24.2 is coming

galaxy/Dockerfile

@@ -15,7 +15,7 @@ ENV GALAXY_ROOT_DIR=/galaxy \
     GALAXY_VIRTUAL_ENV=/galaxy_venv \
     GALAXY_HOME=/home/galaxy \
     GALAXY_CONDA_PREFIX=/tool_deps/_conda \
-    MINIFORGE_VERSION=24.3.0-0
+    MINIFORGE_VERSION=24.9.2-0
 
 
 # Install miniforge and then virtualenv from conda
@@ -39,7 +39,7 @@ RUN curl -s -L https://github.com/conda-forge/miniforge/releases/download/$MINIF
 
 FROM build_base AS build_galaxy
 
-ARG GALAXY_RELEASE=release_24.1
+ARG GALAXY_RELEASE=release_24.2
 ARG GALAXY_REPO=https://github.com/galaxyproject/galaxy
 
 ENV NODE_OPTIONS=--max-old-space-size=4096
@@ -191,6 +191,8 @@ ENV GALAXY_CONFIG_MANAGED_CONFIG_DIR=$EXPORT_DIR/${GALAXY_ROOT_DIR#/}/database/c
     GALAXY_CONFIG_BOOTSTRAP_ADMIN_API_KEY=HSNiugRFvgT574F43jZ7N9F3 \
     GALAXY_CONFIG_BRAND="Galaxy Docker Build" \
     GALAXY_CONFIG_STATIC_ENABLED=False \
+    GALAXY_CONFIG_FILE_SOURCE_TEMPPLATES=$GALAXY_CONFIG_DIR/file_source_templates.yml \
+    GALAXY_CONFIG_VAULT_CONFIG_FILE=$GALAXY_CONFIG_DIR/vault_conf.yml \
     GALAXY_INTERACTIVE_TOOLS_CONFIG_FILE=$GALAXY_CONFIG_DIR/tool_conf_interactive.xml \
     # The following ENV var can be used to set the number of gunicorn workers
     GUNICORN_WORKERS=2 \

galaxy/ansible/files/production_b2drop.yml

@@ -0,0 +1,28 @@
+- id: b2drop
+  version: 0
+  name: B2DROP
+  description: |
+    B2DROP is a Nextcloud to sync and share your research data.
+  variables:
+    username:
+      label: Username / Account Name
+      type: string
+      help: |
+        The username or account name to use to connect to B2DROP. This is not your email address but the name show in the URL of your profile page.
+    writable:
+      label: Writable?
+      type: boolean
+      default: false
+      help: Allow Galaxy to write data to B2DROP.
+  secrets:
+    password:
+      label: Password
+      help: |
+        The password to use to connect to B2DROP.
+  configuration:
+    type: webdav
+    url: 'https://b2drop.bsc.es'
+    root: '/remote.php/dav/files/{{ variables.username }}'
+    login: '{{ variables.username }}'
+    writable: '{{ variables.writable }}'
+    password: '{{ secrets.password }}'

galaxy/ansible/galaxy_file_source_templates.yml

@@ -0,0 +1,25 @@
+- hosts: localhost
+  connection: local
+  remote_user: root
+  tasks:
+    - name: Install fs.webdavfs for Galaxy's file source plugins
+      pip:
+        name: "fs.webdavfs"
+        extra_args: "--index-url https://wheels.galaxyproject.org/simple/ --extra-index-url https://pypi.python.org/simple"
+        virtualenv: "{{ galaxy_venv_dir }}"
+      environment:
+        PYTHOPATH: null
+        VIRTUAL_ENV: "{{ galaxy_venv_dir }}"
+      become_user: "{{ galaxy_user_name }}"
+
+    - name: "Setup user configurable file source templates, also called BYOD"
+      template: src=file_source_templates.yml.j2 dest={{ galaxy_file_source_templates_config_file }} owner={{ galaxy_user_name }} group={{ galaxy_user_name }}
+
+    - name: "Copy B2Drop file source template"
+      ansible.builtin.copy:
+        src: "./files/production_b2drop.yml"
+        dest: "{{ galaxy_config_dir }}/production_b2drop.yml"
+        owner: "{{ galaxy_user_name }}"
+        group: "{{ galaxy_user_name }}"
+        mode: '0644'
+

