Galaxy servers playbook

sn06.yml → galaxy.yml

@@ -1,50 +1,8 @@
 ---
-- name: UseGalaxy.eu
-  hosts: sn06
+- name: Configure Galaxy servers
+  hosts: galaxy:!sn06.galaxyproject.eu
   become: true
   become_user: root
-  vars:
-    # The full internal name.
-    hostname: sn06.galaxyproject.eu
-    # The nginx user needed into the galaxyproject.nginx role
-    nginx_conf_user: galaxy
-    # This server has multiple CNAMEs that are important. Additionally it
-    # provides proxying for many of the other services run by Galaxy Europe.
-    # These server_names are passed to certbot. They generally should not need
-    # to be updated unless you add a new domain. They *only* work with the
-    # route53 provider, so if we want to do usegalaxy.xy, it may require
-    # refactoring / multiple certbot runs.
-    #
-    #
-    # The best way to expand them is to run the playbook, it will leave a message with the command it would have run (look for `skipped, since /etc/letsencrypt/renewal/usegalaxy.eu.conf exists`)
-    #
-    # Then take this command to the command line (root@sn04) and run it with `--expand`. E.g. (DO NOT COPY PASTE (in case the config changes))
-    #
-    # $ /opt/certbot/bin/certbot certonly --non-interactive --dns-route53 \
-    #     -m [email protected] --agree-tos -d 'usegalaxy.eu,*.usegalaxy.eu,galaxyproject.eu,*.galaxyproject.eu,*.interactivetoolentrypoint.interactivetool.usegalaxy.eu,*.interactivetoolentrypoint.interactivetool.live.usegalaxy.eu,*.interactivetoolentrypoint.interactivetool.test.usegalaxy.eu' --expand
-    # Saving debug log to /var/log/letsencrypt/letsencrypt.log
-    # Credentials found in config file: ~/.aws/config
-    # ....
-    # IMPORTANT NOTES:
-    #  - Congratulations! Your certificate and chain have been saved at:
-    #
-    # And you're done expanding the certs.
-    #
-    # The nginx user needed into the galaxyproject.nginx role
-    server_names:
-      - "usegalaxy.eu"
-      - "*.usegalaxy.eu"
-      - "galaxyproject.eu"
-      - "*.galaxyproject.eu"
-      - "*.interactivetoolentrypoint.interactivetool.usegalaxy.eu"
-      - "*.interactivetoolentrypoint.interactivetool.live.usegalaxy.eu"
-      - "*.interactivetoolentrypoint.interactivetool.test.usegalaxy.eu"
-      - "*.aqua.usegalaxy.eu"
-      - "*.interactivetoolentrypoint.interactivetool.aqua.usegalaxy.eu"
-      - "*.ecology.usegalaxy.eu"
-      - "*.interactivetoolentrypoint.interactivetool.ecology.usegalaxy.eu"
-      - "*.earth-system.usegalaxy.eu"
-      - "*.interactivetoolentrypoint.interactivetool.earth-system.usegalaxy.eu"
   vars_files:
     - group_vars/tiaas.yml # All of the training infrastructure
     - group_vars/gxconfig.yml # The base galaxy configuration
@@ -63,68 +21,38 @@
     - mounts/mountpoints.yml
   handlers:
     - name: Restart Galaxy
-      shell: |
-        cd /opt/galaxy/ && source /opt/galaxy/.bashrc  && /usr/bin/gxadmin gunicorn handler-restart && sudo -u galaxy /usr/bin/galaxy-sync-to-nfs && systemctl restart galaxy-handler@* && systemctl restart galaxy-workflow-scheduler@*
+      shell:
+        chdir: /opt/galaxy
+        cmd: |
+          source /opt/galaxy/.bashrc && \
+            /usr/bin/gxadmin gunicorn handler-restart && \
+            sudo -u galaxy /usr/bin/galaxy-sync-to-nfs && \
+            systemctl restart galaxy-handler@* && \
+            systemctl restart galaxy-workflow-scheduler@*
       listen: "restart galaxy"
   pre_tasks:
-    - name: Install Dependencies
-      package:
+    # TODO: Use usegalaxy_eu.packages to manage role dependencies.
+    - name: Install dependencies.
+      ansible.builtin.package:
         name:
-          [
-            "git",
-            "postgresql",
-            "python3-psycopg2",
-            "python3-virtualenv",
-            "bc",
-            "python38",
-            "python38-devel",
-          ]
-      become: true
+          - git
