galaxyproject.cloudman-galaxy-setup

This role sets up Galaxy to work with CloudMan.

Requirements

There are no specific requirements, but it's meant to be used with the larger CloudMan playbook. You might also want to look at the Galaxy Tools role because it's helpful to run after this role.

Variables

Optional Variables

Some of these variables should match similarly named ones in the CloudMan playbook.

• galaxyFS_base_dir: (default: /mnt/galaxy) The main path for the Galaxy file system.
• galaxy_user_name: (default: galaxy) The system username for Galaxy.
• galaxy_server_dir: (default: /mnt/galaxy/galaxy-app) The main location where the Galaxy application is stored.
• galaxy_venv_dir: (default: {{ galaxy_server_dir }}/.venv) The location of the virtual environment for Galaxy.
• galaxy_config_file: (default: {{ galaxy_server_dir }}/config/galaxy.ini) The main configuration file for Galaxy.
• cmg_setup_files: A list of files to copy from this role to Galaxy’s source tree. Check defaults/main.yml for the default files.
• cmg_extra_files: A way to copy additional user-defined files into Galaxy’s source tree. This starts as an empty list, but should be formatted like cmg_setup_files.

Control-flow Variables

Use these variables to control which parts of the role you want to run:

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

Dependencies

No dependencies.

Example Playbook

To use this role, create a playbook file named playbook.yml like this (assuming the role is in the directory roles/galaxyprojectdotorg.cloudman-galaxy-setup):

- hosts: galaxyFS-builder
  become: yes
  roles:
    - role: galaxyprojectdotorg.cloudman-galaxy-setup
      become_user: "{{ galaxy_user_name }}"

Next, create a hosts file:

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

Finally, run the playbook like this:

$ ansible-playbook playbook.yml -i hosts