From bd847412a0207833060909e237a6789137de03bc Mon Sep 17 00:00:00 2001
From: Enis Afgan <afgane@gmail.com>
Date: Thu, 6 Feb 2025 15:32:52 -0500
Subject: [PATCH 1/5] Add config options for tool dependency installs

---
 .../InstallationSettings.test.js              | 15 +++++++++
 .../InstallationSettings.vue                  | 12 +++++--
 doc/source/admin/galaxy_options.rst           | 33 +++++++++++++++++++
 doc/source/dev/faq.rst                        | 13 +++++++-
 lib/galaxy/config/sample/galaxy.yml.sample    | 17 ++++++++--
 lib/galaxy/config/schemas/config_schema.yml   | 21 ++++++++++++
 lib/galaxy/managers/configuration.py          |  5 ++-
 7 files changed, 108 insertions(+), 8 deletions(-)

diff --git a/client/src/components/Toolshed/RepositoryDetails/InstallationSettings.test.js b/client/src/components/Toolshed/RepositoryDetails/InstallationSettings.test.js
index 29094f7574f0..c17b1fc0910a 100644
--- a/client/src/components/Toolshed/RepositoryDetails/InstallationSettings.test.js
+++ b/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);
     });
 });
diff --git a/client/src/components/Toolshed/RepositoryDetails/InstallationSettings.vue b/client/src/components/Toolshed/RepositoryDetails/InstallationSettings.vue
index b726ffa8cf5a..ef86345d7531 100644
--- a/client/src/components/Toolshed/RepositoryDetails/InstallationSettings.vue
+++ b/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,
         };
diff --git a/doc/source/admin/galaxy_options.rst b/doc/source/admin/galaxy_options.rst
index 9caac0e4f7fc..f49b80fcfc9b 100644
--- a/doc/source/admin/galaxy_options.rst
+++ b/doc/source/admin/galaxy_options.rst
@@ -5747,4 +5747,37 @@
 :Type: int
 
 
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+``install_tool_dependencies``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    Install tool dependencies when installing tools from the Tool
+    Shed.
+:Default: ``true``
+:Type: bool
+
+
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+``install_repository_dependencies``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    Install repository dependencies when installing tools from the
+    Tool Shed.
+:Default: ``true``
+:Type: bool
+
+
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+``install_resolver_dependencies``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    Install resolver dependencies when installing tools from the Tool
+    Shed.
+:Default: ``true``
+:Type: bool
+
+
 
diff --git a/doc/source/dev/faq.rst b/doc/source/dev/faq.rst
index a483495b8b46..00ec4dccc93f 100644
--- a/doc/source/dev/faq.rst
+++ b/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.
diff --git a/lib/galaxy/config/sample/galaxy.yml.sample b/lib/galaxy/config/sample/galaxy.yml.sample
index 6035d7266b35..342f8b1ec071 100644
--- a/lib/galaxy/config/sample/galaxy.yml.sample
+++ b/lib/galaxy/config/sample/galaxy.yml.sample
@@ -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
@@ -3067,3 +3067,14 @@ galaxy:
   # affects s3fs file sources.
   #file_source_listings_expiry_time: 60
 
+  # Install tool dependencies when installing tools from the Tool Shed.
+  #install_tool_dependencies: true
+
+  # Install repository dependencies when installing tools from the Tool
+  # Shed.
+  #install_repository_dependencies: true
+
+  # Install resolver dependencies when installing tools from the Tool
+  # Shed.
+  #install_resolver_dependencies: true
+
diff --git a/lib/galaxy/config/schemas/config_schema.yml b/lib/galaxy/config/schemas/config_schema.yml
index d43c647fa571..222aff3fb10e 100644
--- a/lib/galaxy/config/schemas/config_schema.yml
+++ b/lib/galaxy/config/schemas/config_schema.yml
@@ -4240,3 +4240,24 @@ mapping:
           Number of seconds before file source content listings are refreshed. Shorter times will result in more
           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.
+
+      install_repository_dependencies:
+        type: bool
+        default: true
+        required: false
+        desc: |
+          Install repository dependencies when installing tools from the Tool Shed.
+
+      install_resolver_dependencies:
+        type: bool
+        default: true
+        required: false
+        desc: |
+          Install resolver dependencies when installing tools from the Tool Shed.
diff --git a/lib/galaxy/managers/configuration.py b/lib/galaxy/managers/configuration.py
index f30118d2fbf3..56288cecc0a7 100644
--- a/lib/galaxy/managers/configuration.py
+++ b/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,
         }
 
