diff --git a/config/galaxy.ini.sample b/config/galaxy.ini.sample
index 43dbf738559..ef07ff6d049 100644
--- a/config/galaxy.ini.sample
+++ b/config/galaxy.ini.sample
@@ -210,7 +210,7 @@ paste.app_factory = galaxy.web.buildapp:app_factory
 #conda_auto_install = False
 # Set to True to instruct Galaxy to install Conda from the web automatically
 # if it cannot find a local copy and conda_exec is not configured.
-#conda_auto_init = False
+#conda_auto_init = True
 # You must set this to True if conda_prefix and job_working_directory are not on the same
 # volume, or some conda dependencies will fail to execute at job runtime.
 # Conda will copy packages content instead of creating hardlinks or symlinks.
diff --git a/config/local_conda_mapping.yml.sample b/config/local_conda_mapping.yml.sample
new file mode 100644
index 00000000000..383ce4836c6
--- /dev/null
+++ b/config/local_conda_mapping.yml.sample
@@ -0,0 +1,2 @@
+# See $GALAXY_ROOT/lib/galaxy/tools/deps/default_conda_mapping.yml for example mapping - 
+# additional site-specific mappings can be added to config/conda_mapping.yml.
diff --git a/lib/galaxy/config.py b/lib/galaxy/config.py
index 8b709f384f0..dea393a0bf8 100644
--- a/lib/galaxy/config.py
+++ b/lib/galaxy/config.py
@@ -32,6 +32,46 @@ from .version import VERSION_MAJOR
 log = logging.getLogger( __name__ )
 
 
+PATH_DEFAULTS = dict(
+    auth_config_file=['config/auth_conf.xml', 'config/auth_conf.xml.sample'],
+    data_manager_config_file=['config/data_manager_conf.xml', 'data_manager_conf.xml', 'config/data_manager_conf.xml.sample'],
+    datatypes_config_file=['config/datatypes_conf.xml', 'datatypes_conf.xml', 'config/datatypes_conf.xml.sample'],
+    external_service_type_config_file=['config/external_service_types_conf.xml', 'external_service_types_conf.xml', 'config/external_service_types_conf.xml.sample'],
+    job_config_file=['config/job_conf.xml', 'job_conf.xml'],
+    tool_destinations_config_file=['config/tool_destinations.yml', 'config/tool_destinations.yml.sample'],
+    job_metrics_config_file=['config/job_metrics_conf.xml', 'job_metrics_conf.xml', 'config/job_metrics_conf.xml.sample'],
+    dependency_resolvers_config_file=['config/dependency_resolvers_conf.xml', 'dependency_resolvers_conf.xml'],
+    job_resource_params_file=['config/job_resource_params_conf.xml', 'job_resource_params_conf.xml'],
+    migrated_tools_config=['migrated_tools_conf.xml', 'config/migrated_tools_conf.xml'],
+    object_store_config_file=['config/object_store_conf.xml', 'object_store_conf.xml'],
+    openid_config_file=['config/openid_conf.xml', 'openid_conf.xml', 'config/openid_conf.xml.sample'],
+    shed_data_manager_config_file=['shed_data_manager_conf.xml', 'config/shed_data_manager_conf.xml'],
+    shed_tool_data_table_config=['shed_tool_data_table_conf.xml', 'config/shed_tool_data_table_conf.xml'],
+    tool_sheds_config_file=['config/tool_sheds_conf.xml', 'tool_sheds_conf.xml', 'config/tool_sheds_conf.xml.sample'],
+    workflow_schedulers_config_file=['config/workflow_schedulers_conf.xml', 'config/workflow_schedulers_conf.xml.sample'],
+    modules_mapping_files=['config/environment_modules_mapping.yml', 'config/environment_modules_mapping.yml.sample'],
+    local_conda_mapping_file=['config/local_conda_mapping.yml', 'config/local_conda_mapping.yml.sample'],
+)
+
+PATH_LIST_DEFAULTS = dict(
+    tool_data_table_config_path=['config/tool_data_table_conf.xml', 'tool_data_table_conf.xml', 'config/tool_data_table_conf.xml.sample'],
+    # rationale:
+    # [0]: user has explicitly created config/tool_conf.xml but did not
+    #      move their existing shed_tool_conf.xml, don't use
+    #      config/shed_tool_conf.xml, which is probably the empty
+    #      version copied from the sample, or else their shed tools
+    #      will disappear
+    # [1]: user has created config/tool_conf.xml and, having passed
+    #      [0], probably moved their shed_tool_conf.xml as well
+    # [2]: user has done nothing, use the old files
+    # [3]: fresh install
+    tool_config_file=['config/tool_conf.xml,shed_tool_conf.xml',
+                      'config/tool_conf.xml,config/shed_tool_conf.xml',
+                      'tool_conf.xml,shed_tool_conf.xml',
+                      'config/tool_conf.xml.sample,config/shed_tool_conf.xml']
+)
+
+
 def resolve_path( path, root ):
     """If 'path' is relative make absolute by prepending 'root'"""
     if not os.path.isabs( path ):
@@ -39,12 +79,34 @@ def resolve_path( path, root ):
     return path
 
 
+def find_path(kwargs, var, root):
+    """Find a configuration path that may exist at different defaults."""
+    defaults = PATH_DEFAULTS[var]
+
+    if kwargs.get(var, None) is not None:
+        path = kwargs.get(var)
+    else:
+        for default in defaults:
+            if os.path.exists(resolve_path(default, root)):
+                path = default
+                break
+        else:
+            path = defaults[-1]
+
+    return resolve_path(path, root)
+
+
+def find_root(kwargs):
+    root = kwargs.get('root_dir', '.')
+    return root
+
+
 class Configuration( object ):
     deprecated_options = ( 'database_file', )
 
     def __init__( self, **kwargs ):
         self.config_dict = kwargs
-        self.root = kwargs.get( 'root_dir', '.' )
+        self.root = find_root(kwargs)
 
         # Resolve paths of other config files
         self.__parse_config_file_options( kwargs )
@@ -329,23 +391,22 @@ class Configuration( object ):
         self.tool_ngram_minsize = kwargs.get( "tool_ngram_minsize", 3 )
         self.tool_ngram_maxsize = kwargs.get( "tool_ngram_maxsize", 4 )
         # Location for tool dependencies.
-        # Location for tool dependencies.
-        tool_dependency_dir = kwargs.get( "tool_dependency_dir", "database/dependencies" )
-        if tool_dependency_dir.lower() == "none":
-            tool_dependency_dir = None
-
-        if tool_dependency_dir is not None:
-            self.tool_dependency_dir = resolve_path( tool_dependency_dir, self.root )
-            # Setting the following flag to true will ultimately cause tool dependencies
-            # to be located in the shell environment and used by the job that is executing
-            # the tool.
-            self.use_tool_dependencies = True
+        use_tool_dependencies, tool_dependency_dir, use_cached_dependency_manager, tool_dependency_cache_dir, precache_dependencies = \
+            parse_dependency_options(kwargs, self.root, self.dependency_resolvers_config_file)
+        self.use_tool_dependencies = use_tool_dependencies
+        self.tool_dependency_dir = tool_dependency_dir
+        self.use_cached_dependency_manager = use_cached_dependency_manager
+        self.tool_dependency_cache_dir = tool_dependency_cache_dir
+        self.precache_dependencies = precache_dependencies
+        # Deployers may either specify a complete list of mapping files or get the default for free and just
+        # specify a local mapping file to adapt and extend the default one.
+        if "conda_mapping_files" in kwargs:
+            self.conda_mapping_files = kwargs["conda_mapping_files"]
         else:
-            self.tool_dependency_dir = None
-            self.use_tool_dependencies = os.path.exists(self.dependency_resolvers_config_file)
-        self.use_cached_dependency_manager = string_as_bool(kwargs.get("use_cached_dependency_manager", 'False'))
-        self.tool_dependency_cache_dir = kwargs.get( 'tool_dependency_cache_dir', os.path.join(self.tool_dependency_dir, '_cache'))
-        self.precache_dependencies = string_as_bool(kwargs.get("precache_dependencies", 'True'))
+            self.conda_mapping_files = [
+                self.local_conda_mapping_file,
+                os.path.join(self.root, "lib", "galaxy", "tools", "deps", "resolvers", "default_conda_mapping.yml"),
+            ]
 
