Ansible role for building the GVL machine image.
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README.md

This Ansible role is for building the machine image required to run the GVL. It is likely to be used in the context of the larger GVL playbook. Visit the GVL Playbook repository for overall build instructions for the GVL.

If you do not plan to make any customisations of the GVL build, and you are using an OpenStack based cloud, you do not need to build the image yourself and can download a publicly available image instead. See the GVL Playbook repo for a list of pre-built images.

Requirements

The role has been developed and tested on Ubuntu 14.04. It requires sudo access.

Dependencies

This role depends on the cloudman-image role, which in turn depends on several other roles. To satisfy these requirements it is necessary to install the required roles with the following commands (this will download the given roles from Ansible Galaxy and place them in roles subdirectory; unfortunately, Ansible does not have an option to have this done automatically):

$ ansible-galaxy install -r requirements_roles.txt -p roles

Role variables

All of the listed variabls are stored in defaults/main.yml. Check that file for all the available variables.

Individual variables can be set or overridden by setting them directly in a playbook for this role (see an example below for vnc_password). Alternatively, they can be set by creating group_vars directory in the root directory of the playbook used to execute this role and placing a file with the variables there. Note that the name of this file must match the value of hosts setting in the corresponding playbook (e.g., image-builder for the sample playbook provided below).

Required variables

  • vnc_password: a password that will be baked into the image and used as a bridge bewteen VNC and noVNC servers
  • psql_galaxyftp_password: a password that will also be baked into the image and allows Galaxy to authenticate FTP users

Optional variables

  • galaxy_user_name: (default: galaxy) system username to be used for Galaxy
  • galaxyFS_base_dir: (default: /mnt/galaxy) the base path under which the galaxy file system will be placed
  • galaxy_server_dir: (default: "{{ galaxyFS_base_dir }}/galaxy-app") the location where the Galaxy application will be placed
  • galaxy_db_dir: (default: "{{ galaxyFS_base_dir }}/db") the location wher Galaxy's PostgreSQL database will be placed
  • galaxy_db_port: (default: 5930) the port set for Galaxy's PostgrSQL database
  • postgresql_bin_dir: (default: /usr/lib/postgresql/9.3/bin) the path where PostgreSQL binary files are stored. This path will be added to $PATH.
  • nginx_upload_store_path: (default: "{{ galaxyFS_base_dir }}/upload_store") the path to which Nginx's configuration for the upload_store will be set
  • indicesFS_base_dir: (default: /mnt/galaxyIndices) the path where Galaxy reference genomes indices will be stored. Also Galaxy Data Managers will be installed here (via the Tool Shed, as designed by Galaxy).

Control flow variables

The following variables can be set to either yes or no to indicate if the given part of the role should be executed:

  • cm_install_packages: (default: yes) install system level packages
  • cm_system_environment: (default: yes) setup system-level configurations
  • cm_system_tools: (default: yes) install given tools system wide
  • cm_install_s3fs: (default: yes) whether to install S3FS or not
  • cm_configure_nginx: (default: yes) whether to configure Nginx
  • cm_install_proftpd: (default: yes) whether to install ProFTPd server
  • cm_install_novnc: (default: no) whether to install and configure VNC and noVNC bridge for in-browser remote desktop. Note that there are issues with setting this on AWS due to how AWS exposes graphics card hardware.
  • cm_install_r_packages: (default: yes) whether to install R and Bioconductor packages
  • cleanup: (default: no) whether to clean up the instance and make it ready for bundling into an image. This must be set before an image is created!
  • only_cleanup: (default: no) when set, only the cleanup tasks will run and no other. This is primarily intended to be set as a command line variable.

Example playbook

To use the role, it is necessary to launch a cloud instance, create a hosts file that contains access information for the instance, for example:

[image-builder]
130.56.250.204 ansible_ssh_private_key_file=key.pem ansible_ssh_user=ubuntu

Next, set any variables as desired and place the role into a playbook file (e.g., playbook.yml). This playbook assumes the role has been placed into roles/galaxyprojectdotorg.cloudman-image directory:

- hosts: image-builder
  become: yes
  roles:
    - galaxyprojectdotorg.cloudman-image
      vnc_password: <some_password>
      psql_galaxyftp_password: <a_different_password>

Finally, run the playbook with:

$ ansible-playbook playbook.yml -i hosts [--extra-vars cleanup=yes]

NOTE: setting the cleanup variable will disable ssh access to the current instance! While this is not set as the default value, an instance must be cleaned before creating an image.

Upon completion, an image can be created using the cloud console.