Galaxy-tools (deprecated)¶
This ansible role has been cloned from the official galaxyproject.galaxy-tools, with small changes.
This Ansible role is for automated installation of tools from a Tool Shed into Galaxy.
When run, this role will create an execution environment, install ephemeris and invoke the shed-install command to install desired tools into Galaxy. The list of tools to install is provided in files/tool_list.yaml file.
Example Playbook¶
To use the role, you need to create a playbook and include the role in it.
- hosts: localhost
gather_facts: False
connection: local
vars:
galaxy_tools_tool_list_files: [ "files/sample_tool_list.yaml" ]
galaxy_tools_galaxy_instance_url: http://127.0.0.1:8080/
# galaxy_tools_api_key: <API key for Galaxy admin user>
roles:
- indigo-dc.galaxy-tools
Example Tool list¶
For each tool you want to install, you must provide tool name
and owner
and one between tool_panel_section_id
and tool_panel_section_label
in the yaml tool list.
---
api_key: <Admin user API key from galaxy_instance>
galaxy_instance: <Galaxy instance IP>
tools:
- name: fastqc
owner: devteam
tool_panel_section_label: 'Tools'
install_resolver_dependencies: True
install_tool_dependencies: False
- name: 'bowtie_wrappers'
owner: 'devteam'
tool_panel_section_label: 'Tools'
install_resolver_dependencies: True
install_tool_dependencies: False
Variables¶
Required variables¶
Only one of the two variables is requried (if both are set, the API key takes precedence and a bootstrap user is not created):
galaxy_tools_api_key
: the Galaxy API key for an admin user on the target Galaxy instance (not required if the bootstrap user is being created)
galaxy_tools_admin_user_password
: a password for the Galaxy bootstrap user (required only if galaxy_install_bootstrap_user variable is set)
Optional variables¶
See defaults/main.yml for the available variables and their defaults.
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:
galaxy_tools_install_tools
: (default: yes) whether or not to run the tools installation script
galaxy_tools_create_bootstrap_user
: (default: no) whether or not to create a bootstrap Galaxy admin user
galaxy_tools_delete_bootstrap_user
: (default: no) whether or not to delete a bootstrap Galaxy admin user
References¶
galaxyproject.galaxy-tools: https://github.com/galaxyproject/ansible-galaxy-tools
Ephemeris: https://github.com/galaxyproject/ephemeris
galaxy-tools-playbook: https://github.com/afgane/galaxy-tools-playbook