         self.enable_beta_mulled_containers = string_as_bool( kwargs.get( 'enable_beta_mulled_containers', 'False' ) )
         containers_resolvers_config_file = kwargs.get( 'containers_resolvers_config_file', None )
@@ -558,56 +619,11 @@ class Configuration( object ):
         """
         Backwards compatibility for config files moved to the config/ dir.
         """
-        defaults = dict(
-            auth_config_file=[ 'config/auth_conf.xml', 'config/auth_conf.xml.sample' ],
-            data_manager_config_file=[ 'config/data_manager_conf.xml', 'data_manager_conf.xml', 'config/data_manager_conf.xml.sample' ],
-            datatypes_config_file=[ 'config/datatypes_conf.xml', 'datatypes_conf.xml', 'config/datatypes_conf.xml.sample' ],
-            external_service_type_config_file=[ 'config/external_service_types_conf.xml', 'external_service_types_conf.xml', 'config/external_service_types_conf.xml.sample' ],
-            job_config_file=[ 'config/job_conf.xml', 'job_conf.xml' ],
-            tool_destinations_config_file=[ 'config/tool_destinations.yml', 'config/tool_destinations.yml.sample' ],
-            job_metrics_config_file=[ 'config/job_metrics_conf.xml', 'job_metrics_conf.xml', 'config/job_metrics_conf.xml.sample' ],
-            dependency_resolvers_config_file=[ 'config/dependency_resolvers_conf.xml', 'dependency_resolvers_conf.xml' ],
-            job_resource_params_file=[ 'config/job_resource_params_conf.xml', 'job_resource_params_conf.xml' ],
-            migrated_tools_config=[ 'migrated_tools_conf.xml', 'config/migrated_tools_conf.xml' ],
-            object_store_config_file=[ 'config/object_store_conf.xml', 'object_store_conf.xml' ],
-            openid_config_file=[ 'config/openid_conf.xml', 'openid_conf.xml', 'config/openid_conf.xml.sample' ],
-            shed_data_manager_config_file=[ 'shed_data_manager_conf.xml', 'config/shed_data_manager_conf.xml' ],
-            shed_tool_data_table_config=[ 'shed_tool_data_table_conf.xml', 'config/shed_tool_data_table_conf.xml' ],
-            tool_sheds_config_file=[ 'config/tool_sheds_conf.xml', 'tool_sheds_conf.xml', 'config/tool_sheds_conf.xml.sample' ],
-            workflow_schedulers_config_file=['config/workflow_schedulers_conf.xml', 'config/workflow_schedulers_conf.xml.sample'],
-        )
 
-        listify_defaults = dict(
-            tool_data_table_config_path=[ 'config/tool_data_table_conf.xml', 'tool_data_table_conf.xml', 'config/tool_data_table_conf.xml.sample' ],
-            # rationale:
-            # [0]: user has explicitly created config/tool_conf.xml but did not
-            #      move their existing shed_tool_conf.xml, don't use
-            #      config/shed_tool_conf.xml, which is probably the empty
-            #      version copied from the sample, or else their shed tools
-            #      will disappear
-            # [1]: user has created config/tool_conf.xml and, having passed
-            #      [0], probably moved their shed_tool_conf.xml as well
-            # [2]: user has done nothing, use the old files
-            # [3]: fresh install
-            tool_config_file=[ 'config/tool_conf.xml,shed_tool_conf.xml',
-                               'config/tool_conf.xml,config/shed_tool_conf.xml',
-                               'tool_conf.xml,shed_tool_conf.xml',
-                               'config/tool_conf.xml.sample,config/shed_tool_conf.xml' ]
-        )
+        for var in PATH_DEFAULTS:
+            setattr( self, var, find_path( kwargs, var, self.root ) )
 
-        for var, defaults in defaults.items():
-            if kwargs.get( var, None ) is not None:
-                path = kwargs.get( var )
-            else:
-                for default in defaults:
-                    if os.path.exists( resolve_path( default, self.root ) ):
-                        path = default
-                        break
-                else:
-                    path = defaults[-1]
-            setattr( self, var, resolve_path( path, self.root ) )
-
-        for var, defaults in listify_defaults.items():
+        for var, defaults in PATH_LIST_DEFAULTS.items():
             paths = []
             if kwargs.get( var, None ) is not None:
                 paths = listify( kwargs.get( var ) )
@@ -758,6 +774,31 @@ class Configuration( object ):
         return [ parse( v ) for v in allowed_origin_hostnames if v ]
 
 
+def parse_dependency_options(kwargs, root, dependency_resolvers_config_file):
+    # Location for tool dependencies.
+    tool_dependency_dir = kwargs.get("tool_dependency_dir", "database/dependencies")
+    if tool_dependency_dir.lower() == "none":
+        tool_dependency_dir = None
+
+    if tool_dependency_dir is not None:
+        tool_dependency_dir = resolve_path(tool_dependency_dir, root)
+        # Setting the following flag to true will ultimately cause tool dependencies
+        # to be located in the shell environment and used by the job that is executing
+        # the tool.
+        use_tool_dependencies = True
+        tool_dependency_cache_dir = kwargs.get('tool_dependency_cache_dir', os.path.join(tool_dependency_dir, '_cache'))
+        use_cached_dependency_manager = string_as_bool(kwargs.get("use_cached_dependency_manager", 'False'))
+        precache_dependencies = string_as_bool(kwargs.get("precache_dependencies", 'True'))
+    else:
+        tool_dependency_dir = None
+        use_tool_dependencies = os.path.exists(dependency_resolvers_config_file)
+        tool_dependency_cache_dir = None
+        precache_dependencies = False
+        use_cached_dependency_manager = False
+
+    return use_tool_dependencies, tool_dependency_dir, use_cached_dependency_manager, tool_dependency_cache_dir, precache_dependencies
+
+
 def get_database_engine_options( kwargs, model_prefix='' ):
     """
     Allow options for the SQLAlchemy database engine to be passed by using
@@ -787,15 +828,21 @@ def get_database_engine_options( kwargs, model_prefix='' ):
 
 
 def configure_logging( config ):
-    """
-    Allow some basic logging configuration to be read from ini file.
+    """Allow some basic logging configuration to be read from ini file.
+
+    This should be able to consume either a galaxy.config.Configuration object
+    or a simple dictionary of configuration variables.
     """
     # Get root logger
     root = logging.getLogger()
     # PasteScript will have already configured the logger if the
     # 'loggers' section was found in the config file, otherwise we do
     # some simple setup using the 'log_*' values from the config.
-    paste_configures_logging = config.global_conf_parser.has_section( "loggers" )
+    parser = getattr(config, "global_conf_parser", None)
+    if parser:
+        paste_configures_logging = config.global_conf_parser.has_section( "loggers" )
+    else:
+        paste_configures_logging = False
     auto_configure_logging = not paste_configures_logging and string_as_bool( config.get( "auto_configure_logging", "True" ) )
     if auto_configure_logging:
         format = config.get( "log_format", "%(name)s %(levelname)s %(asctime)s %(message)s" )
@@ -826,7 +873,7 @@ def configure_logging( config ):
         handler.setFormatter( formatter )
         root.addHandler( handler )
     # If sentry is configured, also log to it
-    if config.sentry_dsn:
+    if getattr(config, "sentry_dsn", None):
         from raven.handlers.logging import SentryHandler
         sentry_handler = SentryHandler( config.sentry_dsn )
         sentry_handler.setLevel( logging.WARN )
diff --git a/lib/galaxy/model/orm/scripts.py b/lib/galaxy/model/orm/scripts.py
index d7fce87ecb2..a7a922341cd 100644
--- a/lib/galaxy/model/orm/scripts.py
+++ b/lib/galaxy/model/orm/scripts.py
@@ -2,9 +2,8 @@
 Code to support database helper scripts (create_db.py, manage_db.py, etc...).
 """
 import logging
-import os.path
 
