Resolve a bunch of merge conflicts.

lib/galaxy/app.py

@@ -34,9 +34,11 @@ class UniverseApplication( object ):
         #Load security policy
         self.security_agent = self.model.security_agent
         # Start the job queue
-        job_dispatcher = jobs.DefaultJobDispatcher( self )
-        self.job_queue = jobs.JobQueue( self, job_dispatcher )
-        self.job_stop_queue = jobs.JobStopQueue( self, job_dispatcher )
+        self.job_manager = jobs.JobManager( self )
+        # FIXME: These are exposed directly for backward compatibility
+        self.job_queue = self.job_manager.job_queue
+        self.job_stop_queue = self.job_manager.job_stop_queue
+        # Heartbeat and memdump for thread / heap profiling
         self.heartbeat = None
         self.memdump = None
         # Start the heartbeat process if configured and available
@@ -51,7 +53,6 @@ class UniverseApplication( object ):
             if memdump.Memdump:
                 self.memdump = memdump.Memdump()
     def shutdown( self ):
-        self.job_stop_queue.shutdown()
-        self.job_queue.shutdown()
+        self.job_manager.shutdown()
         if self.heartbeat:
             self.heartbeat.shutdown()

lib/galaxy/config.py

@@ -67,6 +67,11 @@ class Configuration( object ):
         self.library_import_dir = kwargs.get( 'library_import_dir', None )
         if self.library_import_dir is not None and not os.path.exists( self.library_import_dir ):
             raise ConfigurationError( "library_import_dir specified in config (%s) does not exist" % self.library_import_dir )
+        # Configuration options for taking advantage of nginx features
+        self.nginx_x_accel_redirect_base = kwargs.get( 'nginx_x_accel_redirect_base', False )
+        self.nginx_upload_location = kwargs.get( 'nginx_upload_store', False )
+        if self.nginx_upload_location:
+            self.nginx_upload_location = os.path.abspath( self.nginx_upload_location )
         # Parse global_conf and save the parser
         global_conf = kwargs.get( 'global_conf', None )
         global_conf_parser = ConfigParser.ConfigParser()
@@ -81,6 +86,11 @@ class Configuration( object ):
         self.datatypes_config = kwargs.get( 'datatypes_config_file', 'datatypes_conf.xml' )
     def get( self, key, default ):
         return self.config_dict.get( key, default )
+    def get_bool( self, key, default ):
+        if key in self.config_dict:
+            return string_as_bool( key )
+        else:
+            return default
     def check( self ):
         # Check that required directories exist
         for path in self.root, self.file_path, self.tool_path, self.tool_data_path, self.template_path, self.job_working_directory:

lib/galaxy/jobs/__init__.py

@@ -17,6 +17,27 @@ log = logging.getLogger( __name__ )
 # States for running a job. These are NOT the same as data states
 JOB_WAIT, JOB_ERROR, JOB_INPUT_ERROR, JOB_INPUT_DELETED, JOB_OK, JOB_READY, JOB_DELETED = 'wait', 'error', 'input_error', 'input_deleted', 'ok', 'ready', 'deleted'
 
+class JobManager( object ):
+    """
+    Highest level interface to job management.
+    
+    TODO: Currently the app accesses "job_queue" and "job_stop_queue" directly.
+          This should be decoupled. 
+    """
+    def __init__( self, app ):
+        self.app = app
+        if self.app.config.get_bool( "enable_job_running", True ):
+            # The dispatcher launches the underlying job runners
+            self.dispatcher = DefaultJobDispatcher( app )
+            # Queues for starting and stopping jobs
+            self.job_queue = JobQueue( app, self.dispatcher )
+            self.job_stop_queue = JobStopQueue( app, self.dispatcher )
+        else:
+            self.job_queue = self.job_stop_queue = NoopQueue()
+    def shutdown( self ):
+        self.job_queue.shutdown()
+        self.job_stop_queue.shutdown()
+
 class Sleeper( object ):
     """
     Provides a 'sleep' method that sleeps for a number of seconds *unless*
@@ -443,7 +464,7 @@ class JobWrapper( object ):
         # custom post process setup
         inp_data = dict( [ ( da.name, da.dataset ) for da in job.input_datasets ] )
         out_data = dict( [ ( da.name, da.dataset ) for da in job.output_datasets ] )
-        param_dict = dict( [ ( p.name, p.value ) for p in job.parameters ] ) # why not re-use self.param_dict here?
+        param_dict = dict( [ ( p.name, p.value ) for p in job.parameters ] ) # why not re-use self.param_dict here? ##dunno...probably should, this causes tools.parameters.basic.UnvalidatedValue to be used in following methods instead of validated and transformed values during i.e. running workflows
         param_dict = self.tool.params_from_strings( param_dict, self.app )
         # Check for and move associated_files
         self.tool.collect_associated_files(out_data)
@@ -594,50 +615,12 @@ class JobStopQueue( object ):
             pass  
 
         for job in jobs:
-            # jobs in a non queued/running/new state do not need to be stopped
-            if job.state not in [ model.Job.states.QUEUED, model.Job.states.RUNNING, model.Job.states.NEW ]:
-                return
-            # job has multiple datasets that aren't parent/child and not all of them are deleted.
-            if not self.check_if_output_datasets_deleted( job.id ):
-                return
-            self.mark_deleted( job.id )
             # job is in JobQueue or FooJobRunner, will be dequeued due to state change above
             if job.job_runner_name is None:
                 return
             # tell the dispatcher to stop the job
             self.dispatcher.stop( job )
 
-    def check_if_output_datasets_deleted( self, job_id ):
-        job = model.Job.get( job_id )
-        for dataset_assoc in job.output_datasets:
-            dataset = dataset_assoc.dataset
-            dataset.refresh()
-            #only the originator of the job can delete a dataset to cause
-            #cancellation of the job, no need to loop through history_associations
-            if not dataset.deleted:
-                return False
-        return True
-
-    def mark_deleted( self, job_id ):
-        job = model.Job.get( job_id )
-        job.refresh()
-        job.state = job.states.DELETED
-        job.info = "Job output deleted by user before job completed."
-        job.flush()
-        for dataset_assoc in job.output_datasets:
-            dataset = dataset_assoc.dataset
-            dataset.refresh()
-            dataset.deleted = True
-            dataset.state = dataset.states.DISCARDED
-            dataset.dataset.flush()
-            for dataset in dataset.dataset.history_associations:
-                #propagate info across shared datasets
-                dataset.deleted = True
-                dataset.blurb = 'deleted'
-                dataset.peek = 'Job deleted'
-                dataset.info = 'Job output deleted by user before job completed'
-                dataset.flush()
-
     def put( self, job ):
         self.queue.put( job )
 