galaxy/ansible/galaxy_object_store_templates.yml

@@ -0,0 +1,6 @@
+- hosts: localhost
+  connection: local
+  remote_user: root
+  tasks:
+    - name: "Setup user configurable object store templates, also called BYOS"
+      template: src=object_store_templates.yml.j2 dest={{ galaxy_object_store_templates_config_file }} owner={{ galaxy_user_name }} group={{ galaxy_user_name }}

galaxy/ansible/galaxy_vault_config.yml

@@ -0,0 +1,12 @@
+- hosts: localhost
+  connection: local
+  remote_user: root
+# You should change this key in production. You can generate Fernet keys with:
+#from cryptography.fernet import Fernet
+#Fernet.generate_key().decode('utf-8')
+  vars:
+    galaxy_vault_encryption_keys:
+      - pwiL08wXlpkBm-_Dr75aw1_uOPVA3HET1y7xrpynhKU=
+  tasks:
+    - name: "Configure Galaxy vault"
+      template: src=vault_conf.yml.j2 dest={{ galaxy_vault_config_file }} owner={{ galaxy_user_name }} group={{ galaxy_user_name }}

galaxy/ansible/group_vars/all.yml

@@ -16,6 +16,9 @@ galaxy_pbs: false
 galaxy_k8s_jobs: false
 galaxy_supervisor: true
 galaxy_job_metrics: true
+galaxy_file_source_templates: true
+galaxy_object_store_templates: true
+galaxy_vault_config: true
 galaxy_scripts: true
 galaxy_domain: "localhost"  # This is used by letsencrypt and Interactive Tools, set it to the domain name under which galaxy can be reached
 galaxy_startup: true
@@ -59,17 +62,20 @@ galaxy_k8s_jobs_pull_policy: IfNotPresent
 
 # Point at the existing Galaxy configuration.
 galaxy_server_dir: "/galaxy"
-galaxy_job_conf_path: "{{ galaxy_server_dir }}/config/job_conf.xml"
-galaxy_container_resolvers_conf_path: "{{ galaxy_server_dir }}/config/container_resolvers_conf.yml"
-galaxy_job_metrics_conf_path: "{{ galaxy_server_dir }}/config/job_metrics_conf.yml"
+galaxy_config_dir: "{{ galaxy_server_dir }}/config"
+galaxy_job_conf_path: "{{ galaxy_config_dir }}/job_conf.xml"
+galaxy_container_resolvers_conf_path: "{{ galaxy_config_dir }}/container_resolvers_conf.yml"
+galaxy_job_metrics_conf_path: "{{ galaxy_config_dir }}/job_metrics_conf.yml"
+galaxy_file_source_templates_config_file: "{{ galaxy_config_dir }}/file_source_templates.yml"
+galaxy_object_store_templates_config_file: "{{ galaxy_config_dir }}/object_store_templates.yml"
+galaxy_vault_config_file: "{{ galaxy_config_dir }}/vault_conf.yml"
 galaxy_user_name: "galaxy"
 galaxy_home_dir: "/home/{{ galaxy_user_name }}"
 galaxy_source_shellrc: false
 galaxy_user_shellrc: "{{ galaxy_home_dir }}/.bashrc"
 galaxy_logs_dir: "{{ galaxy_home_dir }}/"
 galaxy_venv_dir: "{{ galaxy_home_dir }}/venv"
 
-galaxy_config_dir: "{{ galaxy_server_dir }}/config"
 galaxy_config_file: "{{ galaxy_config_dir }}/galaxy.yml"
 galaxy_toolshed_config_file: "{{ galaxy_config_dir }}/tool_shed.yml"
 galaxy_tool_data_table_config_file: "{{ galaxy_config_dir }}/tool_data_table_conf.xml"