-from galaxy.util.properties import load_app_properties
+from galaxy.util.properties import find_config_file, load_app_properties
 
 
 log = logging.getLogger( __name__ )
@@ -40,25 +39,21 @@ DATABASE = {
 }
 
 
-def read_config_file_arg( argv, default, old_default ):
+def read_config_file_arg( argv, default, old_default, cwd=None ):
+    config_file = None
     if '-c' in argv:
         pos = argv.index( '-c' )
         argv.pop(pos)
         config_file = argv.pop( pos )
-    else:
-        if not os.path.exists( default ) and os.path.exists( old_default ):
-            config_file = old_default
-        elif os.path.exists( default ):
-            config_file = default
-        else:
-            config_file = default + ".sample"
-    return config_file
+
+    return find_config_file( default, old_default, config_file, cwd=cwd )
 
 
 def get_config( argv, cwd=None ):
     """
     Read sys.argv and parse out repository of migrations and database url.
 
+    >>> import os
     >>> from ConfigParser import SafeConfigParser
     >>> from tempfile import mkdtemp
     >>> config_dir = mkdtemp()
@@ -89,16 +84,11 @@ def get_config( argv, cwd=None ):
 
     default = database_defaults.get( 'config_file', DEFAULT_CONFIG_FILE )
     old_default = database_defaults.get( 'old_config_file' )
-    if cwd is not None:
-        default = os.path.join( cwd, default )
-        old_default = os.path.join( cwd, old_default )
-    config_file = read_config_file_arg( argv, default, old_default )
+    config_file = read_config_file_arg( argv, default, old_default, cwd=cwd )
     repo = database_defaults[ 'repo' ]
     config_prefix = database_defaults.get( 'config_prefix', DEFAULT_CONFIG_PREFIX )
     config_override = database_defaults.get( 'config_override', 'GALAXY_CONFIG_' )
     default_sqlite_file = database_defaults[ 'default_sqlite_file' ]
-    if cwd:
-        config_file = os.path.join( cwd, config_file )
 
     properties = load_app_properties( ini_file=config_file, config_prefix=config_override )
 
diff --git a/lib/galaxy/tools/deps/__init__.py b/lib/galaxy/tools/deps/__init__.py
index 6f254d3965a..b03f33db229 100644
--- a/lib/galaxy/tools/deps/__init__.py
+++ b/lib/galaxy/tools/deps/__init__.py
@@ -19,26 +19,12 @@ from .requirements import (
     ToolRequirements
 )
 from .resolvers import NullDependency
-from .resolvers.conda import CondaDependencyResolver, DEFAULT_ENSURE_CHANNELS
+from .resolvers.conda import CondaDependencyResolver
 from .resolvers.galaxy_packages import GalaxyPackageDependencyResolver
 from .resolvers.tool_shed_packages import ToolShedPackageDependencyResolver
 
 log = logging.getLogger( __name__ )
 
-# TODO: Load these from the plugins. Would require a two step initialization of
-# DependencyManager - where the plugins are loaded first and then the config
-# is parsed and sent through.
-EXTRA_CONFIG_KWDS = {
-    'conda_prefix': None,
-    'conda_exec': None,
-    'conda_debug': None,
-    'conda_ensure_channels': DEFAULT_ENSURE_CHANNELS,
-    'conda_auto_install': False,
-    'conda_auto_init': False,
-    'conda_copy_dependencies': False,
-    'precache_dependencies': True,
-}
-
 CONFIG_VAL_NOT_FOUND = object()
 
 
@@ -47,15 +33,9 @@ def build_dependency_manager( config ):
         dependency_manager_kwds = {
             'default_base_path': config.tool_dependency_dir,
             'conf_file': config.dependency_resolvers_config_file,
+            'app_config': config,
         }
-        for key, default_value in EXTRA_CONFIG_KWDS.items():
-            value = getattr(config, key, CONFIG_VAL_NOT_FOUND)
-            if value is CONFIG_VAL_NOT_FOUND and hasattr(config, "config_dict"):
-                value = config.config_dict.get(key, CONFIG_VAL_NOT_FOUND)
-            if value is CONFIG_VAL_NOT_FOUND:
-                value = default_value
-            dependency_manager_kwds[key] = value
-        if config.use_cached_dependency_manager:
+        if getattr(config, "use_cached_dependency_manager", False):
             dependency_manager_kwds['tool_dependency_cache_dir'] = config.tool_dependency_cache_dir
             dependency_manager = CachedDependencyManager(**dependency_manager_kwds)
         else:
@@ -90,7 +70,7 @@ class DependencyManager( object ):
     and should each contain a file 'env.sh' which can be sourced to make the
     dependency available in the current shell environment.
     """
-    def __init__( self, default_base_path, conf_file=None, **extra_config ):
+    def __init__( self, default_base_path, conf_file=None, app_config={} ):
         """
         Create a new dependency manager looking for packages under the paths listed
         in `base_paths`.  The default base path is app.config.tool_dependency_dir.
@@ -99,11 +79,30 @@ class DependencyManager( object ):
             log.warning( "Path '%s' does not exist, ignoring", default_base_path )
         if not os.path.isdir( default_base_path ):
             log.warning( "Path '%s' is not directory, ignoring", default_base_path )
-        self.extra_config = extra_config
+        self.__app_config = app_config
         self.default_base_path = os.path.abspath( default_base_path )
         self.resolver_classes = self.__resolvers_dict()
         self.dependency_resolvers = self.__build_dependency_resolvers( conf_file )
 
+    def get_resolver_option(self, resolver, key, explicit_resolver_options={}):
+        """Look in resolver-specific settings for option and then fallback to global settings.
+        """
+        default = resolver.config_options.get(key)
+        config_prefix = resolver.resolver_type
+        global_key = "%s_%s" % (config_prefix, key)
+        value = explicit_resolver_options.get(key, CONFIG_VAL_NOT_FOUND)
+        if value is CONFIG_VAL_NOT_FOUND:
+            if isinstance(self.__app_config, dict):
+                value = self.__app_config.get(global_key, CONFIG_VAL_NOT_FOUND)
+            else:
+                value = getattr(self.__app_config, global_key, CONFIG_VAL_NOT_FOUND)
+        if value is CONFIG_VAL_NOT_FOUND and hasattr(self.__app_config, "config_dict"):
+            value = self.__app_config.config_dict.get(global_key, CONFIG_VAL_NOT_FOUND)
+        if value is CONFIG_VAL_NOT_FOUND:
+            value = default
+
+        return value
+
     def dependency_shell_commands( self, requirements, **kwds ):
         requirement_to_dependency = self.requirements_to_dependencies(requirements, **kwds)
         return [dependency.shell_commands(requirement) for requirement, dependency in requirement_to_dependency.items()]
@@ -141,6 +140,7 @@ class DependencyManager( object ):
             # Check requirements all at once
             all_unmet = len(requirement_to_dependency) == 0
             if all_unmet and hasattr(resolver, "resolve_all"):
+                # TODO: Handle specs.
                 dependencies = resolver.resolve_all(resolvable_requirements, **kwds)
                 if dependencies:
                     assert len(dependencies) == len(resolvable_requirements)
@@ -155,7 +155,7 @@ class DependencyManager( object ):
                 if requirement in requirement_to_dependency:
                     continue
 