@@ -652,3 +635,12 @@ class JobStopQueue( object ):
             self.queue.put( self.STOP_SIGNAL )
             self.sleeper.wake()
             log.info( "job stopper stopped" )
+
+class NoopQueue( object ):
+    """
+    Implements the JobQueue / JobStopQueue interface but does nothing
+    """
+    def put( self, *args ):
+        return
+    def shutdown( self ):
+        return

lib/galaxy/model/__init__.py

@@ -94,7 +94,35 @@ class Job( object ):
         tool = app.toolbox.tools_by_id[self.tool_id]
         param_dict = tool.params_from_strings( param_dict, app )
         return param_dict
-                
+    def check_if_output_datasets_deleted( self ):
+        """
+        Return true if all of the output datasets associated with this job are
+        in the deleted state
+        """
+        for dataset_assoc in self.output_datasets:
+            dataset = dataset_assoc.dataset
+            # only the originator of the job can delete a dataset to cause
+            # cancellation of the job, no need to loop through history_associations
+            if not dataset.deleted:
+                return False
+        return True
+    def mark_deleted( self ):
+        """
+        Mark this job as deleted, and mark any output datasets as discarded.
+        """
+        self.state = Job.states.DELETED
+        self.info = "Job output deleted by user before job completed."
+        for dataset_assoc in self.output_datasets:
+            dataset = dataset_assoc.dataset
+            dataset.deleted = True
+            dataset.state = dataset.states.DISCARDED
+            for dataset in dataset.dataset.history_associations:
+                # propagate info across shared datasets
+                dataset.deleted = True
+                dataset.blurb = 'deleted'
+                dataset.peek = 'Job deleted'
+                dataset.info = 'Job output deleted by user before job completed'
+
 class JobParameter( object ):
     def __init__( self, name, value ):
         self.name = name

lib/galaxy/model/mapping.py

@@ -356,7 +356,7 @@ StoredWorkflowMenuEntry.table = Table( "stored_workflow_menu_entry", metadata,
 
 MetadataFile.table = Table( "metadata_file", metadata, 
     Column( "id", Integer, primary_key=True ),
-    Column( "name", String ),
+    Column( "name", TEXT ),
     Column( "hda_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True, nullable=True ),
     Column( "lda_id", Integer, ForeignKey( "library_folder_dataset_association.id" ), index=True, nullable=True ),
     Column( "create_time", DateTime, default=now ),

lib/galaxy/tools/__init__.py

@@ -676,7 +676,7 @@ class Tool:
             # on the standard run form) or "URL" (a parameter provided by
             # external data source tools). 
             if "runtool_btn" not in incoming and "URL" not in incoming:
-                return "tool_form.tmpl", dict( errors={}, tool_state=state, param_values={}, incoming={} )
+                return "tool_form.mako", dict( errors={}, tool_state=state, param_values={}, incoming={} )
         # Process incoming data
         if not( self.check_values ):
             # If `self.check_values` is false we don't do any checking or
@@ -702,20 +702,20 @@ class Tool:
             # error messages
             if errors:
                 error_message = "One or more errors were found in the input you provided. The specific errors are marked below."    
-                return "tool_form.tmpl", dict( errors=errors, tool_state=state, incoming=incoming, error_message=error_message )
+                return "tool_form.mako", dict( errors=errors, tool_state=state, incoming=incoming, error_message=error_message )
             # If we've completed the last page we can execute the tool
             elif state.page == self.last_page:
                 out_data = self.execute( trans, incoming=params )
-                return 'tool_executed.tmpl', dict( out_data=out_data )
+                return 'tool_executed.mako', dict( out_data=out_data )
             # Otherwise move on to the next page
             else:
                 state.page += 1
                 # Fill in the default values for the next page
                 self.fill_in_new_state( trans, self.inputs_by_page[ state.page ], state.inputs )
-                return 'tool_form.tmpl', dict( errors=errors, tool_state=state )
+                return 'tool_form.mako', dict( errors=errors, tool_state=state )
         else:
             # Just a refresh, render the form with updated state and errors.
-            return 'tool_form.tmpl', dict( errors=errors, tool_state=state )
+            return 'tool_form.mako', dict( errors=errors, tool_state=state )
       
     def update_state( self, trans, inputs, state, incoming, prefix="", context=None,
                       update_only=False, old_errors={}, changed_dependencies={} ):
@@ -797,7 +797,7 @@ class Tool:
                 # Deal with the 'test' element and see if it's value changed
                 test_param_key = group_prefix + input.test_param.name
                 test_param_error = None
-                test_incoming = incoming.get( test_param_key, None )
+                test_incoming = get_incoming_value( incoming, test_param_key, None )
                 if test_param_key not in incoming \
                    and "__force_update__" + test_param_key not in incoming \
                    and update_only:
@@ -878,7 +878,7 @@ class Tool:
                         except:
                             pass
                     if not incoming_value_generated:
-                        incoming_value = incoming.get( key, None )
+                        incoming_value = get_incoming_value( incoming, key, None )
                     value, error = check_param( trans, input, incoming_value, context )
                     if input.dependent_params and state[ input.name ] != value:
                         # We need to keep track of changed dependency parametrs ( parameters
@@ -948,7 +948,10 @@ class Tool:
                 # Regular tool parameter
                 value = input_values[ input.name ]
                 if isinstance( value, UnvalidatedValue ):
-                    value = input.from_html( value.value, None, context )
+                    if value.value is None: #if value.value is None, it could not have been submited via html form and therefore .from_html can't be guaranteed to work
+                        value = None
+                    else:
+                        value = input.from_html( value.value, None, context )
                     # Then do any further validation on the value
                     input.validate( value, None )
                     input_values[ input.name ] = value
@@ -1361,3 +1364,12 @@ def json_fix( val ):
     else:
         return val
     
+def get_incoming_value( incoming, key, default ):
+    if "__" + key + "__is_composite" in incoming:
+        composite_keys = incoming["__" + key + "__keys"].split()
+        value = dict()
+        for composite_key in composite_keys:
+            value[composite_key] = incoming[key + "_" + composite_key]
+        return value
+    else:
+        return incoming.get( key, default )

lib/galaxy/tools/actions/upload.py

@@ -26,12 +26,22 @@ class UploadToolAction( object ):
         temp_name = ""
         data_list = []
 