galaxy/ansible/provision.yml

@@ -70,3 +70,16 @@
 - import_playbook: galaxy_job_metrics.yml
   when: galaxy_job_metrics | bool
   tags: galaxy_job_metrics
+
+- import_playbook: galaxy_file_source_templates.yml
+  when: galaxy_file_source_templates | bool
+  tags: galaxy_file_source_templates
+
+- import_playbook: galaxy_object_store_templates.yml
+  when: galaxy_object_store_templates | bool
+  tags: galaxy_object_store_templates
+
+- import_playbook: galaxy_vault_config.yml
+  when: galaxy_vault_config | bool
+  tags: galaxy_vault_config
+

galaxy/ansible/rabbitmq.yml

@@ -2,7 +2,7 @@
   connection: local
   remote_user: root
   vars:
-    rabbitmq_version: 4.0.3
+    rabbitmq_version: 4.0.4
     rabbitmq_apt_repository: "deb [signed-by=/etc/apt/trusted.gpg.d/rabbitmq-9F4587F226208342.gpg] https://ppa1.rabbitmq.com/rabbitmq/rabbitmq-server/deb/{{ ansible_distribution | lower }} {{ ansible_distribution_release }} main"
     rabbitmq_apt_gpg_url: https://github.com/rabbitmq/signing-keys/releases/download/3.0/cloudsmith.rabbitmq-server.9F4587F226208342.key
     erlang_apt_repository: "deb [signed-by=/etc/apt/trusted.gpg.d/erlang-E495BB49CC4BBE5B.gpg] https://ppa1.rabbitmq.com/rabbitmq/rabbitmq-erlang/deb/{{ ansible_distribution | lower }} {{ ansible_distribution_release }} main"

galaxy/ansible/templates/file_source_templates.yml.j2

@@ -0,0 +1,10 @@
+- include: "{{ galaxy_server_dir }}/lib/galaxy/files/templates/examples/production_azure.yml"
+- include: "{{ galaxy_server_dir }}/lib/galaxy/files/templates/examples/production_ftp.yml"
+- include: "{{ galaxy_server_dir }}/lib/galaxy/files/templates/examples/production_s3fs.yml"
+- include: "{{ galaxy_server_dir }}/lib/galaxy/files/templates/examples/production_aws_private_bucket.yml"
+- include: "{{ galaxy_server_dir }}/lib/galaxy/files/templates/examples/production_aws_public_bucket.yml"
+- include: "{{ galaxy_server_dir }}/lib/galaxy/files/templates/examples/production_azure.yml"
+- include: "{{ galaxy_server_dir }}/lib/galaxy/files/templates/examples/production_dropbox.yml"
+- include: "{{ galaxy_server_dir }}/lib/galaxy/files/templates/examples/production_google_drive.yml"
+- include: "{{ galaxy_server_dir }}/lib/galaxy/files/templates/examples/production_webdav.yml"
+- include: "{{ galaxy_config_dir }}/production_b2drop.yml"

galaxy/ansible/templates/object_store_templates.yml.j2

@@ -0,0 +1,8 @@
+# This is a catalog file for all the user object store templates
+- include: "{{ galaxy_server_dir }}/lib/galaxy/objectstore/templates/examples/production_azure_blob.yml"
+- include: "{{ galaxy_server_dir }}/lib/galaxy/objectstore/templates/examples/production_aws_s3.yml"
+- include: "{{ galaxy_server_dir }}/lib/galaxy/objectstore/templates/examples/production_generic_s3.yml"
+- include: "{{ galaxy_server_dir }}/lib/galaxy/objectstore/templates/examples/production_gcp_s3.yml"
+- include: "{{ galaxy_server_dir }}/lib/galaxy/objectstore/templates/examples/cloudflare.yml"
+- include: "{{ galaxy_server_dir }}/lib/galaxy/objectstore/templates/examples/onedata.yml"
+- include: "{{ galaxy_server_dir }}/lib/galaxy/objectstore/templates/examples/minio_just_buckets.yml"

galaxy/ansible/templates/vault_conf.yml.j2

@@ -0,0 +1,11 @@
+type: database
+path_prefix: /galaxy
+# Encryption keys must be valid fernet keys
+# To generate a valid key:
+#
+# Use the ascii string value as a key
+# For more details, see: https://cryptography.io/en/latest/fernet/#
+encryption_keys:
+{% for encryption_key in galaxy_vault_encryption_keys %}
+  - {{ encryption_key }}
+{% endfor %}