-                dependency = resolver.resolve( requirement.name, requirement.version, requirement.type, **kwds )
+                dependency = resolver.resolve( requirement, **kwds )
                 if require_exact and not dependency.exact:
                     continue
 
@@ -210,8 +210,8 @@ class DependencyManager( object ):
 
 
 class CachedDependencyManager(DependencyManager):
-    def __init__(self, default_base_path, conf_file=None, **extra_config):
-        super(CachedDependencyManager, self).__init__(default_base_path=default_base_path, conf_file=conf_file, **extra_config)
+    def __init__(self, default_base_path, conf_file=None, app_config={}):
+        super(CachedDependencyManager, self).__init__(default_base_path=default_base_path, conf_file=conf_file, app_config=app_config)
 
     def build_cache(self, requirements, **kwds):
         resolved_dependencies = self.requirements_to_dependencies(requirements, **kwds)
@@ -240,7 +240,7 @@ class CachedDependencyManager(DependencyManager):
         resolved_dependencies = self.requirements_to_dependencies(requirements, **kwds)
         cacheable_dependencies = [dep for dep in resolved_dependencies.values() if dep.cacheable]
         hashed_dependencies_dir = self.get_hashed_dependencies_path(cacheable_dependencies)
-        if not os.path.exists(hashed_dependencies_dir) and self.extra_config['precache_dependencies']:
+        if not os.path.exists(hashed_dependencies_dir) and self.__app_config.getattr("precache_dependencies", False):
             # Cache not present, try to create it
             self.build_cache(requirements, **kwds)
         if os.path.exists(hashed_dependencies_dir):
diff --git a/lib/galaxy/tools/deps/requirements.py b/lib/galaxy/tools/deps/requirements.py
index bb2cfaa612f..bdb0ae0451a 100644
--- a/lib/galaxy/tools/deps/requirements.py
+++ b/lib/galaxy/tools/deps/requirements.py
@@ -1,9 +1,12 @@
+import copy
+
 from galaxy.util import (
     asbool,
     xml_text,
 )
 from galaxy.util.oset import OrderedSet
 
+
 DEFAULT_REQUIREMENT_TYPE = "package"
 DEFAULT_REQUIREMENT_VERSION = None
 
@@ -14,29 +17,69 @@ class ToolRequirement( object ):
     run (for example, a program, package, or library).  Requirements can
     optionally assert a specific version.
     """
-    def __init__( self, name=None, type=None, version=None ):
+    def __init__( self, name=None, type=None, version=None, specs=[] ):
         self.name = name
         self.type = type
         self.version = version
+        self.specs = specs
 
     def to_dict( self ):
-        return dict(name=self.name, type=self.type, version=self.version)
+        specs = [s.to_dict() for s in self.specs]
+        return dict(name=self.name, type=self.type, version=self.version, specs=specs)
+
+    def copy( self ):
+        return copy.deepcopy( self )
 
     @staticmethod
     def from_dict( dict ):
         version = dict.get( "version", None )
         name = dict.get("name", None)
         type = dict.get("type", None)
-        return ToolRequirement( name=name, type=type, version=version )
+        specs = [RequirementSpecification.from_dict(s) for s in dict.get("specs", [])]
+        return ToolRequirement( name=name, type=type, version=version, specs=specs )
 
     def __eq__(self, other):
-        return self.name == other.name and self.type == other.type and self.version == other.version
+        return self.name == other.name and self.type == other.type and self.version == other.version and self.specs == other.specs
 
     def __ne__(self, other):
         return not self.__eq__(other)
 
     def __hash__(self):
-        return hash((self.name, self.type, self.version))
+        return hash((self.name, self.type, self.version, frozenset(self.specs)))
+
+
+class RequirementSpecification(object):
+    """Refine a requirement using a URI."""
+
+    def __init__(self, uri, version=None):
+        self.uri = uri
+        self.version = version
+
+    @property
+    def specifies_version(self):
+        return self.version is not None
+
+    @property
+    def short_name(self):
+        return self.uri.split("/")[-1]
+
+    def to_dict(self):
+        return dict(uri=self.uri, version=self.version)
+
+    @staticmethod
+    def from_dict(dict):
+        uri = dict.get["uri"]
+        version = dict.get("version", None)
+        return RequirementSpecification(uri=uri, version=version)
+
+    def __eq__(self, other):
+        return self.uri == other.uri and self.version == other.version
+
+    def __ne__(self, other):
+        return not self.__eq__(other)
+
+    def __hash__(self):
+        return hash((self.uri, self.version))
 
 
 class ToolRequirements(object):
diff --git a/lib/galaxy/tools/deps/resolvers/__init__.py b/lib/galaxy/tools/deps/resolvers/__init__.py
index c24c107887a..eb6fecbeaed 100644
--- a/lib/galaxy/tools/deps/resolvers/__init__.py
+++ b/lib/galaxy/tools/deps/resolvers/__init__.py
@@ -5,6 +5,9 @@ from abc import (
     abstractproperty,
 )
 
+import yaml
+
+from galaxy.util import listify
 from galaxy.util.dictifiable import Dictifiable
 
 from ..requirements import ToolRequirement
@@ -22,10 +25,11 @@ class DependencyResolver(Dictifiable, object):
     # resolution.
     disabled = False
     resolves_simple_dependencies = True
+    config_options = {}
     __metaclass__ = ABCMeta
 
     @abstractmethod
-    def resolve( self, name, version, type, **kwds ):
+    def resolve( self, requirement, **kwds ):
         """Given inputs describing dependency in the abstract yield a Dependency object.
 
         The Dependency object describes various attributes (script, bin,
@@ -37,17 +41,14 @@ class DependencyResolver(Dictifiable, object):
         request version is 'default'.)
         """
 
-    def _get_config_option(self, key, dependency_resolver, default=None, config_prefix=None, **kwds):
-        """ Look in resolver-specific settings for option and then fallback to
-        global settings.
+
+class MultipleDependencyResolver:
+    """Variant of DependencyResolver that can optionally resolve multiple dependencies together."""
+
+    @abstractmethod
+    def resolve_all( self, requirements, **kwds ):
+        """Given multiple requirements yield Dependency objects if and only if they may all be resolved together.
         """
-        global_key = "%s_%s" % (config_prefix, key)
-        if key in kwds:
-            return kwds.get(key)
-        elif global_key in dependency_resolver.extra_config:
-            return dependency_resolver.extra_config.get(global_key)
-        else:
-            return default
 
 
 class ListableDependencyResolver:
@@ -67,6 +68,116 @@ class ListableDependencyResolver:
         return ToolRequirement(name=name, type="package", version=version)
 
