Add config options for tool dependency installs

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
 

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
 

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.