Fix dependency ordering broken in #2917.

We will store dependencies in an OrderedDict, matching the order of `<requirements>`.

Fixes an issue where an R library was being sourced before R itself during shell command generation, the sourcing of R afterwards overwrote the `R_LIBS` env setting.

lib/galaxy/tools/deps/__init__.py

@@ -5,6 +5,8 @@
 import logging
 import os.path
 
+from collections import OrderedDict
+
 from galaxy.util import plugin_config
 
 from .resolvers import NullDependency
@@ -97,7 +99,7 @@ def requirements_to_dependencies(self, requirements, **kwds):
         Takes a list of requirements and returns a dictionary
         with requirements as key and dependencies as value.
         """
-        requirement_to_dependency = dict()
+        requirement_to_dependency = OrderedDict()
         for requirement in requirements:
             if requirement.type in [ 'package', 'set_environment' ]:
                 dependency = self.find_dep( name=requirement.name,