 
+class MappableDependencyResolver:
+    """Mix this into a ``DependencyResolver`` to allow mapping files.
+
+    Mapping files allow adapting generic requirements to specific local implementations.
+    """
+
+    def _setup_mapping(self, dependency_manager, **kwds):
+        mapping_files = dependency_manager.get_resolver_option(self, "mapping_files", explicit_resolver_options=kwds)
+        mappings = []
+        if mapping_files:
+            mapping_files = listify(mapping_files)
+            for mapping_file in mapping_files:
+                mappings.extend(MappableDependencyResolver._mapping_file_to_list(mapping_file))
+        self._mappings = mappings
+
+    @staticmethod
+    def _mapping_file_to_list(mapping_file):
+        with open(mapping_file, "r") as f:
+            raw_mapping = yaml.load(f) or []
+            return map(RequirementMapping.from_dict, raw_mapping)
+
+    def _expand_mappings(self, requirement):
+        for mapping in self._mappings:
+            if requirement.name == mapping.from_name:
+                if mapping.from_version is not None and mapping.from_version != requirement.version:
+                    continue
+
+                requirement = requirement.copy()
+                requirement.name = mapping.to_name
+                if mapping.to_version is not None:
+                    requirement.version = mapping.to_version
+
+                break
+
+        return requirement
+
+
+class RequirementMapping(object):
+
+    def __init__(self, from_name, from_version, to_name, to_version):
+        self.from_name = from_name
+        self.from_version = from_version
+        self.to_name = to_name
+        self.to_version = to_version
+
+    @staticmethod
+    def from_dict(raw_mapping):
+        from_raw = raw_mapping.get("from")
+        if isinstance(from_raw, dict):
+            from_name = from_raw.get("name")
+            from_version = str(from_raw.get("version"))
+        else:
+            from_name = from_raw
+            from_version = None
+
+        to_raw = raw_mapping.get("to")
+        if isinstance(to_raw, dict):
+            to_name = to_raw.get("name", from_name)
+            to_version = str(to_raw.get("version"))
+        else:
+            to_name = to_raw
+            to_version = None
+
+        return RequirementMapping(from_name, from_version, to_name, to_version)
+
+
+class SpecificationAwareDependencyResolver:
+    """Mix this into a :class:`DependencyResolver` to implement URI specification matching.
+
+    Allows adapting generic requirements to more specific URIs - to tailor name
+    or version to specified resolution system.
+    """
+    __metaclass__ = ABCMeta
+
+    @abstractmethod
+    def _expand_specs(self, requirement):
+        """Find closest matching specification for discovered resolver and return new concrete requirement."""
+
+
+class SpecificationPatternDependencyResolver:
+    """Implement the :class:`SpecificationAwareDependencyResolver` with a regex pattern."""
+
+    @abstractproperty
+    def _specification_pattern(self):
+        """Pattern of URI to match against."""
+
+    def _find_specification(self, specs):
+        pattern = self._specification_pattern
+        for spec in specs:
+            if pattern.match(spec.uri):
+                return spec
+        return None
+
+    def _expand_specs(self, requirement):
+        name = requirement.name
+        version = requirement.version
+        specs = requirement.specs
+
+        spec = self._find_specification(specs)
+        if spec is not None:
+            name = spec.short_name
+            version = spec.version or version
+
+            requirement = requirement.copy()
+            requirement.name = name
+            requirement.version = version
+
+        return requirement
+
+
 class InstallableDependencyResolver:
     """ Mix this into a ``DependencyResolver`` and implement to indicate
     the dependency resolver can attempt to install new dependencies.
diff --git a/lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py b/lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py
index 5585de56c42..a6b4cde4520 100644
--- a/lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py
+++ b/lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py
@@ -29,7 +29,8 @@ class HomebrewToolShedDependencyResolver(
         self._init_homebrew(**kwds)
         self._init_base_path(dependency_manager, **kwds)
 
-    def resolve(self, name, version, type, **kwds):
+    def resolve(self, requirement, **kwds):
+        name, version, type = requirement.name, requirement.version, requirement.type
         if type != "package":
             return NullDependency(version=version, name=name)
         if version is None:
diff --git a/lib/galaxy/tools/deps/resolvers/conda.py b/lib/galaxy/tools/deps/resolvers/conda.py
index f6fe1d3925f..87a5ec14f53 100644
--- a/lib/galaxy/tools/deps/resolvers/conda.py
+++ b/lib/galaxy/tools/deps/resolvers/conda.py
@@ -5,6 +5,7 @@ incompatible changes coming.
 
 import logging
 import os
+import re
 
 import galaxy.tools.deps.installable
 
@@ -28,7 +29,10 @@ from ..resolvers import (
     DependencyResolver,
     InstallableDependencyResolver,
     ListableDependencyResolver,
+    MappableDependencyResolver,
+    MultipleDependencyResolver,
     NullDependency,
+    SpecificationPatternDependencyResolver,
 )
 
 
@@ -39,16 +43,27 @@ DEFAULT_ENSURE_CHANNELS = "iuc,bioconda,r,defaults,conda-forge"
 log = logging.getLogger(__name__)
 
 
-class CondaDependencyResolver(DependencyResolver, ListableDependencyResolver, InstallableDependencyResolver):
+class CondaDependencyResolver(DependencyResolver, MultipleDependencyResolver, ListableDependencyResolver, InstallableDependencyResolver, SpecificationPatternDependencyResolver, MappableDependencyResolver):
     dict_collection_visible_keys = DependencyResolver.dict_collection_visible_keys + ['conda_prefix', 'versionless', 'ensure_channels', 'auto_install']
     resolver_type = "conda"
+    config_options = {
+        'prefix': None,
+        'exec': None,
+        'debug': None,
+        'ensure_channels': DEFAULT_ENSURE_CHANNELS,
+        'auto_install': False,
+        'auto_init': True,
+        'copy_dependencies': False,
+    }
+    _specification_pattern = re.compile(r"https\:\/\/anaconda.org\/\w+\/\w+")
 
     def __init__(self, dependency_manager, **kwds):
+        self._setup_mapping(dependency_manager, **kwds)
         self.versionless = _string_as_bool(kwds.get('versionless', 'false'))
         self.dependency_manager = dependency_manager
 
         def get_option(name):
-            return self._get_config_option(name, dependency_manager, config_prefix="conda", **kwds)
+            return dependency_manager.get_resolver_option(self, name, explicit_resolver_options=kwds)
 
         # Conda context options (these define the environment)
         conda_prefix = get_option("prefix")
@@ -133,6 +148,8 @@ class CondaDependencyResolver(DependencyResolver, ListableDependencyResolver, In
 
         conda_targets = []
         for requirement in requirements:
+            requirement = self._expand_requirement(requirement)
+
             version = requirement.version
             if self.versionless:
                 version = None
@@ -170,7 +187,10 @@ class CondaDependencyResolver(DependencyResolver, ListableDependencyResolver, In
             assert len(conda_targets) == 1
             return conda_targets[0].install_environment
 
-    def resolve(self, name, version, type, **kwds):
+    def resolve(self, requirement, **kwds):
+        requirement = self._expand_requirement(requirement)
+        name, version, type = requirement.name, requirement.version, requirement.type
+
         # Check for conda just not being there, this way we can enable
         # conda by default and just do nothing in not configured.
         if not os.path.isdir(self.conda_context.conda_prefix):
@@ -218,6 +238,9 @@ class CondaDependencyResolver(DependencyResolver, ListableDependencyResolver, In
             preserve_python_environment=preserve_python_environment,
         )
 
+    def _expand_requirement(self, requirement):
+        return self._expand_specs(self._expand_mappings(requirement))
+
     def list_dependencies(self):
         for install_target in installed_conda_targets(self.conda_context):
             name = install_target.package
diff --git a/lib/galaxy/tools/deps/resolvers/default_conda_mapping.yml b/lib/galaxy/tools/deps/resolvers/default_conda_mapping.yml
new file mode 100644
index 00000000000..9b1e59e7a6b
--- /dev/null
+++ b/lib/galaxy/tools/deps/resolvers/default_conda_mapping.yml
@@ -0,0 +1,5 @@
+- from: R
+  to: r-base
+- from: blast+
+  to: blast
+  
\ No newline at end of file
diff --git a/lib/galaxy/tools/deps/resolvers/galaxy_packages.py b/lib/galaxy/tools/deps/resolvers/galaxy_packages.py
index 858ff0faf98..8e1a1145030 100644
--- a/lib/galaxy/tools/deps/resolvers/galaxy_packages.py
+++ b/lib/galaxy/tools/deps/resolvers/galaxy_packages.py
@@ -16,6 +16,7 @@ from ..resolvers import (
     Dependency,
     DependencyResolver,
     ListableDependencyResolver,
+    MappableDependencyResolver,
     NullDependency,
 )
 