-        if 'filename' in dir( data_file ):
+        if 'local_filename' in dir( data_file ):
+            # Use the existing file
             try:
                 file_name = data_file.filename
                 file_name = file_name.split( '\\' )[-1]
                 file_name = file_name.split( '/' )[-1]
-                data_list.append( self.add_file( trans, data_file.file, file_name, file_type, dbkey, space_to_tab=space_to_tab ) )
+                data_list.append( self.add_file( trans, data_file.local_filename, file_name, file_type, dbkey, space_to_tab=space_to_tab ) )
+            except Exception, e:
+                return self.upload_empty( trans, "Error:", str( e ) )
+        elif 'filename' in dir( data_file ):
+            try:
+                file_name = data_file.filename
+                file_name = file_name.split( '\\' )[-1]
+                file_name = file_name.split( '/' )[-1]
+                temp_name = sniff.stream_to_file( data_file.file )
+                data_list.append( self.add_file( trans, temp_name, file_name, file_type, dbkey, space_to_tab=space_to_tab ) )
             except Exception, e:
                 return self.upload_empty( trans, "Error:", str( e ) )
         if url_paste not in [ None, "" ]:
@@ -53,7 +63,8 @@ class UploadToolAction( object ):
                         if not NAME:
                             NAME = line
                         try:
-                            data_list.append( self.add_file( trans, urllib.urlopen( line ), NAME, file_type, dbkey, info=INFO, space_to_tab=space_to_tab ) )
+                            temp_name = sniff.stream_to_file( urllib.urlopen( line ) )
+                            data_list.append( self.add_file( trans, temp_name, NAME, file_type, dbkey, info="uploaded url", space_to_tab=space_to_tab ) )
                         except Exception, e:
                             return self.upload_empty( trans, "Error:", str( e ) )
             else:
@@ -65,7 +76,8 @@ class UploadToolAction( object ):
                         break
                 if is_valid:
                     try:
-                        data_list.append( self.add_file( trans, StringIO.StringIO( url_paste ), 'Pasted Entry', file_type, dbkey, info="pasted entry", space_to_tab=space_to_tab ) )
+                        temp_name = sniff.stream_to_file( StringIO.StringIO( url_paste ) )
+                        data_list.append( self.add_file( trans, temp_name, 'Pasted Entry', file_type, dbkey, info="pasted entry", space_to_tab=space_to_tab ) )
                     except Exception, e:
                         return self.upload_empty( trans, "Error:", str( e ) )
                 else:
@@ -90,9 +102,8 @@ class UploadToolAction( object ):
         trans.app.model.flush()
         return dict( output=data )
 
-    def add_file( self, trans, file_obj, file_name, file_type, dbkey, info=None, space_to_tab=False ):
+    def add_file( self, trans, temp_name, file_name, file_type, dbkey, info=None, space_to_tab=False ):
         data_type = None
-        temp_name = sniff.stream_to_file( file_obj )
         
         # See if we have an empty file
         if not os.path.getsize( temp_name ) > 0:

lib/galaxy/tools/parameters/__init__.py

@@ -16,9 +16,7 @@ def check_param( trans, param, incoming_value, param_values ):
     value = incoming_value
     error = None
     try:
-        if param.name == 'file_data':
-            pass
-        elif value is not None or isinstance(param, DataToolParameter):
+        if value is not None or isinstance(param, DataToolParameter):
             # Convert value from HTML representation
             value = param.from_html( value, trans, param_values )
             # Allow the value to be converted if neccesary

lib/galaxy/tools/parameters/basic.py

@@ -2,10 +2,11 @@
 Basic tool parameters.
 """
 
-import logging, string, sys, os
+import logging, string, sys, os, os.path
 from elementtree.ElementTree import XML, Element
 from galaxy import config, datatypes, util
 from galaxy.web import form_builder
+from galaxy.util.bunch import Bunch
 import validation, dynamic_options
 # For BaseURLToolParameter
 from galaxy.web import url_for
@@ -291,6 +292,23 @@ class FileToolParameter( ToolParameter ):
         self.name = elem.get( 'name' )
     def get_html_field( self, trans=None, value=None, other_values={}  ):
         return form_builder.FileField( self.name )
+    def from_html( self, value, trans=None, other_values={} ):
+        # Middleware or proxies may encode files in special ways (TODO: this
+        # should be pluggable)
+        if type( value ) == dict:
+            upload_location = self.tool.app.config.nginx_upload_location
+            assert upload_location, \
+                "Request appears to have been processed by nginx_upload_module \
+                but Galaxy is not configured to recgonize it"
+            # Check that the file is in the right location
+            local_filename = os.path.abspath( value['path'] )
+            assert local_filename.startswith( upload_location ), \
+                "Filename provided by nginx is not in correct directory"
+            value = Bunch(
+                filename = value["name"],
+                local_filename = local_filename
+            )
+        return value
     def get_required_enctype( self ):
         """
         File upload elements require the multipart/form-data encoding

lib/galaxy/tools/parameters/dynamic_options.py

@@ -102,7 +102,7 @@ class DataMetaFilter( Filter ):
             if self.multiple:
                 return dataset_value in file_value.split( self.separator )
             return file_value == dataset_value
-        assert self.ref_name in other_values or trans.workflow_building_mode, "Required dependency '%s' not found in incoming values" % self.ref_name
+        assert self.ref_name in other_values or ( trans is not None and trans.workflow_building_mode), "Required dependency '%s' not found in incoming values" % self.ref_name
         ref = other_values.get( self.ref_name, None )
         if not isinstance( ref, self.dynamic_option.tool_param.tool.app.model.HistoryDatasetAssociation ):
             return [] #not a valid dataset
@@ -146,9 +146,9 @@ class ParamValueFilter( Filter ):
     def get_dependency_name( self ):
         return self.ref_name
     def filter_options( self, options, trans, other_values ):
-        if trans.workflow_building_mode: return []
+        if trans is not None and trans.workflow_building_mode: return []
+        assert self.ref_name in other_values, "Required dependency '%s' not found in incoming values" % self.ref_name
         ref = str( other_values.get( self.ref_name, None ) )
-        assert ref is not None, "Required dependency '%s' not found in incoming values" % self.ref_name
         rval = []
         for fields in options:
             if ( self.keep and fields[self.column] == ref ) or ( not self.keep and fields[self.column] != ref ):

lib/galaxy/web/controllers/root.py

@@ -305,6 +305,28 @@ class RootController( BaseController ):
         else:
             return trans.show_error_message( "You do not have permission to edit this dataset's (%s) attributes." % id )
 