 

From 3a8d5aeb39fd32c507370118143828e994e35361 Mon Sep 17 00:00:00 2001
From: Enis Afgan <afgane@gmail.com>
Date: Thu, 6 Feb 2025 16:09:54 -0500
Subject: [PATCH 2/5] Lint

---
 client/README.md                                       | 10 ++++++++++
 .../RepositoryDetails/InstallationSettings.test.js     |  6 +++---
 2 files changed, 13 insertions(+), 3 deletions(-)

diff --git a/client/README.md b/client/README.md
index 667eb23b05e4..532fad8661fe 100644
--- a/client/README.md
+++ b/client/README.md
@@ -122,6 +122,16 @@ 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, from the `client` folder, run the
+following commands as appropriate to ensure all the code is properly formatted:
+
+    yarn prettier --check .
+    yarn prettier --write .
+    yarn prettier --write src/components/MyComponent.js
+
 ### Running the tests
 
 #### At Build-Time
diff --git a/client/src/components/Toolshed/RepositoryDetails/InstallationSettings.test.js b/client/src/components/Toolshed/RepositoryDetails/InstallationSettings.test.js
index c17b1fc0910a..15b0c28035bf 100644
--- a/client/src/components/Toolshed/RepositoryDetails/InstallationSettings.test.js
+++ b/client/src/components/Toolshed/RepositoryDetails/InstallationSettings.test.js
@@ -10,10 +10,10 @@ jest.mock("@/composables/config", () => ({
         config: {
             install_tool_dependencies: true,
             install_repository_dependencies: true,
-            install_resolver_dependencies: true
+            install_resolver_dependencies: true,
         },
-        isConfigLoaded: true
-    })
+        isConfigLoaded: true,
+    }),
 }));
 
 const localVue = getLocalVue();

From 0de4174a15e4ecc5f316d75928979d89db15a407 Mon Sep 17 00:00:00 2001
From: Enis Afgan <afgane@gmail.com>
Date: Fri, 7 Feb 2025 09:09:31 -0500
Subject: [PATCH 3/5] Update client/README.md

Co-authored-by: Nuwan Goonasekera <2070605+nuwang@users.noreply.github.com>
---
 client/README.md | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/client/README.md b/client/README.md
index 532fad8661fe..afa67060c0c1 100644
--- a/client/README.md
+++ b/client/README.md
@@ -125,12 +125,11 @@ for isolating test functionality.
 ### Linting
 
 We use [Prettier](https://prettier.io/) to enforce code style and best
-practices. Before submitting a pull request, from the `client` folder, run the
-following commands as appropriate to ensure all the code is properly formatted:
+practices. Before submitting a pull request, run the following commands
+as appropriate to ensure all the code is properly formatted:
 
-    yarn prettier --check .
-    yarn prettier --write .
-    yarn prettier --write src/components/MyComponent.js
+    make client-lint
+    make client-format
 
 ### Running the tests
 

From 1214692a16c8b8fb921d4a2a0c02f789a14e48da Mon Sep 17 00:00:00 2001
From: Enis Afgan <afgane@gmail.com>
Date: Fri, 7 Feb 2025 09:49:35 -0500
Subject: [PATCH 4/5] Update descriptions of the install options

---
 doc/source/admin/galaxy_options.rst         | 20 +++++++++++++++++---
 lib/galaxy/config/sample/galaxy.yml.sample  | 18 ++++++++++++++++--
 lib/galaxy/config/schemas/config_schema.yml | 20 ++++++++++++++++++--
 3 files changed, 51 insertions(+), 7 deletions(-)

diff --git a/doc/source/admin/galaxy_options.rst b/doc/source/admin/galaxy_options.rst
index f49b80fcfc9b..74a34eda3880 100644
--- a/doc/source/admin/galaxy_options.rst
+++ b/doc/source/admin/galaxy_options.rst
@@ -5753,7 +5753,13 @@
 
 :Description:
     Install tool dependencies when installing tools from the Tool
-    Shed.
+    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
 
@@ -5764,7 +5770,11 @@
 
 :Description:
     Install repository dependencies when installing tools from the
-    Tool Shed.
+    Tool Shed. These are other Tool Shed repositories that the tool
+    being installed depends on. Repository dependencies ensure that
+    all necessary components are installed for the tool to work
+    correctly within the Galaxy environment. This option should be set
+    to false if containerized versions of tools are used.
 :Default: ``true``
 :Type: bool
 