@@ -66,11 +67,13 @@ class BaseGalaxyPackageDependencyResolver(DependencyResolver, UsesToolDependency
         self.versionless = str(kwds.get('versionless', "false")).lower() == "true"
         self._init_base_path( dependency_manager, **kwds )
 
-    def resolve( self, name, version, type, **kwds ):
+    def resolve(self, requirement, **kwds):
         """
         Attempt to find a dependency named `name` at version `version`. If version is None, return the "default" version as determined using a
         symbolic link (if found). Returns a triple of: env_script, base_path, real_version
         """
+        name, version, type = requirement.name, requirement.version, requirement.type
+
         if version is None or self.versionless:
             exact = not self.versionless or version is None
             return self._find_dep_default( name, type=type, exact=exact, **kwds )
@@ -101,9 +104,17 @@ class BaseGalaxyPackageDependencyResolver(DependencyResolver, UsesToolDependency
         return NullDependency(version=version, name=name)
 
 
-class GalaxyPackageDependencyResolver(BaseGalaxyPackageDependencyResolver, ListableDependencyResolver):
+class GalaxyPackageDependencyResolver(BaseGalaxyPackageDependencyResolver, ListableDependencyResolver, MappableDependencyResolver):
     resolver_type = "galaxy_packages"
 
+    def __init__(self, dependency_manager, **kwds):
+        super(GalaxyPackageDependencyResolver, self).__init__(dependency_manager, **kwds)
+        self._setup_mapping(dependency_manager, **kwds)
+
+    def resolve(self, requirement, **kwds):
+        requirement = self._expand_mappings(requirement)
+        return super(GalaxyPackageDependencyResolver, self).resolve(requirement, **kwds)
+
     def list_dependencies(self):
         base_path = self.base_path
         for package_name in listdir(base_path):
diff --git a/lib/galaxy/tools/deps/resolvers/homebrew.py b/lib/galaxy/tools/deps/resolvers/homebrew.py
index 395eb1eb518..2a9781d3904 100644
--- a/lib/galaxy/tools/deps/resolvers/homebrew.py
+++ b/lib/galaxy/tools/deps/resolvers/homebrew.py
@@ -39,7 +39,9 @@ class HomebrewDependencyResolver(DependencyResolver, UsesHomebrewMixin):
 
         self._init_homebrew(**kwds)
 
-    def resolve(self, name, version, type, **kwds):
+    def resolve(self, requirement, **kwds):
+        name, version, type = requirement.name, requirement.version, requirement.type
+
         if type != "package":
             return NullDependency(version=version, name=name)
 
diff --git a/lib/galaxy/tools/deps/resolvers/modules.py b/lib/galaxy/tools/deps/resolvers/modules.py
index 227abb72a9c..0cbbc5764f8 100644
--- a/lib/galaxy/tools/deps/resolvers/modules.py
+++ b/lib/galaxy/tools/deps/resolvers/modules.py
@@ -13,7 +13,12 @@ from subprocess import PIPE, Popen
 
 from six import StringIO
 
-from ..resolvers import Dependency, DependencyResolver, NullDependency
+from ..resolvers import (
+    Dependency,
+    DependencyResolver,
+    MappableDependencyResolver,
+    NullDependency,
+)
 
 log = logging.getLogger( __name__ )
 
@@ -24,11 +29,12 @@ DEFAULT_MODULE_PREFETCH = "true"
 UNKNOWN_FIND_BY_MESSAGE = "ModuleDependencyResolver does not know how to find modules by [%s], find_by should be one of %s"
 
 
-class ModuleDependencyResolver(DependencyResolver):
+class ModuleDependencyResolver(DependencyResolver, MappableDependencyResolver):
     dict_collection_visible_keys = DependencyResolver.dict_collection_visible_keys + ['base_path', 'modulepath']
     resolver_type = "modules"
 
     def __init__(self, dependency_manager, **kwds):
+        self._setup_mapping(dependency_manager, **kwds)
         self.versionless = _string_as_bool(kwds.get('versionless', 'false'))
         find_by = kwds.get('find_by', 'avail')
         prefetch = _string_as_bool(kwds.get('prefetch', DEFAULT_MODULE_PREFETCH))
@@ -51,7 +57,10 @@ class ModuleDependencyResolver(DependencyResolver):
             module_path = DEFAULT_MODULE_PATH
         return module_path
 
-    def resolve( self, name, version, type, **kwds ):
+    def resolve(self, requirement, **kwds):
+        requirement = self._expand_mappings(requirement)
+        name, version, type = requirement.name, requirement.version, requirement.type
+
         if type != "package":
             return NullDependency(version=version, name=name)
 
diff --git a/lib/galaxy/util/properties.py b/lib/galaxy/util/properties.py
index f2de11b3ae2..b5743dc0ef2 100644
--- a/lib/galaxy/util/properties.py
+++ b/lib/galaxy/util/properties.py
@@ -10,6 +10,28 @@ from six import iteritems
 from six.moves.configparser import ConfigParser
 
 
+def find_config_file(default, old_default, explicit, cwd=None):
+    if cwd is not None:
+        default = os.path.join(cwd, default)
+        old_default = os.path.join(cwd, old_default)
+        if explicit is not None:
+            explicit = os.path.join(cwd, explicit)
+
+    if explicit:
+        if os.path.exists(explicit):
+            config_file = explicit
+        else:
+            raise Exception("Problem determining Galaxy's configuration - the specified configuration file cannot be found.")
+    else:
+        if not os.path.exists( default ) and os.path.exists( old_default ):
+            config_file = old_default
+        elif os.path.exists( default ):
+            config_file = default
+        else:
+            config_file = default + ".sample"
+    return config_file
+
+
 def load_app_properties(
     kwds={},
     ini_file=None,
@@ -97,4 +119,4 @@ class NicerConfigParser(ConfigParser):
                 raise
 
 
-__all__ = ('load_app_properties', 'NicerConfigParser')
+__all__ = ('find_config_file', 'load_app_properties', 'NicerConfigParser')
diff --git a/run.sh b/run.sh
index 039047a87b8..9d7dbdfb211 100755
--- a/run.sh
+++ b/run.sh
@@ -14,6 +14,7 @@ then
     . $GALAXY_LOCAL_ENV_FILE
 fi
 
+INITIALIZE_TOOL_DEPENDENCIES=1  # Install Conda if needed.
 # Pop args meant for common_startup.sh
 while :
 do
@@ -22,6 +23,10 @@ do
             common_startup_args="$common_startup_args $1"
             shift
             ;;
+        --skip-tool-dependency-initialization)
+            INITIALIZE_TOOL_DEPENDENCIES=0
+            shift
+            ;;
         --skip-venv)
             skip_venv=1
             common_startup_args="$common_startup_args $1"
@@ -98,6 +103,11 @@ if [ -z "$GALAXY_CONFIG_FILE" ]; then
     export GALAXY_CONFIG_FILE
 fi
 