+    def __delete_dataset( self, trans, id ):
+        data = self.app.model.HistoryDatasetAssociation.get( id )
+        if data:
+            # Walk up parent datasets to find the containing history
+            topmost_parent = data
+            while topmost_parent.parent:
+                topmost_parent = topmost_parent.parent
+            assert topmost_parent in trans.history.datasets, "Data does not belong to current history"
+            # Mark deleted and cleanup
+            data.mark_deleted()
+            data.clear_associated_files()
+            trans.log_event( "Dataset id %s marked as deleted" % str(id) )
+            if data.parent_id is None and len( data.creating_job_associations ) > 0:
+                # Mark associated job for deletion
+                job = data.creating_job_associations[0].job
+                if job.state not in [ model.Job.states.QUEUED, model.Job.states.RUNNING, model.Job.states.NEW ]:
+                    return
+                # Are *all* of the job's other output datasets deleted?
+                if job.check_if_output_datasets_deleted():
+                    job.mark_deleted()                
+            self.app.model.flush()
+
     @web.expose
     def delete( self, trans, id = None, show_deleted_on_refresh = False, **kwd):
         if id:
@@ -315,55 +337,20 @@ class RootController( BaseController ):
             history = trans.get_history()
             for id in dataset_ids:
                 try:
-                    int( id )
+                    id = int( id )
                 except:
                     continue
-                data = self.app.model.HistoryDatasetAssociation.get( id )
-                if data:
-                    # Walk up parent datasets to find the containing history
-                    topmost_parent = data
-                    while topmost_parent.parent:
-                        topmost_parent = topmost_parent.parent
-                    assert topmost_parent in history.datasets, "Data does not belong to current history"
-                    # Mark deleted and cleanup
-                    data.mark_deleted()
-                    data.clear_associated_files()
-                    self.app.model.flush()
-                    trans.log_event( "Dataset id %s marked as deleted" % str(id) )
-                    if data.parent_id is None:
-                        try:
-                            self.app.job_stop_queue.put( data.creating_job_associations[0].job )
-                        except IndexError:
-                            pass    # upload tool will cause this since it doesn't have a job
+                self.__delete_dataset( trans, id )
         return self.history( trans, show_deleted = show_deleted_on_refresh )
         
     @web.expose
     def delete_async( self, trans, id = None, **kwd):
         if id:
             try:
-                int( id )
+                id = int( id )
             except:
                 return "Dataset id '%s' is invalid" %str( id )
-            history = trans.get_history()
-            data = self.app.model.HistoryDatasetAssociation.get( id )
-            if data:
-                # Walk up parent datasets to find the containing history
-                topmost_parent = data
-                while topmost_parent.parent:
-                    topmost_parent = topmost_parent.parent
-                assert topmost_parent in history.datasets, "Data does not belong to current history"
-                # Mark deleted and cleanup
-                data.mark_deleted()
-                data.clear_associated_files()
-                self.app.model.flush()
-                trans.log_event( "Dataset id %s marked as deleted async" % str(id) )
-                if data.parent_id is None:
-                    try:
-                        self.app.job_stop_queue.put( data.creating_job_associations[0].job )
-                    except IndexError:
-                        pass    # upload tool will cause this since it doesn't have a job
-            else:
-                return "Dataset id '%s' is invalid" %str( id )
+            self.__delete_dataset( trans, id )
         return "OK"
 
     ## ---- History management -----------------------------------------------

lib/galaxy/web/framework/base.py

@@ -5,6 +5,7 @@ A simple WSGI application/framework.
 import socket
 import types
 import logging
+import os.path
 import sys
 
 from Cookie import SimpleCookie
@@ -132,16 +133,16 @@ class WebApplication( object ):
         if callable( body ):
             # Assume the callable is another WSGI application to run
             return body( environ, start_response )
+        elif isinstance( body, types.FileType ):
+            # Stream the file back to the browser
+            return send_file( start_response, trans, body )
         else:
             start_response( trans.response.wsgi_status(), 
                             trans.response.wsgi_headeritems() )
             return self.make_body_iterable( trans, body )
         
     def make_body_iterable( self, trans, body ):
-        if isinstance( body, types.FileType ):
-            # Stream the file back to the browser
-            return iterate_file( body )
-        elif isinstance( body, ( types.GeneratorType, list, tuple ) ):
+        if isinstance( body, ( types.GeneratorType, list, tuple ) ):
             # Recursively stream the iterable
             return flatten( body )
         elif isinstance( body, basestring ):
@@ -302,6 +303,20 @@ class Response( object ):
 
 CHUNK_SIZE = 2**16
 
+def send_file( start_response, trans, body ):
+    # If configured use X-Accel-Redirect header for nginx
+    base = trans.app.config.nginx_x_accel_redirect_base
+    if base:
+        trans.response.headers['X-Accel-Redirect'] = \
+            base + os.path.abspath( body.name )
+        body = [ "" ]
+    # Fall back on sending the file in chunks
+    else:
+        body = iterate_file( body )
+    start_response( trans.response.wsgi_status(), 
+                    trans.response.wsgi_headeritems() )
+    return body
+
 def iterate_file( file ):
     """
     Progressively return chunks from `file`.

scripts/cleanup_datasets/cleanup_datasets.py

@@ -191,8 +191,6 @@ def purge_histories( h, d, m, cutoff_time, remove_from_disk ):
                             if errmsg:
                                 errors = True
                                 print errmsg
-                            else:
-                                print "%s" % dataset.file_name
                         else:
                             dataset.purged = True
                             dataset.flush()
@@ -264,7 +262,6 @@ def purge_datasets( d, m, cutoff_time, remove_from_disk ):
                print errmsg
             else:
                 dataset_count += 1
-                print "%s" % dataset.file_name
         else:
             dataset.purged = True
             dataset.file_size = 0
@@ -314,6 +311,7 @@ def purge_dataset( dataset, m ):
             else:
                 # Remove dataset file from disk
                 os.unlink( dataset.file_name )
+                print "%s" % dataset.file_name
                 # Mark all associated MetadataFiles as deleted and purged and remove them from disk
                 print "The following metadata files associated with dataset '%s' have been purged" % dataset.file_name
                 for hda in dataset.history_associations:

scripts/scramble/scripts/pbs_python.py

@@ -27,6 +27,9 @@ for dir in [ "build", "dist" ]:
         print "scramble(): removing dir:", dir
         shutil.rmtree( dir )
 
+# the build process doesn't set an rpath for libtorque
+os.environ['LD_RUN_PATH'] = os.environ['LIBTORQUE_DIR']
+
 print "scramble(): Running pbs_python configure script"
 p = subprocess.Popen( args = "sh configure --with-pbsdir=%s" % os.environ['LIBTORQUE_DIR'], shell = True )
 r = p.wait()

templates/tool_executed.mako

@@ -4,37 +4,31 @@
 <head>
 <title>Galaxy</title>
 <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
-<link href="$h.url_for('/static/style/base.css')" rel="stylesheet" type="text/css" />
+<link href="${h.url_for('/static/style/base.css')}" rel="stylesheet" type="text/css" />
 <script type="text/javascript">
   var inside_galaxy_frameset = false;
 
