regalaxy_tools_install.yml

---
- hosts: galaxyservers
  become: true
  become_user: root
  tasks:
    ## Install required Galaxy tools
    - name: Install required tools - create Ephemeris venv
      ansible.builtin.shell:
        cmd: python3 -m venv ~/ephemeris_venv
    - name: Install required tools - install Ephemeris
      ansible.builtin.shell:
        cmd: source ~/ephemeris_venv/bin/activate && pip install ephemeris
    - name: Install required tools - install Galaxy tools
      ansible.builtin.shell:
        cmd: ~/ephemeris_venv/bin/shed-tools install -g https://{{ inventory_hostname }}{{ csnt_galaxy_url_prefix }} -a {{ api_key }} -t {{ playbook_dir }}/files/{{ inventory_hostname }}/regalaxy_tool_list.yaml
      when: "inventory_hostname in ['repeatexplorer-elixir.cerit-sc.cz', 'galaxy-re.grid.cesnet.cz']"
    - name: Set-up pre-defined integrated_tool_panel config file on RE instance only
      ansible.builtin.copy:
        src: "{{ playbook_dir }}/files/{{ inventory_hostname }}/regalaxy_integrated_tool_panel.xml"
        dest: "{{ galaxy_mutable_config_dir }}/integrated_tool_panel.xml"
        owner: "{{ galaxy_user_name }}"
        group: "{{ galaxy_user_group_name }}"
        mode: '0644'
        backup: true
      when: "inventory_hostname in ['repeatexplorer-elixir.cerit-sc.cz', 'galaxy-re.grid.cesnet.cz']"
    - name: Restart galaxy
      become: true
      become_user: root
      ansible.builtin.command: galaxyctl restart