+if [ $INITIALIZE_TOOL_DEPENDENCIES -eq 1 ]; then
+    # Install Conda environment if needed.
+    python ./scripts/manage_tool_dependencies.py -c "$GALAXY_CONFIG_FILE" init_if_needed
+fi
+
 if [ -n "$GALAXY_RUN_ALL" ]; then
     servers=$(sed -n 's/^\[server:\(.*\)\]/\1/  p' "$GALAXY_CONFIG_FILE" | xargs echo)
     if [ -z "$stop_daemon_arg_set" -a -z "$daemon_or_restart_arg_set" ]; then
diff --git a/scripts/manage_tool_dependencies.py b/scripts/manage_tool_dependencies.py
new file mode 100644
index 00000000000..07b5b8802ca
--- /dev/null
+++ b/scripts/manage_tool_dependencies.py
@@ -0,0 +1,87 @@
+import argparse
+import os.path
+import sys
+
+sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, 'lib')))
+
+from galaxy.util.properties import find_config_file, load_app_properties
+from galaxy.config import (
+    configure_logging,
+    find_path,
+    find_root,
+    parse_dependency_options,
+)
+from galaxy.tools.deps import CachedDependencyManager, DependencyManager, NullDependencyManager
+
+DESCRIPTION = "Script to manage tool dependencies (with focus on a Conda environments)."
+
+
+def main(argv=None):
+    """Entry point for conversion process."""
+    if argv is None:
+        argv = sys.argv[1:]
+    args = _arg_parser().parse_args(argv)
+    action = args.action
+    action_func = ACTIONS[action]
+    action_func(args)
+
+
+def _init_if_needed(args):
+    kwargs = _app_properties(args)
+
+    # If conda_auto_init is set, simply building the Conda resolver will call handle installation.
+    _build_dependency_manager_no_config(kwargs)
+
+
+def _app_properties(args):
+    config_file = find_config_file("config/galaxy.ini", "universe_wsgi.ini", args.config_file)
+    app_properties = load_app_properties(ini_file=config_file)
+    return app_properties
+
+
+def _arg_parser():
+    parser = argparse.ArgumentParser(description=DESCRIPTION)
+    parser.add_argument('action', metavar='ACTION', type=str,
+                        choices=ACTIONS.keys(),
+                        help='action to perform')
+    parser.add_argument("-c", "--config-file", default=None)
+    return parser
+
+
+def _build_dependency_manager_no_config(kwargs):
+    """Simplified variant of build_dependency_manager from galaxy.tools.deps.
+
+    The canonical factory method requires a full Galaxy configuration object
+    which we do not have available in this script (an optimization).
+    """
+    configure_logging(kwargs)
+    root = find_root(kwargs)
+    dependency_resolvers_config_file = find_path(kwargs, "dependency_resolvers_config_file", root)
+    use_dependencies, tool_dependency_dir, use_cached_dependency_manager, tool_dependency_cache_dir, precache_dependencies = \
+        parse_dependency_options(kwargs, root, dependency_resolvers_config_file)
+
+    if not use_dependencies:
+        dependency_manager = NullDependencyManager()
+    else:
+        dependency_manager_kwds = {
+            'default_base_path': tool_dependency_dir,
+            'conf_file': dependency_resolvers_config_file,
+            'app_config': kwargs,
+        }
+
+        if use_cached_dependency_manager:
+            dependency_manager_kwds['tool_dependency_cache_dir'] = tool_dependency_cache_dir
+            dependency_manager = CachedDependencyManager(**dependency_manager_kwds)
+        else:
+            dependency_manager = DependencyManager( **dependency_manager_kwds )
+
+    return dependency_manager
+
+
+ACTIONS = {
+    "init_if_needed": _init_if_needed,
+}
+
+
+if __name__ == '__main__':
+    main()
diff --git a/test/functional/tools/legacy_r.xml b/test/functional/tools/legacy_r.xml
new file mode 100644
index 00000000000..5d70feede9f
--- /dev/null
+++ b/test/functional/tools/legacy_r.xml
@@ -0,0 +1,14 @@
+<tool id="legacy_R" name="legacy_R" version="0.1.0">
+    <command detect_errors="exit_code"><![CDATA[
+        R --version > $out_file1
+    ]]></command>
+    <requirements>
+        <requirement type="package">R</requirement>
+    </requirements>
+    <inputs>
+        <param name="input1" type="text" value="The value" />
+    </inputs>
+    <outputs>
+        <data name="out_file1" format="txt" />
+    </outputs>
+</tool>
diff --git a/test/functional/tools/samples_tool_conf.xml b/test/functional/tools/samples_tool_conf.xml
index d678c8be35d..02677a581bd 100644
--- a/test/functional/tools/samples_tool_conf.xml
+++ b/test/functional/tools/samples_tool_conf.xml
@@ -124,6 +124,8 @@
     <tool file="for_tours/filtering.xml" />
   </section>
 
+  <!-- Tools for dependency and container testing. -->
+  <tool file="legacy_r.xml" />
   <tool file="mulled_example_multi_1.xml" />
   <tool file="mulled_example_conflict.xml" />
 
diff --git a/test/integration/test_resolvers.py b/test/integration/test_resolvers.py
index 5c36fd30fbe..a676a299ca3 100644
--- a/test/integration/test_resolvers.py
+++ b/test/integration/test_resolvers.py
@@ -4,6 +4,9 @@ import shutil
 from tempfile import mkdtemp
 
 from base import integration_util
+from base.populators import (
+    DatasetPopulator,
+)
 
 GNUPLOT = {u'version': u'4.6', u'type': u'package', u'name': u'gnuplot'}
 
@@ -71,6 +74,20 @@ class CondaResolutionIntegrationTestCase(integration_util.IntegrationTestCase):
         response = create_response.json()
         self._assert_dependency_type(response)
 
+    def test_legacy_r_mapping( self ):
+        """
+        """
+        dataset_populator = DatasetPopulator(self.galaxy_interactor)
+        history_id = dataset_populator.new_history()
+        payload = dataset_populator.run_tool_payload(
+            tool_id="legacy_R",
+            inputs={},
+            history_id=history_id,
+        )
+        create_response = self._post( "tools", data=payload )
+        self._assert_status_code_is( create_response, 200 )
+        dataset_populator.wait_for_history( history_id, assert_ok=True )
+
     def test_dependency_status_installed_not_exact( self ):
         """
         GET request to dependency_resolvers/dependency with GNUPLOT dependency.
diff --git a/test/unit/tools/test_tool_deps.py b/test/unit/tools/test_tool_deps.py
index 2f4bda30fcb..1c18eedf29e 100644
--- a/test/unit/tools/test_tool_deps.py
+++ b/test/unit/tools/test_tool_deps.py
@@ -40,7 +40,7 @@ def test_tool_dependencies():
             if sub == "env.sh":
                 __touch( os.path.join( p, "env.sh" ) )
 
-        dm = DependencyManager( default_base_path=base_path )
+        dm = __dependency_manager_for_base_path( default_base_path=base_path )
         dependency = dm.find_dep( "dep1", "1.0" )
         assert dependency.script == os.path.join( base_path, 'dep1', '1.0', 'env.sh' )
         assert dependency.path == os.path.join( base_path, 'dep1', '1.0' )
@@ -70,7 +70,7 @@ TEST_VERSION = "0.5.9"
 def test_toolshed_set_enviornment_requiremetns():
     with __test_base_path() as base_path:
         test_repo = __build_test_repo('set_environment')
-        dm = DependencyManager( default_base_path=base_path )
+        dm = __dependency_manager_for_base_path( default_base_path=base_path )
         env_settings_dir = os.path.join(base_path, "environment_settings", TEST_REPO_NAME, TEST_REPO_USER, TEST_REPO_NAME, TEST_REPO_CHANGESET)
         os.makedirs(env_settings_dir)
         dependency = dm.find_dep( TEST_REPO_NAME, version=None, type='set_environment', installed_tool_dependencies=[test_repo] )
@@ -81,7 +81,7 @@ def test_toolshed_set_enviornment_requiremetns():
 def test_toolshed_package_requirements():
     with __test_base_path() as base_path:
         test_repo = __build_test_repo('package', version=TEST_VERSION)
-        dm = DependencyManager( default_base_path=base_path )
+        dm = __dependency_manager_for_base_path( default_base_path=base_path )
         package_dir = __build_ts_test_package(base_path)
         dependency = dm.find_dep( TEST_REPO_NAME, version=TEST_VERSION, type='package', installed_tool_dependencies=[test_repo] )
         assert dependency.version == TEST_VERSION
@@ -90,7 +90,7 @@ def test_toolshed_package_requirements():
 