-  if ( parent.frames && parent.frames.galaxy_history )
-  {
-      parent.frames.galaxy_history.location.href="$h.url_for( controller='root', action='history' )";
-    
+  if ( parent.frames && parent.frames.galaxy_history ) {
+      parent.frames.galaxy_history.location.href="${h.url_for( controller='root', action='history' )}";
       inside_galaxy_frameset = true;
   }
   
-  if ( parent.handle_minwidth_hint )
-  {
+  if ( parent.handle_minwidth_hint ) {
       parent.handle_minwidth_hint( -1 );
   }
 
-  function main()
-  {
+  function main() {
     // If called from outside the galaxy frameset, redirect there
-    #if $tool.options.refresh
-      if ( ! inside_galaxy_frameset )
-      {
+    %if tool.options.refresh:
+      if ( ! inside_galaxy_frameset ) {
         setTimeout( "refresh()", 1000 );
         document.getElementById( "refresh_message" ).style.display = "block";
       }
-    #end if
+    %endif
   }
 
-  function refresh()
-  {
-    top.location.href = '$request.base';
+  function refresh() {
+    top.location.href = '${request.base}';
   }
 
 </script>
@@ -43,14 +37,13 @@
 
 <body onLoad="main()">
 
-
 <div class="donemessage">
 
 <p>The following job has been succesfully added to the queue:</p>
 
-#for $data in $out_data.values
-   <div style="padding: 10px"><b> $data.hid: $data.name</b></div>
-#end for
+%for data in out_data.values():
+   <div style="padding: 10px"><b> ${data.hid}: ${data.name}</b></div>
+%endfor
 
 <p>
 You can check the status of queued jobs and view the resulting 
@@ -59,9 +52,9 @@ the status will change from 'running' to 'finished' if completed
 succesfully or 'error' if problems were encountered.
 </p>
 
-#if $tool.options.refresh
-<p id="refresh_message" style="display: none;">You are now being redirected back to <a href="$request.base">Galaxy</a></div>
-#end if
+%if tool.options.refresh:
+<p id="refresh_message" style="display: none;">You are now being redirected back to <a href="${request.base}">Galaxy</a></div>
+%endif
 
 </div>
 

templates/tool_form.mako

@@ -0,0 +1,194 @@
+<!-- -->
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+
+<%
+from galaxy.util.expressions import ExpressionContext 
+%>
+
+<html>
+
+<head>
+<title>Galaxy</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
+<link href="${h.url_for('/static/style/base.css')}" rel="stylesheet" type="text/css" />
+<script type='text/javascript' src="${h.url_for('/static/scripts/jquery.js')}"> </script>
+<script type="text/javascript">
+$( function() {
+    $( "select[@refresh_on_change='true']").change( function() {
+        $( "#tool_form" ).submit();
+    });
+});
+%if not add_frame.debug:
+    if( window.name != "galaxy_main" ) {
+        location.replace( '${h.url_for( controller='root', action='index', tool_id=tool.id )}' );
+    }
+%endif
+</script>
+</head>
+
+<body>
+
+<%def name="do_inputs( inputs, tool_state, errors, prefix, other_values=None )">
+  <% other_values = ExpressionContext( tool_state, other_values ) %>
+    %for input_index, input in enumerate( inputs.itervalues() ):
+        %if input.type == "repeat":
+          <div class="repeat-group">
+              <div class="form-title-row"><b>${input.title_plural}</b></div>
+              <% repeat_state = tool_state[input.name] %>
+              %for i in range( len( repeat_state ) ):
+                <div class="repeat-group-item">
+                <%
+                if input.name in errors:
+                    rep_errors = errors[input.name][i]
+                else:
+                    rep_errors = dict()
+                index = repeat_state[i]['__index__']
+                %>
+                <div class="form-title-row"><b>${input.title} ${i + 1}</b></div>
+                ${do_inputs( input.inputs, repeat_state[i], rep_errors, prefix + input.name + "_" + str(index) + "|", other_values )}
+                <div class="form-row"><input type="submit" name="${prefix}${input.name}_${index}_remove" value="Remove ${input.title} ${i+1}"></div>
+                </div>
+              %endfor
+              <div class="form-row"><input type="submit" name="${prefix}${input.name}_add" value="Add new ${input.title}"></div>
+          </div>
+        %elif input.type == "conditional":
+            <%
+            group_state = tool_state[input.name]
+            group_errors = errors.get( input.name, {} )
+            current_case = group_state['__current_case__']
+            group_prefix = prefix + input.name + "|"
+            %>
+            ${row_for_param( group_prefix, input.test_param, group_state, group_errors, other_values )}
+            ${do_inputs( input.cases[current_case].inputs, group_state, group_errors, group_prefix, other_values )}
+        %else:
+            ${row_for_param( prefix, input, tool_state, errors, other_values )}
+        %endif
+    %endfor  
+</%def>
+
+<%def name="row_for_param( prefix, param, parent_state, parent_errors, other_values )">
+    <%
+    if parent_errors.has_key( param.name ):
+        cls = "form-row form-row-error"
+    else:
+        cls = "form-row"
+    %>
+    <div class="${cls}">
+        <% label = param.get_label() %>
+        %if label:
+            <label>
+                ${label}:
+            </label>
+        %endif
+        <%
+        field = param.get_html_field( trans, parent_state[ param.name ], other_values )
+        field.refresh_on_change = param.refresh_on_change
+        %>
+        <div style="float: left; width: 250px; margin-right: 10px;">${field.get_html( prefix )}</div>
+        %if parent_errors.has_key( param.name ):
+        <div style="float: left; color: red; font-weight: bold; padding-top: 1px; padding-bottom: 3px;">
+            <div style="width: 300px;"><img style="vertical-align: middle;" src="${h.url_for('/static/style/error_small.png')}">&nbsp;<span style="vertical-align: middle;">${parent_errors[param.name]}</span></div>
+        </div>
+        %endif
+        
+        %if param.help:
+        <div class="toolParamHelp" style="clear: both;">
+            ${param.help}
+        </div>
+        %endif
+
+        <div style="clear: both"></div>
+                
+    </div>
+</%def>
+
+%if add_frame.from_noframe:
+    <div class="warningmessage">
+    <strong>Welcome to Galaxy</strong>
+    <hr/>
+    It appears that you found this tool from a link outside of Galaxy.
+    If you're not familiar with Galaxy, please consider visiting the
+    <a href="${h.url_for( controller='root' )}" target="_top">welcome page</a>.
+    To learn more about what Galaxy is and what it can do for you, please visit
+    the <a href="$add_frame.wiki_url" target="_top">Galaxy wiki</a>.
+    </div>
+    <br/>
+%endif
+
+<div class="toolForm" id="$tool.id">
+  %if tool.has_multiple_pages:
+  <div class="toolFormTitle">${tool.name} (step ${tool_state.page+1} of ${tool.npages})</div>
+  %else:
+  <div class="toolFormTitle">${tool.name}</div>
+  %endif
+  <div class="toolFormBody">
+  <form id="tool_form" name="tool_form" action="${h.url_for( tool.action )}" enctype="${tool.enctype}" target="${tool.target}" method="${tool.method}">
+    <input type="hidden" name="tool_id" value="${tool.id}">
+    <input type="hidden" name="tool_state" value="${util.object_to_string( tool_state.encode( tool, app ) )}">
+    
+    %if tool.display_by_page[tool_state.page]:
+        ${trans.fill_template_string( tool.display_by_page[tool_state.page], other_values=tool.get_param_html_map( trans, tool_state.page, tool_state.inputs ) )}
+        <input type="submit" class="primary-button" name="runtool_btn" value="Execute">
+        
+    %else:
+        
+          <div style="display: none;">
+            %if tool_state.page == tool.last_page:
+            <input type="submit" class="primary-button" name="runtool_btn" value="Execute">
+            %else:
+            <input type="submit" class="primary-button" name="runtool_btn" value="Next step">
+            %endif
+          </div>
+          ${do_inputs( tool.inputs_by_page[ tool_state.page ], tool_state.inputs, errors, "" )}
+          <div class="form-row">
+            %if tool_state.page == tool.last_page:
+            <input type="submit" class="primary-button" name="runtool_btn" value="Execute">
+            %else:
+            <input type="submit" class="primary-button" name="runtool_btn" value="Next step">
+            %endif
+          </div>    
+        
+    %endif    
+
+  </form>
+  </div>
+</div>
+
+%if tool.help:
+<div class="toolHelp">
+     <div class="toolHelpBody">
+     %if tool.has_multiple_pages:
+        ${tool.help_by_page[tool_state.page]}
+     %else:
+     ${tool.help}
+     %endif
+     </div>        
+</div>
+%endif
+
+</body>
+
+<script type="text/javascript">
+   $( function() {
+       $( 'li > ul' ).each( function( i ) {
+           if ( $( this )[0].className == 'toolParameterExpandableCollapsable' )
+           {
+               var parent_li = $( this ).parent( 'li' );
+               var sub_ul = $( this ).remove();
+               parent_li.find( 'span' ).wrapInner( '<a/>' ).find( 'a' ).click( function() {
+                 sub_ul.toggle();
+                 $( this )[0].innerHTML = ( sub_ul[0].style.display=='none' ) ? '[+]' : '[-]';
+               });
+               parent_li.append( sub_ul );
+           }
+       });
+       $( 'ul ul' ).each( function(i) {
+           if ( $( this )[0].className == 'toolParameterExpandableCollapsable' && this.attributes.getNamedItem( 'default_state' ).value == 'collapsed' )
+           {
+               $( this ).hide();
+           }
+       });
+   });
+</script>
+
+</html>

