install.yml

---

- name: Deploy miarka software
  hosts: deploy
  connection: local

  # These three variables needs to be overriden when calling ansible-playbook.
  #
  # Call with e.g. "ansible-playbook install.yml -e deployment_environment=staging -e deployment_version=foo".
  # If devel then the version will always be set to USERNAME_BRANCHNAME.
  # If staging or production then the playbook will halt if the folder version already exists.
  # I.e. the user will then manually have to remove the directory, OR add "-e deployment_override=true"
  # to deploy into an already existing folder.
  #
  # /vulpes/ngi/production/<latest|current> will link to /vulpes/ngi/production/<github release>
  # /vulpes/ngi/staging/ will contain a folder wild-wild-west which will be world writeable ON THE RECIEVING end. I.e. the
  # sync script will change the permissions? This is to make sure that not everyone that is able to login to miarka3 can
  # upload data into the cluster.

  pre_tasks:
    - fail:
        msg: "You must specify '-e site=<upps | sthlm>'"
      when: site is not defined or site is not in [ "upps", "sthlm" ]

    - include: tasks/set-paths.yml
      tags: always

    - include_vars:
        dir: env_vars
        files_matching: site_(all|{{ site }})_env_(all|{{ deployment_environment }}).yml$
      tags: always

    - include_vars:
        dir: env_secrets
        files_matching: site_(all|{{ site }})_env_(all|{{ deployment_environment }}).yml$
      tags: always

    - name: create {{ proj_root }} folder and configure setgid
      file:
        path: "{{ proj_root }}"
        group: "{{ ngi_group }}"
        state: directory
        recurse: no
        mode: g+rwXs,o-rwx
      when: deployment_environment in ["staging", "devel"]
      tags: always

    - name: create folder and configure setgid
      file:
        path: "{{ item }}"
        group: "{{ ngi_sw_group }}"
        state: directory
        recurse: no
        mode: g+rwXs,o=rX
      tags: always
      with_items:
        - "{{ root_path }}"
        - "{{ ngi_containers }}"
        - "{{ igenomes_dir }}"

    - name: initiate list of static folders that must be created on the target, after deployment
      set_fact:
        static_folders:
          - "{{ proj_root }}/{{ uppmax_project }}"
          - "{{ ngi_pipeline_path }}"
          - "{{ ngi_pipeline_nobackup }}"
          - "{{ ngi_pipeline_workdir }}"
          - "{{ ngi_log_path }}"
          - "{{ static_ngi_pipeline_path }}"
          - "{{ static_ngi_pipeline_nobackup }}"
          - "{{ static_ngi_log_path }}"
          - "{{ ngi_softlinks }}"
      tags: always

    - name: initiate list of static commands that must be run on the target, after deployment
      set_fact:
        static_commands: []
      tags: always

  environment:
    "{{ tools_path }}"

  roles:
    - { role: setup_base_config, tags: setup_base_config }
    - { role: ngi_pipeline, tags: ngi_pipeline }
    - { role: func_accounts, tags: func_accounts }
    - { role: nextflow, tags: nextflow }
    - { role: tarzan, tags: tarzan }
    - { role: taca, tags: taca }
    - { role: ngi_reports, tags: ngi_reports }
    - { role: multiqc, tags: multiqc }
    - { role: arteria-checksum-ws, tags: arteria-checksum }
    - { role: arteria-checkqc-ws, tags: arteria-checkqc }
    - { role: arteria-delivery-ws, tags: arteria-delivery }
    - { role: arteria-sequencing-report-ws, tags: arteria-sequencing-report }
    - { role: snpseq-metadata-service, tags: snpseq-metadata-service }
    - { role: standalone_scripts, tags: standalone_scripts }
    - { role: misc-tools, tags: misc-tools }
    - { role: archive-upload-ws, tags: archive-upload }
    - { role: archive-verify-ws, tags: archive-verify }
    - { role: nf-core, tags: nf-core }
    - { role: kraken2, tags: kraken2 }

  tasks:

    - name: Add miarka_provision version to deployed tools files
      lineinfile:
        dest: "{{ deployed_tool_versions }}"
        line: "-- Deployed at {{ ansible_date_time.iso8601 }}, miarka_provision ({{ (branch_name, branch_tag, branch_hash) | join('.') }}), by {{ deploy_user }} --"
      tags: always

    - name: create script for creating static folders
      template:
        src: create_static_contents.sh.j2
        dest: "{{ ngi_resources }}/create_static_contents_{{ site }}.sh"
        mode: +x
      tags: always

    - name: set correct file permission for everything in the deployment
      file:
        path: "{{ item }}"
        group: "{{ ngi_sw_group }}"
        state: directory
        recurse: yes
        mode: g+rwX,o=rX
      tags: always
      with_items:
        - "{{ root_path }}"
        - "{{ ngi_containers }}"
        - "{{ igenomes_dir }}"

  post_tasks:

    - debug:
        msg: Finished deploying to {{ root_path }}