 def test_toolshed_tools_fallback_on_manual_dependencies():
     with __test_base_path() as base_path:
-        dm = DependencyManager( default_base_path=base_path )
+        dm = __dependency_manager_for_base_path( default_base_path=base_path )
         test_repo = __build_test_repo('package', version=TEST_VERSION)
         env_path = __setup_galaxy_package_dep(base_path, "dep1", "1.0")
         dependency = dm.find_dep( "dep1", version="1.0", type='package', installed_tool_dependencies=[test_repo] )
@@ -100,7 +100,7 @@ def test_toolshed_tools_fallback_on_manual_dependencies():
 
 def test_toolshed_greater_precendence():
     with __test_base_path() as base_path:
-        dm = DependencyManager( default_base_path=base_path )
+        dm = __dependency_manager_for_base_path( default_base_path=base_path )
         test_repo = __build_test_repo('package', version=TEST_VERSION)
         ts_package_dir = __build_ts_test_package(base_path)
         gx_env_path = __setup_galaxy_package_dep(base_path, TEST_REPO_NAME, TEST_VERSION)
@@ -142,13 +142,7 @@ def test_tool_requirements():
 
 def test_module_dependency_resolver():
     with __test_base_path() as temp_directory:
-        module_script = os.path.join(temp_directory, "modulecmd")
-        __write_script(module_script, '''#!/bin/sh
-cat %s/example_output 1>&2;
-''' % temp_directory)
-        with open(os.path.join(temp_directory, "example_output"), "w") as f:
-            # Subset of module avail from MSI cluster.
-            f.write('''
+        module_script = _setup_module_command(temp_directory, '''
 -------------------------- /soft/modules/modulefiles ---------------------------
 JAGS/3.2.0-gcc45
 JAGS/3.3.0-gcc4.7.2
@@ -168,19 +162,87 @@ advisor/2013/update1    intel/11.1.075          mkl/10.2.1.017
 advisor/2013/update2    intel/11.1.080          mkl/10.2.5.035
 advisor/2013/update3    intel/12.0              mkl/10.2.7.041
 ''')
-        resolver = ModuleDependencyResolver(None, modulecmd=module_script)
-        module = resolver.resolve( name="R", version=None, type="package" )
+        resolver = ModuleDependencyResolver(_SimpleDependencyManager(), modulecmd=module_script)
+        module = resolver.resolve( ToolRequirement( name="R", version=None, type="package" ) )
         assert module.module_name == "R"
         assert module.module_version is None
 
-        module = resolver.resolve( name="R", version="3.0.1", type="package" )
+        module = resolver.resolve( ToolRequirement( name="R", version="3.0.1", type="package" ) )
         assert module.module_name == "R"
         assert module.module_version == "3.0.1"
 
-        module = resolver.resolve( name="R", version="3.0.4", type="package" )
+        module = resolver.resolve( ToolRequirement( name="R", version="3.0.4", type="package" ) )
         assert isinstance(module, NullDependency)
 
 
+def test_module_resolver_with_mapping():
+    with __test_base_path() as temp_directory:
+        module_script = _setup_module_command(temp_directory, '''
+-------------------------- /soft/modules/modulefiles ---------------------------
+blast/2.24
+''')
+        mapping_file = os.path.join(temp_directory, "mapping")
+        with open(mapping_file, "w") as f:
+            f.write('''
+- from: blast+
+  to: blast
+''')
+
+        resolver = ModuleDependencyResolver(_SimpleDependencyManager(), modulecmd=module_script, mapping_files=mapping_file)
+        module = resolver.resolve( ToolRequirement( name="blast+", version="2.24", type="package" ) )
+        assert module.module_name == "blast"
+        assert module.module_version == "2.24", module.module_version
+
+
+def test_module_resolver_with_mapping_versions():
+    with __test_base_path() as temp_directory:
+        module_script = _setup_module_command(temp_directory, '''
+-------------------------- /soft/modules/modulefiles ---------------------------
+blast/2.22.0-mpi
+blast/2.23
+blast/2.24.0-mpi
+''')
+        mapping_file = os.path.join(temp_directory, "mapping")
+        with open(mapping_file, "w") as f:
+            f.write('''
+- from:
+    name: blast+
+    version: 2.24
+  to:
+    name: blast
+    version: 2.24.0-mpi
+- from:
+    name: blast
+    version: 2.22
+  to:
+    version: 2.22.0-mpi
+''')
+
+        resolver = ModuleDependencyResolver(_SimpleDependencyManager(), modulecmd=module_script, mapping_files=mapping_file)
+        module = resolver.resolve( ToolRequirement( name="blast+", version="2.24", type="package" ) )
+        assert module.module_name == "blast"
+        assert module.module_version == "2.24.0-mpi", module.module_version
+
+        resolver = ModuleDependencyResolver(_SimpleDependencyManager(), modulecmd=module_script, mapping_files=mapping_file)
+        module = resolver.resolve( ToolRequirement( name="blast+", version="2.23", type="package" ) )
+        assert isinstance(module, NullDependency)
+
+        module = resolver.resolve( ToolRequirement( name="blast", version="2.22", type="package" ) )
+        assert module.module_name == "blast"
+        assert module.module_version == "2.22.0-mpi", module.module_version
+
+
+def _setup_module_command(temp_directory, contents):
+    module_script = os.path.join(temp_directory, "modulecmd")
+    __write_script(module_script, '''#!/bin/sh
+cat %s/example_output 1>&2;
+''' % temp_directory)
+    with open(os.path.join(temp_directory, "example_output"), "w") as f:
+        # Subset of module avail from MSI cluster.
+        f.write(contents)
+    return module_script
+
+
 def test_module_dependency():
     with __test_base_path() as temp_directory:
         # Create mock modulecmd script that just exports a variable
@@ -219,7 +281,7 @@ def test_shell_commands_built():
     # Test that dependency manager builds valid shell commands for a list of
     # requirements.
     with __test_base_path() as base_path:
-        dm = DependencyManager( default_base_path=base_path )
+        dm = __dependency_manager_for_base_path( default_base_path=base_path )
         __setup_galaxy_package_dep( base_path, TEST_REPO_NAME, TEST_VERSION, contents="export FOO=\"bar\"" )
         mock_requirements = ToolRequirements([{'type': 'package', 'version': TEST_VERSION, 'name': TEST_REPO_NAME}])
         commands = dm.dependency_shell_commands( mock_requirements )
@@ -411,5 +473,15 @@ def __dependency_manager(xml_content):
         f = tempfile.NamedTemporaryFile()
         f.write(xml_content)
         f.flush()
-        dm = DependencyManager( default_base_path=base_path, conf_file=f.name )
+        dm = __dependency_manager_for_base_path( default_base_path=base_path, conf_file=f.name )
         yield dm
+
+
+def __dependency_manager_for_base_path(default_base_path, conf_file=None ):
+    return DependencyManager( default_base_path=default_base_path, conf_file=conf_file, app_config={"conda_auto_init": False} )
+
+
+class _SimpleDependencyManager(object):
+
+    def get_resolver_option(self, resolver, key, explicit_resolver_options={}):
+        return explicit_resolver_options.get(key)