Don't use QB3 cluster in examples

Switch all example SGE usage from the obsolete QB3
cluster to the current Wynton cluster.

doc/backend.rst

@@ -30,7 +30,7 @@ For any web service, the :class:`Job` class must first be subclassed and then
 one or more of its methods implemented to actually do the work of running jobs.
 For example, the :meth:`Job.run` method will be called by the backend when
 the job starts; it is expected to start the job running on the cluster,
-typically by using an :class:`SGERunner` object. There are similar methods
+typically by using a :class:`WyntonSGERunner` object. There are similar methods
 that can be used to do extra processing before the job starts
 (:meth:`Job.preprocess`), after it finishes running on the cluster
 (:meth:`Job.postprocess` and :meth:`Job.finalize`) or when the job is moved
@@ -53,7 +53,7 @@ job output should simply indicate what the problem is).
    in the subclass. For example, to run a new job, call
    :meth:`Job.reschedule_run`, not the :meth:`Job.run` method directly.
 
-As mentioned above, an :class:`SGERunner` class is provided that takes care of
+As mentioned above, a :class:`WyntonSGERunner` class is provided that takes care of
 the details of running a script on the cluster and checking if it has
 completed. Typically the script run here should use the local /scratch disk
 on the cluster nodes if possible - this is not implemented automatically by
@@ -176,7 +176,7 @@ The example below demonstrates a simple :class:`Job` subclass that, given a
 set of PDB files from the frontend, runs an SGE job on the cluster that
 extracts all of the HETATM records from each PDB. This is done by
 overriding the :meth:`Job.run` method to pass a set of shell script commands
-to an :class:`SGERunner` instance; this instance is then returned to the
+to an :class:`WyntonSGERunner` instance; this instance is then returned to the
 backend. The backend will then keep track of the SGE job, and notice when
 it finishes.
 

doc/installation.rst

@@ -38,10 +38,10 @@ Prerequisites
 * SGE. The framework expects to be run on a machine that is a submit host to a Sun GridEngine compute cluster
   (or a compatible product, such as `OGE <http://www.oracle.com/us/products/tools/oracle-grid-engine-075549.html>`_
   or `OGS <http://gridscheduler.sourceforge.net/>`_). The framework talks to SGE via DRMAA, so you will also need
-  the `DRMAA Python bindings <https://github.com/pygridtools/drmaa-python>`_. The framework contains classes to
-  talk to the three SGE installations available in the Sali lab - :class:`SGERunner`, :class:`WyntonSGERunner`, and :class:`SaliSGERunner`
-  in :file:`saliweb/python/saliweb/backend/__init__.py`. To work in your environment, add a new subclass to that file
-  (see the implementation of :class:`SaliSGERunner` for an example) setting the `SGE_CELL` and `SGE_ROOT` environment
+  the `DRMAA Python bindings <https://github.com/pygridtools/drmaa-python>`_. The framework contains a class to
+  talk to the SGE installation available in the Sali lab - :class:`WyntonSGERunner`
+  in :file:`saliweb/python/saliweb/backend/__init__.py`. To work in your environment, add a new :class:`SGERunner` subclass to that file
+  (see the implementation of :class:`WyntonSGERunner` for an example) setting the `SGE_CELL` and `SGE_ROOT` environment
   variables appropriately, setting `DRMAA_LIBRARY_PATH` to the location of your :file:`libdrmaa.so` file, setting
   `_runner_name` to a unique value, and setting `_qstat` to the full path to your :file:`qstat` binary.
 

examples/customdb.py

@@ -8,7 +8,7 @@ def __init__(self, jobcls):
 
 
 class Job(saliweb.backend.Job):
-    runnercls = saliweb.backend.SGERunner
+    runnercls = saliweb.backend.WyntonSGERunner
 
     def preprocess(self):
         pdbs = glob.glob("*.pdb")

examples/logging.py

@@ -2,7 +2,7 @@
 import logging
 
 class Job(saliweb.backend.Job):
-    runnercls = saliweb.backend.SGERunner
+    runnercls = saliweb.backend.WyntonSGERunner
 
     def run(self):
         # Uncomment to get all logging output

examples/package.py

@@ -8,7 +8,7 @@ def __init__(self, jobcls):
 
 
 class Job(saliweb.backend.Job):
-    runnercls = saliweb.backend.SGERunner
+    runnercls = saliweb.backend.WyntonSGERunner
 
     def preprocess(self):
         pdbs = glob.glob("*.pdb")

examples/simplejob.py

@@ -4,7 +4,7 @@
 import os
 
 class Job(saliweb.backend.Job):
-    runnercls = saliweb.backend.SGERunner
+    runnercls = saliweb.backend.WyntonSGERunner
 
     def run(self):
         script = """