templates/tool_form.tmpl

@@ -1,191 +0,0 @@
-<!-- -->
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
-
-#from galaxy.util.expressions import ExpressionContext 
-
-<html>
-
-<head>
-<title>Galaxy</title>
-<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
-<link href="$h.url_for('/static/style/base.css')" rel="stylesheet" type="text/css" />
-<script type='text/javascript' src="$h.url_for('/static/scripts/jquery.js')"> </script>
-<script type="text/javascript">
-jQuery( function() {
-    jQuery( "select[@refresh_on_change='true']").change( function() {
-        jQuery( "#tool_form" ).submit();
-    });
-});
-#if not $add_frame.debug
-    if( window.name != "galaxy_main" ) {
-        location.replace( '$h.url_for( controller='root', action='index', tool_id=$tool.id )' );
-    }
-#end if
-</script>
-</head>
-
-<body>
-
-## #if $getVar( 'error_message', None )
-##    <div class="errormessagesmall">$error_message</div>
-##    <p></p>
-## #end if
-
-#def do_inputs( $inputs, $tool_state, $errors, $prefix, $context=None )
-  #set $context = ExpressionContext( $tool_state, $context )
-  #for $input_index, $input in enumerate( $inputs.itervalues() )
-    #if $input.type == "repeat"
-      <div class="repeat-group">
-          <div class="form-title-row"><b>${input.title_plural}</b></div>
-          #set repeat_state = $tool_state[$input.name]
-          #for i in range( len( $repeat_state ) ):
-            <div class="repeat-group-item">
-            #if $input.name in errors
-              #set rep_errors = $errors[$input.name][$i]
-            #else
-              #set rep_errors = dict()
-            #end if
-            #set index = $repeat_state[$i]['__index__']
-            <div class="form-title-row"><b>${input.title} ${i + 1}</b></div>
-            $do_inputs( $input.inputs, $repeat_state[$i], $rep_errors, $prefix + $input.name + "_" + str($index) + "|", $context )
-            <div class="form-row"><input type="submit" name="${prefix}${input.name}_${index}_remove" value="Remove ${input.title} ${i+1}"></div>
-            </div>
-          #end for
-          <div class="form-row"><input type="submit" name="${prefix}${input.name}_add" value="Add new ${input.title}"></div>
-      </div>
-    #elif $input.type == "conditional"
-      #set group_state = $tool_state[$input.name]
-      #set group_errors = $errors.get( $input.name, {} )
-      #set current_case = $group_state['__current_case__']
-      #set group_prefix = $prefix + $input.name + "|"
-      $row_for_param( $group_prefix, $input.test_param, $group_state, $group_errors, $context )
-      $do_inputs( $input.cases[$current_case].inputs, $group_state, $group_errors, $group_prefix, $context )
-    #else
-      $row_for_param( $prefix, $input, $tool_state, $errors, $context )
-    #end if
-  #end for  
-#end def
-
-#def row_for_param( $prefix, $param, $parent_state, $parent_errors, $context )
-    #if $parent_errors.has_key( $param.name ):
-        #set cls = "form-row form-row-error"
-    #else
-        #set cls = "form-row"
-    #end if
-    <div class="$cls">
-        #set label = $param.get_label()
-        #if $label:
-            <label>
-                $label:
-            </label>
-        #end if
-        #set field = $param.get_html_field( $caller, $parent_state[ $param.name ], $context )
-        #set $field.refresh_on_change = $param.refresh_on_change
-        <div style="float: left; width: 250px; margin-right: 10px;">$field.get_html( $prefix )</div>
-        #if $parent_errors.has_key( $param.name ):
-        <div style="float: left; color: red; font-weight: bold; padding-top: 1px; padding-bottom: 3px;">
-            <div style="width: 300px;"><img style="vertical-align: middle;" src="$h.url_for('/static/style/error_small.png')">&nbsp;<span style="vertical-align: middle;">$parent_errors[$param.name]</span></div>
-        </div>
-        #elif $param.help
-        ##<div class="toolParamHelp" style="float: right;">$param.help</div>
-        #end if
-        
-        #if $param.help
-        <div class="toolParamHelp" style="clear: both;">
-            $param.help
-        </div>
-        
-        #end if
-
-        <div style="clear: both"></div>
-                
-    </div>
-#end def
-
-#if $add_frame.from_noframe
-    <div class="warningmessage">
-    <strong>Welcome to Galaxy</strong>
-    <hr/>
-    It appears that you found this tool from a link outside of Galaxy.  If you're not familiar with Galaxy, please consider visiting the <a href="$h.url_for( controller='root' )" target="_top">welcome page</a>.  To learn more about what Galaxy is and what it can do for you, please visit the <a href="$add_frame.wiki_url" target="_top">Galaxy wiki</a>.
-    </div>
-    <br/>
-#end if
-
-<div class="toolForm" id="$tool.id">
-  #if $tool.has_multiple_pages 
-  <div class="toolFormTitle">$tool.name (step #echo $tool_state.page+1 # of $tool.npages)</div>