@@ -5775,7 +5785,11 @@
 
 :Description:
     Install resolver dependencies when installing tools from the Tool
-    Shed.
+    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
 
diff --git a/lib/galaxy/config/sample/galaxy.yml.sample b/lib/galaxy/config/sample/galaxy.yml.sample
index 342f8b1ec071..55c3bb1c322d 100644
--- a/lib/galaxy/config/sample/galaxy.yml.sample
+++ b/lib/galaxy/config/sample/galaxy.yml.sample
@@ -3068,13 +3068,27 @@ galaxy:
   #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.
+  # Shed. These are other Tool Shed repositories that the tool being
+  # installed depends on. Repository dependencies ensure that all
+  # necessary components are installed for the tool to work correctly
+  # within the Galaxy environment. This option should be set to false if
+  # containerized versions of tools are used.
   #install_repository_dependencies: true
 
   # Install resolver dependencies when installing tools from the Tool
-  # Shed.
+  # 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
 
diff --git a/lib/galaxy/config/schemas/config_schema.yml b/lib/galaxy/config/schemas/config_schema.yml
index 222aff3fb10e..5d9ea43585f3 100644
--- a/lib/galaxy/config/schemas/config_schema.yml
+++ b/lib/galaxy/config/schemas/config_schema.yml
@@ -4247,17 +4247,33 @@ mapping:
         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.
+          Install repository dependencies when installing tools from the Tool
+          Shed. These are other Tool Shed repositories that the tool being
+          installed depends on. Repository dependencies ensure that all
+          necessary components are installed for the tool to work correctly
+          within the Galaxy environment. This option should be set to false if
+          containerized versions of tools are used.
 
       install_resolver_dependencies:
         type: bool
         default: true
         required: false
         desc: |
-          Install resolver dependencies when installing tools from the Tool Shed.
+          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.

From d6e508d6cc06101e1cf78d0fbbbf3421308bcf16 Mon Sep 17 00:00:00 2001
From: Enis Afgan <afgane@gmail.com>
Date: Tue, 11 Feb 2025 15:36:56 -0500
Subject: [PATCH 5/5] Correct description for the repository deps option

---
 doc/source/admin/galaxy_options.rst         | 8 ++++----
 lib/galaxy/config/sample/galaxy.yml.sample  | 8 ++++----
 lib/galaxy/config/schemas/config_schema.yml | 8 ++++----
 3 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/doc/source/admin/galaxy_options.rst b/doc/source/admin/galaxy_options.rst
index 74a34eda3880..f9c5eb15f282 100644
--- a/doc/source/admin/galaxy_options.rst
+++ b/doc/source/admin/galaxy_options.rst
@@ -5771,10 +5771,10 @@
 :Description:
     Install repository dependencies when installing tools from the
     Tool Shed. These are other Tool Shed repositories that the tool
-    being installed depends on. Repository dependencies ensure that
-    all necessary components are installed for the tool to work
-    correctly within the Galaxy environment. This option should be set
-    to false if containerized versions of tools are used.
+    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
 
diff --git a/lib/galaxy/config/sample/galaxy.yml.sample b/lib/galaxy/config/sample/galaxy.yml.sample
index 55c3bb1c322d..b8fed5deb551 100644
--- a/lib/galaxy/config/sample/galaxy.yml.sample
+++ b/lib/galaxy/config/sample/galaxy.yml.sample
@@ -3078,10 +3078,10 @@ galaxy:
 
   # Install repository dependencies when installing tools from the Tool
   # Shed. These are other Tool Shed repositories that the tool being
-  # installed depends on. Repository dependencies ensure that all
-  # necessary components are installed for the tool to work correctly
-  # within the Galaxy environment. This option should be set to false if
-  # containerized versions of tools are used.
+  # 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
diff --git a/lib/galaxy/config/schemas/config_schema.yml b/lib/galaxy/config/schemas/config_schema.yml
index 5d9ea43585f3..1af6641a7072 100644
--- a/lib/galaxy/config/schemas/config_schema.yml
+++ b/lib/galaxy/config/schemas/config_schema.yml
@@ -4261,10 +4261,10 @@ mapping:
         desc: |
           Install repository dependencies when installing tools from the Tool
           Shed. These are other Tool Shed repositories that the tool being
-          installed depends on. Repository dependencies ensure that all
-          necessary components are installed for the tool to work correctly
-          within the Galaxy environment. This option should be set to false if
-          containerized versions of tools are used.
+          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