Merge pull request #3358 from jmchilton/dev_merge

Merge latest release 16.10 into dev.

lib/galaxy/tools/__init__.py

@@ -399,6 +399,16 @@ class Tool( object, Dictifiable ):
     def valid_input_states( self ):
         return model.Dataset.valid_input_states
 
+    @property
+    def requires_galaxy_python_environment(self):
+        """Indicates this tool's runtime requires Galaxy's Python environment."""
+        # All special tool types (data source, history import/export, etc...)
+        # seem to require Galaxy's Python.
+        return self.tool_type != "default" or self.id in [
+            "__SET_METADATA__",
+            "upload1",
+        ]
+
     def __get_job_tool_configuration(self, job_params=None):
         """Generalized method for getting this tool's job configuration.
 
@@ -1327,6 +1337,7 @@ class Tool( object, Dictifiable ):
             installed_tool_dependencies=self.installed_tool_dependencies,
             tool_dir=self.tool_dir,
             job_directory=job_directory,
+            preserve_python_environment=self.requires_galaxy_python_environment,
             metadata=metadata,
             tool_instance=self
         )

lib/galaxy/tools/deps/container_resolvers/explicit.py

@@ -20,7 +20,7 @@ class ExplicitContainerResolver(ContainerResolver):
         a correct container.
         """
         for container_description in tool_info.container_descriptions:
-            if self._container_type_enabled(container_description):
-                return True
+            if self._container_type_enabled(container_description, enabled_container_types):
+                return container_description
 
-        return False
+        return None

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

@@ -120,6 +120,8 @@ class CondaDependencyResolver(DependencyResolver, ListableDependencyResolver, In
             conda_target, conda_context=self.conda_context
         )
 
+        preserve_python_environment = kwds.get("preserve_python_environment", False)
+
         job_directory = kwds.get("job_directory", None)
         if not is_installed and self.auto_install and job_directory:
             is_installed = self.install_dependency(name=name, version=version, type=type)
@@ -144,7 +146,8 @@ class CondaDependencyResolver(DependencyResolver, ListableDependencyResolver, In
             conda_environment,
             exact,
             name,
-            version
+            version,
+            preserve_python_environment=preserve_python_environment,
         )
 
     def list_dependencies(self):
@@ -195,7 +198,7 @@ class CondaDependency(Dependency):
     dependency_type = 'conda'
     cacheable = True
 
-    def __init__(self, conda_context, environment_path, exact, name=None, version=None):
+    def __init__(self, conda_context, environment_path, exact, name=None, version=None, preserve_python_environment=False):
         self.activate = conda_context.activate
         self.conda_context = conda_context
         self.environment_path = environment_path
@@ -203,6 +206,7 @@ class CondaDependency(Dependency):
         self._name = name
         self._version = version
         self.cache_path = None
+        self._preserve_python_environment = preserve_python_environment
 
     @property
     def exact(self):
@@ -243,11 +247,19 @@ class CondaDependency(Dependency):
         if not self.cache_path:
             # Build an isolated environment if not using a cached dependency manager
             self.build_environment()
-        return """[ "$CONDA_DEFAULT_ENV" = "%s" ] || . %s '%s' > conda_activate.log 2>&1 """ % (
-            self.environment_path,
-            self.activate,
-            self.environment_path
-        )
+        if self._preserve_python_environment:
+            # On explicit testing the only such requirement I am aware of is samtools - and it seems to work
+            # fine with just appending the PATH as done below. Other tools may require additional
+            # variables in the future.
+            return """export PATH=$PATH:'%s/bin' """ % (
+                self.environment_path,
+            )
+        else:
+            return """[ "$CONDA_DEFAULT_ENV" = "%s" ] || . %s '%s' > conda_activate.log 2>&1 """ % (
+                self.environment_path,
+                self.activate,
+                self.environment_path
+            )
 
 
 def _string_as_bool( value ):