Merge branch 'release_16.01' into dev_merge_0

Conflicts:
	static/scripts/bundled/analysis.bundled.js.map
	static/scripts/bundled/libs.bundled.js
	static/scripts/bundled/libs.bundled.js.map

client/galaxy/scripts/layout/menu.js

@@ -173,7 +173,7 @@ var Collection = Backbone.Collection.extend({
         if ( !Galaxy.user.id ){
             var userTab = {
                 id              : 'user',
-                icon            : 'fa-user',
+                title           : 'User',
                 cls             : 'loggedout-only',
                 tooltip         : 'Account registration or login',
                 menu            : [{
@@ -191,7 +191,7 @@ var Collection = Backbone.Collection.extend({
         } else {
             var userTab = {
                 id              : 'user',
-                icon            : 'fa-user',
+                title           : 'User',
                 cls             : 'loggedin-only',
                 tooltip         : 'Account preferences and saved data',
                 menu            : [{

lib/galaxy/tools/cwl/cwltool_deps.py

@@ -23,10 +23,9 @@ try:
 except ImportError:
     shellescape = None
 
-if job is not None:
-    needs_shell_quoting = job.needs_shell_quoting
-else:
-    needs_shell_quoting = None
+import re
+
+needs_shell_quoting = re.compile(r"""(^$|[\s|&;()<>\'"$@])""").search
 
 
 def ensure_cwltool_available():

lib/galaxy/tools/deps/resolvers/__init__.py

@@ -27,11 +27,11 @@ class DependencyResolver(Dictifiable, object):
         version for instance if the request version is 'default'.)
         """
 
-    def _get_config_option(self, key, dependency_resolver, default=None, prefix=None, **kwds):
+    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.
         """
-        global_key = "%s_%s" % (prefix, key)
+        global_key = "%s_%s" % (config_prefix, key)
         if key in kwds:
             return kwds.get(key)
         elif global_key in dependency_resolver.extra_config:

lib/galaxy/tools/deps/resolvers/conda.py

@@ -42,7 +42,7 @@ class CondaDependencyResolver(DependencyResolver, ListableDependencyResolver, In
         self.versionless = _string_as_bool(kwds.get('versionless', 'false'))
 
         def get_option(name):
-            return self._get_config_option(name, dependency_manager, prefix="conda", **kwds)
+            return self._get_config_option(name, dependency_manager, config_prefix="conda", **kwds)
 
         # Conda context options (these define the environment)
         conda_prefix = get_option("prefix")