+          - postgresql
+          - python3-psycopg2
+          - python3-virtualenv
+          - bc
+          - python38
+          - python38-devel
+        state: present
+
     - name: Set default version of Python
       alternatives:
         name: python
         path: /usr/bin/python3
+
     - name: Disable SELinux
       selinux:
         state: disabled
-    - name: Inject custom Pulsar build in the Galaxy requirements file (HTCondor migration).
-      # This Pulsar build makes the `condor_rm` and `condor_submit` commands configurable.
-      # See https://github.com/kysrpex/pulsar/commits/condor_manager_prefix_option for more details.
-      block:
-        - name: Allocate a temporary directory.
-          ansible.builtin.tempfile:
-            prefix: ansible.galaxyproject.galaxy_requirements_file
-            state: directory
-          changed_when: false
-          register: galaxy_requirements_file_directory
-        - name: Clone Galaxy.
-          git:
-            dest: "{{ galaxy_requirements_file_directory.path }}/galaxy"
-            depth: 1
-            repo: "{{ galaxy_repo }}"
-            version: "{{ galaxy_commit_id }}"
-            executable: "{{ git_executable | default(omit) }}"
-          changed_when: false
-        - name: Retrieve the requirements file.
-          ansible.builtin.copy:
-            remote_src: true
-            src: "{{ galaxy_requirements_file_directory.path }}/galaxy/lib/galaxy/dependencies/pinned-requirements.txt"
-            dest: "{{ galaxy_requirements_file_directory.path }}/requirements.txt"
-          changed_when: false
-        - name: Replace `pulsar-galaxy-lib` with a patched version in the requirements file.
-          ansible.builtin.lineinfile:
-            path: "{{ galaxy_requirements_file_directory.path }}/requirements.txt"
-            regexp: 'pulsar-galaxy-lib'
-            line: 'git+https://github.com/kysrpex/pulsar.git@condor_manager_prefix_option#egg=pulsar-galaxy-lib ; python_version >= "3.7" and python_version < "3.12"'
-        - name: Configure the Galaxy role to use the modified version of the requirements file.
-          ansible.builtin.set_fact:
-            galaxy_requirements_file: "{{ galaxy_requirements_file_directory.path }}/requirements.txt"
-      always:
-        - name: Remove the Galaxy clone.
-          changed_when: false
-          ansible.builtin.file:
-            path: "{{ galaxy_requirements_file_directory.path }}/galaxy"
-            state: absent
+
   post_tasks:
     - name: Append some users to the systemd-journal group
       user:
@@ -135,7 +63,8 @@
         - "{{ galaxy_user.name }}"
         - "telegraf"
         - "stats" # special account to retrieve statistics from the server in read-only mode
-    - name: Set authorized SSH key (galaxy user)
+
+    - name: Set authorized SSH keys (galaxy user)
       ansible.posix.authorized_key:
         user: "{{ galaxy_user.name }}"
         state: present
@@ -148,7 +77,8 @@
         - https://github.com/wm75.keys
         - https://github.com/gmauro.keys
         - "{{ galaxy_user_public_key }}"
-    - name: Set authorized SSH key (stats user)
+
+    - name: Set authorized SSH keys (stats user)
       ansible.posix.authorized_key:
         user: "stats"
         state: present
@@ -180,7 +110,7 @@
 
     ## Install miniconda, create a _galaxy_ environment and install Packages
     ## Galaxy will use the virtualenv from this conda environment (see
-    ## galaxy_virtualenv_command) in the group_vars/sn06.yml
+    ## galaxy_virtualenv_command) in the group_vars/galaxy.yml
     - role: galaxyproject.miniconda
       vars:
         miniconda_prefix: "{{ conda_prefix }}"
@@ -225,9 +155,6 @@
     ## Setup docker
     - geerlingguy.docker
 
-    # HTCondor Cluster setup
-    - usegalaxy_eu.htcondor
-
     # Misc.
     - role: hxr.galaxy-nonreproducible-tools
       become: true