-  #else
-  <div class="toolFormTitle">$tool.name</div>
-  #end if
-  <div class="toolFormBody">
-  <form id="tool_form" name="tool_form" action="$h.url_for( $tool.action )" enctype="$tool.enctype" target="$tool.target" method="$tool.method">
-    <input type="hidden" name="tool_id" value="$tool.id">
-    <input type="hidden" name="tool_state" value="$util.object_to_string( $tool_state.encode( $tool, $app ) )">
-    
-    #if $tool.display_by_page[$tool_state.page]
-        
-        $caller.fill_template_string( $tool.display_by_page[$tool_state.page], context=$tool.get_param_html_map( $caller, $tool_state.page, $tool_state.inputs ) )
-        <input type="submit" class="primary-button" name="runtool_btn" value="Execute">
-        
-    #else
-        
-          <div style="display: none;">
-            #if $tool_state.page == $tool.last_page
-            <input type="submit" class="primary-button" name="runtool_btn" value="Execute">
-            #else
-            <input type="submit" class="primary-button" name="runtool_btn" value="Next step">
-            #end if
-          </div>
-          $do_inputs( $tool.inputs_by_page[ $tool_state.page ], $tool_state.inputs, $errors, "" )
-          <div class="form-row">
-            #if $tool_state.page == $tool.last_page
-            <input type="submit" class="primary-button" name="runtool_btn" value="Execute">
-            #else
-            <input type="submit" class="primary-button" name="runtool_btn" value="Next step">
-            #end if
-          </div>    
-        
-    #end if    
-
-  </form>
-  </div>
-</div>
-
-#if $tool.help
-<div class="toolHelp">
-     <div class="toolHelpBody">
-     #if $tool.has_multiple_pages
-     $tool.help_by_page[$tool_state.page]
-     #else
-     $tool.help
-     #end if
-     </div>        
-</div>
-#end if
-
-</body>
-
-<script type="text/javascript">
-   \$( function() {
-       \$( 'li > ul' ).each( function( i ) {
-           if ( \$( this )[0].className == 'toolParameterExpandableCollapsable' )
-           {
-               var parent_li = \$( this ).parent( 'li' );
-               var sub_ul = \$( this ).remove();
-               parent_li.find( 'span' ).wrapInner( '<a/>' ).find( 'a' ).click( function() {
-                 sub_ul.toggle();
-                 \$( this )[0].innerHTML = ( sub_ul[0].style.display=='none' ) ? '[+]' : '[-]';
-               });
-               parent_li.append( sub_ul );
-           }
-       });
-       \$( 'ul ul' ).each( function(i) {
-           if ( \$( this )[0].className == 'toolParameterExpandableCollapsable' && this.attributes.getNamedItem( 'default_state' ).value == 'collapsed' )
-           {
-               \$( this ).hide();
-           }
-       });
-   });
-</script>
-
-</html>

tools/data_source/microbial_import_code.py

@@ -80,7 +80,7 @@ def load_microbial_data( GALAXY_DATA_INDEX_DIR, sep='\t' ):
     return microbe_info
 
 #post processing, set build for data and add additional data to history
-from galaxy import datatypes, config, jobs 
+from galaxy import datatypes, config, jobs, tools
 from shutil import copyfile
 
 def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr):
@@ -96,7 +96,12 @@ def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr
     #if not (kingdom or group or org):
     if not (kingdom or org):
         print "Parameters are not available."
-    
+    #workflow passes galaxy.tools.parameters.basic.UnvalidatedValue instead of values
+    if isinstance( kingdom, tools.parameters.basic.UnvalidatedValue ):
+        kingdom = kingdom.value
+    if isinstance( org, tools.parameters.basic.UnvalidatedValue ):
+        org = org.value
+    
     GALAXY_DATA_INDEX_DIR = app.config.tool_data_path
     microbe_info = load_microbial_data( GALAXY_DATA_INDEX_DIR, sep='\t' )
     new_stdout = ""

tools/new_operations/complement.xml

@@ -18,6 +18,11 @@
       <param name="allchroms" value="true" />
       <output name="output" file="gops_complement_out.bed" />
     </test>
+    <test>
+      <param name="input1" value="2_mod.bed" ftype="interval"/>
+      <param name="allchroms" value="true" />
+      <output name="output" file="gops_complement_out_diffCols.dat" />
+    </test>
     <test>
       <param name="input1" value="gops_bigint.interval" />
       <param name="allchroms" value="true" />

tools/new_operations/coverage.xml

@@ -19,6 +19,11 @@
       <param name="input2" value="2.bed" />
       <output name="output" file="gops_coverage_out.interval" />
     </test>
+    <test>
+      <param name="input1" value="1.bed" />
+      <param name="input2" value="2_mod.bed" ftype="interval"/>
+      <output name="output" file="gops_coverage_out_diffCols.interval" />
+    </test>
     <test>
       <param name="input1" value="gops_bigint.interval" />
       <param name="input2" value="gops_bigint2.interval" />

