Laniakea Galaxy

Ansible role to install Galaxy 23.0 using roles developed by the Galaxy community.

Requirements

Required roles:

• src: galaxyproject.galaxy version: 0.10.14
• src: galaxyproject.nginx version: 0.7.1
• src: galaxyproject.postgresql version: 1.1.2
• src: galaxyproject.postgresql_objects version: 1.2.0
• src: geerlingguy.pip version: 2.0.0
• src: galaxyproject.miniconda version: 0.3.1
• src: usegalaxy_eu.certbot version: 0.1.11
• src: galaxyproject.tusd version: 0.0.1
• src: galaxyproject.cvmfs version: 0.2.14

Ansible-version

tested with : Ansible 4.10.0 with Ansible core 2.11.12

Tasks

main.yml includes all necessary sub-roles

pre_tasks.yml calls OS-specific set of pre_tasks: for CentOS7 or RockyLinux9

Variables

• Laniakea variables: vars/main.yml
• Default variables (Admin, paths): defaults/mail.yml
• Role-specific varibles are in the tasks files:
  • PostgeSQL: tasks/postgresql_objects.yml
  • NGINX: tasks/nginx.yml
  • Galaxy: tasks/install_galaxy_role_vars.yml
  • TUSD: tasks/tusd.yml and partially in tasks/install_galaxy_role_vars.yml

Local Test Execution

# on a blank VM
# install requirements
sudo yum install -y git pip vim
pip install ansible==4.10.0 ansible-core==2.11.12
# clone repo
git clone <repo_path>
# copy test playbook
cp ansible-role-laniakea-galaxy/tests/test.yml test.yml
# update hostname and asnible user
vim inventory
ansible-galaxy install -r ansible-role-laniakea-galaxy/requirements.yml
cd ../
# run playbook
ansible-playbook -i ansible-role-laniakea-galaxy/inventory test.yml

Logs:

• <galaxy_install_path>/var/gravity/log/ (with the default paths /home/galaxy/galaxy/var/gravity/log/) - Gravity log files:
  • gunicorns
  • handlers
  • celery
  • tusd
  • interactive tools (if enabled)
• sudo journalctl -u galaxy all Galaxy logs (come from supervisor, located at /home/galaxy/galaxy/var/gravity/supervisor/supervisord.log)

Example Playbook

 ---

 - hosts: galaxyservers
   become: true
   vars:
     GALAXY_ADMIN_USERNAME: ""
     GALAXY_ADMIN_PASSWORD: ""
     GALAXY_ADMIN_API_KEY: ""
     GALAXY_ADMIN_EMAIL: ""
   roles:
     - ansible-role-laniakea-galaxy

License

Apache Licence v2

http://www.apache.org/licenses/LICENSE-2.0

Author Information

Pietro Mandreoli email: [email protected] Polina Khmelevskaia: [email protected]