://www.packer.io/docs/

 * https://github.com/flomotlik/packer-example

 * https://github.com/eggsby/docker-ansible-packer