Add config options for tool dependency installs

client/README.md

@@ -122,6 +122,15 @@ utils](https://vue-test-utils.vuejs.org/) to mount individual components in a
 test bed and check them for rendered features. Please use jest-based mocking
 for isolating test functionality.
 
+### Linting
+
+We use [Prettier](https://prettier.io/) to enforce code style and best
+practices. Before submitting a pull request, run the following commands
+as appropriate to ensure all the code is properly formatted:
+
+    make client-lint
+    make client-format
+
 ### Running the tests
 
 #### At Build-Time

client/src/components/Toolshed/RepositoryDetails/InstallationSettings.test.js

@@ -4,6 +4,17 @@ import { getLocalVue } from "tests/jest/helpers";
 import InstallationSettings from "./InstallationSettings";
 
 jest.mock("app");
+// Mock the useConfig composable
+jest.mock("@/composables/config", () => ({
+    useConfig: () => ({
+        config: {
+            install_tool_dependencies: true,
+            install_repository_dependencies: true,
+            install_resolver_dependencies: true,
+        },
+        isConfigLoaded: true,
+    }),
+}));
 
 const localVue = getLocalVue();
 
@@ -28,5 +39,9 @@ describe("InstallationSettings", () => {
         expect(wrapper.find(".title").text()).toBe("Installing 'name'");
         expect(wrapper.find(".description").text()).toBe("long_description");
         expect(wrapper.find(".revision").text()).toBe("owner rev. changesetRevision");
+
+        expect(wrapper.vm.installToolDependencies).toBe(true);
+        expect(wrapper.vm.installRepositoryDependencies).toBe(true);
+        expect(wrapper.vm.installResolverDependencies).toBe(true);
     });
 });

client/src/components/Toolshed/RepositoryDetails/InstallationSettings.vue

@@ -46,6 +46,8 @@
     </b-modal>
 </template>
 <script>
+import { useConfig } from "@/composables/config";
+
 export default {
     props: {
         repo: {
@@ -77,13 +79,17 @@ export default {
             default: false,
         },
     },
+    setup() {
+        const { config, isConfigLoaded } = useConfig(true);
+        return { config, isConfigLoaded };
+    },
     data() {
         return {
             modalShow: true,
             advancedShow: false,
-            installToolDependencies: true,
-            installRepositoryDependencies: true,
-            installResolverDependencies: true,
+            installToolDependencies: this.config.install_tool_dependencies,
+            installRepositoryDependencies: this.config.install_repository_dependencies,
+            installResolverDependencies: this.config.install_resolver_dependencies,
             toolConfig: null,
             toolSection: null,
         };

doc/source/admin/galaxy_options.rst

@@ -5747,6 +5747,53 @@
 :Type: int
 
 
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+``install_tool_dependencies``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    Install tool dependencies when installing tools from the Tool
+    Shed. These are the software packages and libraries required for a
+    tool to function properly. Tool dependencies are typically
+    specified in the tool's XML configuration using <requirement>
+    tags. Galaxy can automatically install these dependencies if the
+    tool_dependency_dir is properly configured in the galaxy.yml file.
+    This option should be set to false if containerized versions of
+    tools are used.
+:Default: ``true``
+:Type: bool
+
+
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+``install_repository_dependencies``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    Install repository dependencies when installing tools from the
+    Tool Shed. These are other Tool Shed repositories that the tool
+    being installed depends on. This is commonly used with tool
+    suites. Repository dependencies ensure that all necessary
+    components are installed for the tool (or suite) to work correctly
+    within the Galaxy environment.
+:Default: ``true``
+:Type: bool
+
+
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+``install_resolver_dependencies``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    Install resolver dependencies when installing tools from the Tool
+    Shed. These are mechanisms used by Galaxy to locate and make
+    available the required software packages for tools. Galaxy uses
+    dependency resolvers (e.g., Conda) to determine how to satisfy
+    tool requirements. This option should be set to false if
+    containerized versions of tools are used.
+:Default: ``true``
+:Type: bool
+
+
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 ``enable_failed_jobs_working_directory_cleanup``
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

doc/source/dev/faq.rst

@@ -1,4 +1,4 @@
-How Do I...
+How Do I ...
 ===========
 
 This section contains a number of smaller topics with links and examples meant
@@ -25,4 +25,15 @@ We have added a Makefile which will let you do this. You can simply run:
 Please see the ``Makefile`` itself for details and other options. There is also a readme at
 ``client/README.md``.
 
+... rebuild the Galaxy configuration schema?
+-------------------------------------------
 
+Galaxy configurations have a schema that is used to validate configuration files. This schema is
+defined in ``lib/galaxy/config/schemas/config_schema.yml``. If you make changes to the schema, to rebuild
+all sample YAML and RST files run
+
+.. code-block:: bash
+
+    make config-rebuild
+
+Then add updated files to your commit.

