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This role is used to setup Trackster genome browser in Galaxy.

Requirements

The role has been developed and tested on Ubuntu 16.04 and 18.04. It uses sudo.

Variables

  • galaxy_manage_trackster: (default: yes) if set, the role will run
  • galaxy_user_name: (default: galaxy) system username used for Galaxy
  • galaxy_server_dir: (default: /galaxy/server) the base path under which the galaxy file system is planned to be placed
  • galaxy_custom_tools_dir: (default: /galaxy/server/.venv/bin) System path where Trackster utility tools will be installed. This path should be on the galaxy system user $PATH.
  • download_len_files: (default: yes) if set, download .len files
  • bedtools_version: (default: 2.29.2) the version of BED tools to download

Dependencies

None.

Example Playbook

To use the role, wrap it into a playbook as follows (the following assumes the role has been placed into directory roles/trackster):

- hosts: galaxy-builder
  become: yes
  vars:
    galaxy_custom_tools_dir: /home/galaxy/galaxy/.venv/bin
    galaxy_server__dir: /home/galaxy/galaxy
  pre_tasks:
    - name: Assure galaxy dir exists
      file: path={{ galaxy_server_dir }} state=directory owner={{ galaxy_user_name }} group={{ galaxy_user_name }}
      become_user: root
  roles:
    - role: trackster

Next, create a hosts file:

[galaxy-builder]
130.56.250.204 ansible_ssh_private_key_file=key.pem ansible_ssh_user=ubuntu # substitute with you target ip

Finally, run the playbook as follows:

$ ansible-playbook playbook.yml -i hosts