galaxyXpand simplification and consistency (#48)

* Gathering common variables in 000_cross_env_vars

* Merging common and specific galaxy_config dictionaries

* Update playbook.yml

* put conda default to 23.11

* add nginx_conf_user variable in the playbook (nginx role )

* nginx reverse proxy stays to port 4000 for dev_gce

* GALAXY release 23.1

* galaxy_manage_systemd "false" in docker group_vars

* simplification of gce and docker envs

* simplify env dev_mississippi

* simplify conect

* Update welcome.html.j2

* simplification of Mississippi environment

* Update welcome.html.j2

* fix Conect welcome page

* fix dev_mississippi welcome page

* simplification of ARTbio environment

.github/workflows/test_playbook.yaml

@@ -75,10 +75,13 @@ jobs:
 
     - name: Sleep for 30 secs and check galaxyctl status
       run: |
+        sudo sed -E -i 's/www-data/galaxy/' /etc/nginx/nginx.conf
+        sudo systemctl restart nginx.service
         sudo galaxyctl graceful
         echo "waiting 30 sec" && sleep 30
+        sudo cat /etc/nginx/nginx.conf
+        sudo cat /home/galaxy/galaxy/config/galaxy.yml
         sudo galaxyctl status
-# sudo su - galaxy -c "source galaxy/.venv/bin/activate && galaxyctl status"
 
     - name: check Galaxy API is alive
       run: |

environments/000_cross_env_vars

@@ -2,16 +2,93 @@
 # Python 3 support
 pip_virtualenv_command: /usr/bin/python3 -m venv
 
-# Common variables needed by all hosts
-galaxy_user_name: galaxy
-galaxy_db_name: galaxy
-
-
-# galaxy (check requirement)
-galaxy_config_perms: 0664
-
 # to install uptime set to 'yes'
 install_uptime: no
 
-# to not install slurm set to 'no'
+# to install slurm set to 'yes'
 install_slurm: yes
+
+# nginx.conf File
+nginx_conf_user: "www-data galaxy"
+
+# systemd
+galaxy_manage_systemd: true
+
+# Galaxy common to all hosts
+galaxy_commit_id: release_23.1
+galaxy_user_name: galaxy
+galaxy_db_name: galaxy
+galaxy_config_perms: 0664
+galaxy_additional_venv_packages: drmaa
+galaxy_create_user: true
+galaxy_separate_privileges: true
+galaxy_privsep_user: "{{ galaxy_user }}"
+galaxy_layout: legacy
+galaxy_root: /home/galaxy
+galaxy_server_dir: "{{ galaxy_root }}/galaxy"
+galaxy_user: {name: galaxy, shell: /bin/bash}
+galaxy_mutable_data_dir: "{{ galaxy_server_dir }}/database"
+galaxy_mutable_config_dir: "{{ galaxy_server_dir }}/config"
+galaxy_config_dir: "{{ galaxy_server_dir }}/config"
+galaxy_config_file: "{{ galaxy_config_dir }}/galaxy.yml"
+galaxy_force_checkout: true
+galaxy_venv_dir: "/home/galaxy/galaxy/.venv"
+miniconda_prefix: "{{ galaxy_tool_dependency_dir }}/_conda"
+miniconda_version: 23.11
+miniconda_channels: ['conda-forge', 'bioconda', 'defaults']
+
+common_galaxy_config:
+  galaxy:
+    admin_users: [email protected],[email protected]
+    builds_file_path: shared/ucsc/builds.txt
+    database_connection: "postgresql:///galaxy?host=/var/run/postgresql"
+    display_servers: hgw1.cse.ucsc.edu,hgw2.cse.ucsc.edu,hgw3.cse.ucsc.edu,hgw4.cse.ucsc.edu,hgw5.cse.ucsc.edu,hgw6.cse.ucsc.edu,hgw7.cse.ucsc.edu,hgw8.cse.ucsc.edu,lowepub.cse.ucsc.edu
+    file_path: datasets
+    job_config_file: "{{ galaxy_config_dir }}/job_conf.yml"
+    object_store_store_by: id
+    tool_data_path: "{{ galaxy_server_dir }}/tool-data"
+    # SQL Performance
+    slow_query_log_threshold: 5
+    enable_per_request_sql_debugging: true
+    # File serving perfomance
+    nginx_x_accel_redirect_base: /_x_accel_redirect
+    static_enabled: false
+    # Automation / Ease of Use / User-facing features
+    watch_job_rules: 'auto'
+    watch_tool_data_dir: true
+    watch_tools: 'true'
+    allow_path_paste: true
+    enable_quotas: true
+    allow_user_dataset_purge: true
+    allow_user_deletion: true
+    show_welcome_with_login: true
+    expose_user_name: true
+    expose_dataset_path: true
+    expose_potentially_sensitive_job_metrics: true
+    # Debugging
+    cleanup_job: onsuccess
+    allow_user_impersonation: true
+    # Tool security
+    outputs_to_working_directory: true
+    new_user_dataset_access_role_default_private: true # Make datasets private by default
+  gravity:
+    process_manager: systemd
+    galaxy_root: "{{ galaxy_server_dir }}"
+    galaxy_user: "{{ galaxy_user_name }}"
+    virtualenv: "{{ galaxy_venv_dir }}"
+    gunicorn:
+      # default galaxyXpand listening option
+      bind: "unix:{{ galaxy_config_dir }}/gunicorn.sock"
+      # default galaxyXpand workers
+      workers: 2
+      # Other options that will be passed to gunicorn
+      extra_args: '--forwarded-allow-ips="*"'
+      # This lets Gunicorn start Galaxy completely before forking which is faster.
+      # https://docs.gunicorn.org/en/stable/settings.html#preload-app
+      preload: true
+    handlers:
+      handler:
+        processes: 2
+        pools:
+          - job-handler
+          - workflow-scheduler