lib/galaxy/config/sample/galaxy.yml.sample

@@ -1,21 +1,21 @@
 # Galaxy is configured by default to be usable in a single-user development
 # environment.  To tune the application for a multi-user production
 # environment, see the documentation at:
-#
+# 
 #  https://docs.galaxyproject.org/en/master/admin/production.html
-#
+# 
 # Throughout this sample configuration file, except where stated otherwise,
 # uncommented values override the default if left unset, whereas commented
 # values are set to the default value.  Relative paths are relative to the root
 # Galaxy directory.
-#
+# 
 # Examples of many of these options are explained in more detail in the Galaxy
 # Community Hub.
-#
+# 
 #   https://galaxyproject.org/admin/config
-#
+# 
 # Config hackers are encouraged to check there before asking for help.
-#
+# 
 # Configuration for Gravity process manager.
 # ``uwsgi:`` section will be ignored if Galaxy is started via Gravity commands (e.g ``./run.sh``, ``galaxy`` or ``galaxyctl``).
 gravity:
@@ -189,9 +189,9 @@ gravity:
     # Public-facing port of the proxy
     # port: 4002
 
-    # Routes file to monitor.
-    # Should be set to the same path as ``interactivetools_map`` in the ``galaxy:`` section. This is ignored if
-    # ``interactivetools_map is set``.
+    # Database to monitor.
+    # Should be set to the same value as ``interactivetools_map`` (or ``interactivetoolsproxy_map``) in the ``galaxy:`` section. This is
+    # ignored if either ``interactivetools_map`` or ``interactivetoolsproxy_map`` are set.
     # sessions: database/interactivetools_map.sqlite
 
     # Include verbose messages in gx-it-proxy
@@ -3067,6 +3067,31 @@ galaxy:
   # affects s3fs file sources.
   #file_source_listings_expiry_time: 60
 
+  # Install tool dependencies when installing tools from the Tool Shed.
+  # These are the software packages and libraries required for a tool to
+  # function properly. Tool dependencies are typically specified in the
+  # tool's XML configuration using <requirement> tags. Galaxy can
+  # automatically install these dependencies if the tool_dependency_dir
+  # is properly configured in the galaxy.yml file. This option should be
+  # set to false if containerized versions of tools are used.
+  #install_tool_dependencies: true
+
+  # Install repository dependencies when installing tools from the Tool
+  # Shed. These are other Tool Shed repositories that the tool being
+  # installed depends on. This is commonly used with tool suites.
+  # Repository dependencies ensure that all necessary components are
+  # installed for the tool (or suite) to work correctly within the
+  # Galaxy environment.
+  #install_repository_dependencies: true
+
+  # Install resolver dependencies when installing tools from the Tool
+  # Shed. These are mechanisms used by Galaxy to locate and make
+  # available the required software packages for tools. Galaxy uses
+  # dependency resolvers (e.g., Conda) to determine how to satisfy tool
+  # requirements. This option should be set to false if containerized
+  # versions of tools are used.
+  #install_resolver_dependencies: true
+
   # Enables the cleanup of failed Galaxy job's working directories. Runs
   # in a Celery task.
   #enable_failed_jobs_working_directory_cleanup: false

lib/galaxy/config/schemas/config_schema.yml

@@ -4241,6 +4241,43 @@ mapping:
           queries while browsing a file sources. Longer times will result in fewer requests to file sources but
           outdated contents might be displayed to the user. Currently only affects s3fs file sources.
 
+      install_tool_dependencies:
+        type: bool
+        default: true
+        required: false
+        desc: |
+          Install tool dependencies when installing tools from the Tool Shed.
+          These are the software packages and libraries required for a tool to
+          function properly. Tool dependencies are typically specified in the
+          tool's XML configuration using <requirement> tags. Galaxy can
+          automatically install these dependencies if the tool_dependency_dir is
+          properly configured in the galaxy.yml file. This option should be set
+          to false if containerized versions of tools are used.
+
+      install_repository_dependencies:
+        type: bool
+        default: true
+        required: false
+        desc: |
+          Install repository dependencies when installing tools from the Tool
+          Shed. These are other Tool Shed repositories that the tool being
+          installed depends on. This is commonly used with tool suites.
+          Repository dependencies ensure that all necessary components are
+          installed for the tool (or suite) to work correctly within the Galaxy
+          environment.
+
+      install_resolver_dependencies:
+        type: bool
+        default: true
+        required: false
+        desc: |
+          Install resolver dependencies when installing tools from the Tool
+          Shed. These are mechanisms used by Galaxy to locate and make available
+          the required software packages for tools. Galaxy uses dependency
+          resolvers (e.g., Conda) to determine how to satisfy tool requirements.
+          This option should be set to false if containerized versions of tools
+          are used.
+
       enable_failed_jobs_working_directory_cleanup:
         type: bool
         default: false

lib/galaxy/managers/configuration.py

@@ -96,7 +96,7 @@ def reload_toolbox(self):
 #   but doesn't have a model like them. It might be better in config.py or a
 #   totally new area, but I'm leaving it in managers for now for class consistency.
 class ConfigSerializer(base.ModelSerializer):
-    """Configuration (galaxy.ini) settings viewable by all users"""
+    """Configuration (galaxy.yml) settings viewable by all users"""
 
     def __init__(self, app):
         super().__init__(app)
@@ -230,6 +230,9 @@ def _config_is_truthy(item, key, **context):
             "help_forum_api_url": _use_config,
             "enable_help_forum_tool_panel_integration": _use_config,
             "llm_api_configured": lambda item, key, **context: bool(item.openai_api_key),
+            "install_tool_dependencies": _use_config,
+            "install_repository_dependencies": _use_config,
+            "install_resolver_dependencies": _use_config,
         }