GCC BOSC 2018

galaxy_ansible_install.sh

#!/bin/bash
sudo pip install ansible
git clone https://github.com/ARTbio/GalaxyKickStart
cd GalaxyKickStart
git checkout 2018-gccbosc
ansible-galaxy install -r requirements_roles.yml -p roles --force
cat <<EOT >> group_vars/gccbosc18.yml
galaxy_root_dir: /srv/galaxy
galaxy_server_dir: "{{ galaxy_root_dir }}/server"
galaxy_venv_dir: "{{ galaxy_root_dir }}/venv"
galaxy_mutable_data_dir: "{{ galaxy_data }}"
proftpd_files_dir: "{{ galaxy_data }}/ftp"
galaxy_config_dir: "{{ galaxy_root_dir }}/config"
galaxy_mutable_config_dir: "{{ galaxy_config_dir }}"
galaxy_shed_tools_dir: "{{ galaxy_root_dir }}/shed_tools"
galaxy_tool_dependency_dir: "{{ galaxy_root_dir }}/dependencies"
tool_dependency_dir: "{{ galaxy_tool_dependency_dir }}"
galaxy_job_conf_path: "{{ galaxy_config_dir }}/job_conf.xml"
galaxy_job_metrics_conf_path: "{{ galaxy_config_dir }}/job_metrics_conf.xml"
nginx_upload_store_path: "{{ galaxy_data }}/upload_store"
tool_data_table_config_path: "{{ galaxy_config_dir }}/tool_data_table_conf.xml,/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml"
len_file_path: "{{ galaxy_config_dir }}/len"
galaxy_log_dir: "{{ galaxy_root_dir }}/log"
supervisor_slurm_config_dir: "{{ galaxy_log_dir }}"

galaxy_manage_trackster: False
galaxy_extras_config_cvmfs: True
galaxy_restart_handler_enabled: True
galaxy_mule_handlers: True
galaxy_handler_processes: 1

galaxy_config_style: yaml
galaxy_config_file: "{{ galaxy_config_dir }}/galaxy.yml"

galaxy_config:
  galaxy:
    database_connection: "{{ galaxy_db }}"
    file_path: "{{ galaxy_data }}/datasets"
    new_file_path: "{{ galaxy_data }}/tmp"
    galaxy_data_manager_data_path: "{{ galaxy_data }}/tool-data"
    job_config_file: "{{ galaxy_job_conf_path }}"
    ftp_upload_dir: "{{ proftpd_files_dir }}"
    ftp_upload_site: ftp://[server IP address]
    tool_data_table_config_path: "{{ tool_data_table_config_path }}"
    len_file_path: "{{ len_file_path }}"
    check_migrate_tools: False
  uwsgi:
    module: galaxy.webapps.galaxy.buildapp:uwsgi_app()
    logfile-chmod: 644


additional_files_list:
  - { src: "extra-files/galaxy-kickstart/logo.png", dest: "{{ galaxy_server_dir }}/static/images/" }
  - { src: "extra-files/tool_sheds_conf.xml", dest: "{{ galaxy_config_dir }}" }
  - { src: "extra-files/cloud_setup/vimrc", dest: "/etc/vim/" }
EOT

cat <<EOT >> inventory
[gccbosc18]
localhost ansible_connection=local
EOT

cat <<EOT >> galaxy.yml
- hosts: all
  become: yes
  gather_facts: False

  environment: "{{ proxy_env }}"

  handlers:
    - include: roles/handlers/galaxy.yml
      static: yes

  pre_tasks:
    - fail: msg="Installed ansible version {{ ansible_version.full }}, but ansible version later than 2.1 required"
      when: "{{ ansible_version.full | version_compare('2.1.0.0', '<') }}"
      tags:
        - always

    - raw: test -e /usr/bin/python || (apt -y update && apt install -y python-minimal)
      tags:
        - always

    - setup: # aka gather_facts
      tags:
        - always

    - set_fact:
        banner_img: "{% if 'jetstream' in group_names %}jetstream_text.png{% else %}gce_text.png{% endif %}"
    - name: Create galaxy system user
      user:
        name: "galaxy"
        home: "/srv/galaxy"
        skeleton: "/etc/skel"
        shell: "/bin/bash"
        system: yes
      tags:
          - always
  roles:

    - role: galaxyprojectdotorg.galaxy-os
      tags:
        - install_galaxy
        - install_packages

    - role: cloud_setup
      when: cloud_setup is defined

    - role: ensure_postgresql_up
      tags:
        - install_galaxy
        - manage_postgres

    - role: natefoo.postgresql_objects
      postgresql_objects_users:
        - name: "{{ galaxy_user_name }}"
          password: "{{ galaxy_user_name }}"
          encrypted: "yes"
      postgresql_objects_databases:
        - name: "{{ galaxy_user_name }}"
          owner: "{{ galaxy_user_name }}"
      become: yes
      become_user: postgres
      tags:
        - install_galaxy
        - manage_postgres

    - role: miniconda-role
      tags: conda
      become: yes
      become_user: "{{ galaxy_user_name }}"

    - role: galaxyprojectdotorg.galaxy
      become: yes
      become_user: "{{ galaxy_user_name }}"
      tags:
        - configure_galaxy
        - install_galaxy

    - role: set_supervisor_env_vars
      tags: env_vars

    - role: copy_additional_files
      tags:
        - install_extras

    # Installs supervisor, nginx and proftpd
    - role: galaxyprojectdotorg.galaxy-extras
      tags:
        - configure_server_stack
        - install_extras

    - role: ensure_postgresql_up
      tags:
        - manage_postgres
        - install_tools

    - role: galaxy.movedata
      tags:
        - persists_galaxy

    - role: galaxyprojectdotorg.trackster
      tags: configure_galaxy

    - role: galaxyprojectdotorg.galaxy-tools
      become: yes
      become_user: "{{ galaxy_user_name }}"
      tags: install_tools

    - role: run_data_manager_role
      tags:
        - install_data_managers
      when: gks_run_data_managers

  post_tasks:
    - name: Clean apt cache to recover some disk space
      shell: apt-get clean

    # htop is a placeholder here; see bug report
    # https://github.com/ansible/ansible-modules-core/issues/4029
    - name: Apt autoremove
      apt: autoremove=yes name=htop
EOT

ansible-playbook -i inventory galaxy.yml --tags "install_galaxy,install_extras"