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This Ansible role is for building the filesystem image required to run the GVL. It is likely to be used in the context of the GVL playbook.

Requirements

This role is largely intended to be used in the context of the larger GVL playbook. It must be run on a machine instance on which the GVL Image Role has already been executed.

Dependencies

This role depends on several roles, as defined in meta/main.yml. 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

Variables

Optional variables

Note that some of these variables should match equally named ones from the GVL playbook.

  • galaxyFS_base_dir: (default: /mnt/galaxy) the base path under which the galaxy file system is planned to be placed
  • galaxy_user_name: (default: galaxy) system username used for Galaxy
  • galaxy_server_dir: (default: /mnt/galaxy/galaxy-app) The default location where the Galaxy application is stored
  • galaxy_venv_dir: (default: {{ galaxy_server_dir }}/.venv) The location of virtual env used by Galaxy
  • galaxy_config_file: (default: {{ galaxy_server_dir }}/config/galaxy.ini) The location of Galaxy's main configuration file
  • cmg_setup_files: A list of files to be copied from this role into Galaxy's source tree. See defaults/main.yml for the defaults.
  • cmg_extra_files: Provides a hook to copy a list of extra, user-defined files into Galaxy's source tree. The default is an empty list, but should be in a format similar to cmg_setup_files.
Control-flow variables

Use the following control-flow variables to decide which parts of the role you'd like to run:

  • cm_setup_galaxy: (default: yes) whether to run the Galaxy setup step

Dependencies

None.

Example Playbook

To use the role, wrap it into a playbook file called playbook.yml as follows (the following assumes the role has been placed into directory roles/galaxyprojectdotorg.cloudman-galaxy-setup):

- hosts: gvl-filesystem-hosts
  become: yes
  roles:
    - role: gvl.ansible.filesystem
      become_user: "{{ galaxy_user_name }}"

Next, create a hosts file:

[gvl-filesystem-hosts]
130.56.250.204 ansible_ssh_private_key_file=key.pem ansible_ssh_user=ubuntu

Finally, run the playbook as follows:

$ ansible-playbook playbook.yml -i hosts

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Ansible role for the Genomics Virtual Lab filesystem

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