Allow per-manager job directories.

Update: Rebased on to the latest master and documentation for this feature in docs/job_managers.rst and linked to this general manager configuration information from app.yml.sample (per excellent request of @mvdbeek).

app.yml.sample

@@ -2,7 +2,8 @@
 ## to an absolute path, such as /tmp/pulsar_staging or C:\\pulsar_staging
 #staging_directory: files/staging
 
-## Configure one or more named managers.
+## Configure one or more named managers (more information on configuring managers
+## can be found at http://pulsar.readthedocs.org/en/latest/job_managers.html).
 #managers:
 #  _default_:
 #    type: queued_python

docs/job_managers.rst

@@ -158,6 +158,9 @@ the Galaxy mailing list.
 More Options
 -------------------------------
 
+Any manager can override the ``staging_directory`` used by setting this
+property in its configuration section.
+
 The ``min_polling_interval: 0.5`` option can be set on any manager to control
 how frequently Pulsar will poll the resource manager for job updates.
 

pulsar/managers/base/__init__.py

@@ -59,7 +59,8 @@ class BaseManager(ManagerInterface):
         self.persistence_directory = getattr(app, 'persistence_directory', None)
         self.lock_manager = locks.LockManager()
         self._directory_maker = DirectoryMaker(kwds.get("job_directory_mode", None))
-        self._setup_staging_directory(app.staging_directory)
+        staging_directory = kwds.get("staging_directory", app.staging_directory)
+        self._setup_staging_directory(staging_directory)
         self.id_assigner = get_id_assigner(kwds.get("assign_ids", None))
         self.__init_galaxy_system_properties(kwds)
         self.debug = str(kwds.get("debug", False)).lower() == "true"