tools/new_operations/intersect.xml

@@ -21,13 +21,27 @@
     <data format="input" name="output" metadata_source="input1" />
   </outputs>
   <code file="operation_filter.py"/>
-  <tests>
+  <tests>
+    <test>
+      <param name="input1" value="1.bed" />
+      <param name="input2" value="2.bed" />
+      <param name="min" value="1" />
+      <param name="returntype" value="" />
+      <output name="output" file="gops_intersect_out.bed" />
+    </test>
     <test>
       <param name="input1" value="1.bed" />
-      <param name="input2" value="2.bed" />
+      <param name="input2" value="2_mod.bed" ftype="interval"/>
       <param name="min" value="1" />
-      <param name="returntype" value="" />
-      <output name="output" file="gops_intersect_out.bed" />
+      <param name="returntype" value="" />
+      <output name="output" file="gops_intersect_diffCols.bed" />
+    </test>
+    <test>
+      <param name="input1" value="1.bed" />
+      <param name="input2" value="2_mod.bed" ftype="interval"/>
+      <param name="min" value="1" />
+      <param name="returntype" value="Overlapping pieces of Intervals" />
+      <output name="output" file="gops_intersect_p_diffCols.bed" />
     </test>
     <test>
       <param name="input1" value="1.bed" />

tools/new_operations/merge.xml

@@ -21,6 +21,11 @@
       <output name="output" file="gops-merge.dat" />
       <param name="returntype" value="true" />
     </test>
+    <test>
+      <param name="input1" value="2_mod.bed" ftype="interval"/>
+      <output name="output" file="gops_merge_diffCols.dat" />
+      <param name="returntype" value="true" />
+    </test>
     <test>
       <param name="input1" value="gops_bigint.interval" />
       <output name="output" file="gops_merge_out2.bed" />

tools/new_operations/subtract.xml

@@ -32,6 +32,13 @@
       <param name="returntype" value="" />
       <output name="output" file="gops-subtract.dat" />
     </test>
+    <test>
+      <param name="input1" value="1.bed" />
+      <param name="input2" value="2_mod.bed" ftype="interval"/>
+      <param name="min" value="1" />
+      <param name="returntype" value="" />
+      <output name="output" file="gops_subtract_diffCols.dat" />
+    </test>
     <test>
       <param name="input1" value="gops_subtract_bigint.bed" />
       <param name="input2" value="2.bed" />

universe_wsgi.ini.sample

@@ -34,7 +34,7 @@ job_queue_cleanup_interval = 30
 # Database connection
 database_file = database/universe.sqlite
 # You may use a SQLAlchemy connection string to specify an external database instead
-## database_connection = postgres:///galaxy_test
+## database_connection = postgres:///galaxy
 ## database_engine_option_echo = true
 ## database_engine_option_echo_pool = true
 ## database_engine_option_pool_size = 10
@@ -93,12 +93,15 @@ mailing_join_addr = galaxy-user-join@bx.psu.edu
 # Write thread status periodically to 'heartbeat.log' (careful, uses disk space rapidly!)
 ## use_heartbeat = True
 
+# Enable the memory debugging interface (careful, negatively impacts server performance)
+## use_memdump = True
+
 # Profiling middleware (cProfile based)
 ## use_profile = True
 
-# Mail
-smtp_server = coltrane.bx.psu.edu
-error_email_to = galaxy-bugs@bx.psu.edu
+# For use by 'report this error' link on error-state datasets
+#smtp_server = smtp.example.org
+#error_email_to = galaxy-bugs@example.org
 
 # Use the new iframe / javascript based layout
 use_new_layout = true
@@ -124,29 +127,34 @@ static_style_dir = %(here)s/static/june_2007_style/blue
 ## wiki_url: replaces the default galaxy main wiki
 ## bugs_email: replaces the default galaxy bugs email list
 #brand = Private local mirror
-#wiki_url=/path/to/my/local/wiki
-#bugs_email=mailto:bugmaster@this.site.com
+#wiki_url = /path/to/my/local/wiki
+#bugs_email = mailto:galaxy-bugs@example.org
 
 # ---- Job Runners ----------------------------------------------------------
 
 # Clustering Galaxy is not a straightforward process and requires a lot of
-# pre-configuration.  See the ClusteringGalaxy Wiki before attempting to set any
-# of these options.  If running normally (without a cluster), do not change
-# anything in this section.
+# pre-configuration.  See the ClusteringGalaxy Wiki before attempting to set
+# any of these options:
+#
+# http://g2.trac.bx.psu.edu/wiki/ClusteringGalaxy
+#
+# If running normally (without a cluster), do not change anything in this
+# section.
 
 # start_job_runners: Comma-separated list of job runners to start.  local is
 # always started.  If left commented, no jobs will be run on the cluster, even
 # if a cluster URL is explicitly defined in the [galaxy:tool_runners] section
-# below.  The only runner currently available is 'pbs'.
+# below.  The runners currently available are 'pbs' and 'sge'.
 #start_job_runners = pbs
 
 # default_cluster_job_runner: The URL for the default runner to use when a tool
 # doesn't explicity define a runner below.  For help on the cluster URL format,
-# see the ClusteringGalaxy Wiki.  Leave commented if not using a cluster job runner.
+# see the ClusteringGalaxy Wiki.  Leave commented if not using a cluster job
+# runner.
 #default_cluster_job_runner = pbs:///
 
 # The PBS options are described in detail in the Galaxy Configuration section of
-# the ClusteringGalaxy Wiki
+# the ClusteringGalaxy Wiki, and are only necessary when using file staging.
 #pbs_application_server = 
 #pbs_stage_path = 
 #pbs_dataset_server = 
@@ -156,8 +164,6 @@ static_style_dir = %(here)s/static/june_2007_style/blue
 [galaxy:tool_runners]
 
 biomart = local:///
-blat2wig = pbs:///blast
-blat_wrapper = pbs:///blast
 encode_db1 = local:///
 encode_import_all_latest_datasets1 = local:///
 encode_import_chromatin_and_chromosomes1 = local:///
@@ -165,13 +171,8 @@ encode_import_gencode1 = local:///
 encode_import_genes_and_transcripts1 = local:///
 encode_import_multi-species_sequence_analysis1 = local:///
 encode_import_transcription_regulation1 = local:///
-generate_coverage_report = pbs:///blast
 hbvar = local:///
-hist_high_quality_score = pbs:///blast
-megablast_wrapper = pbs:///blast
-megablast_xml_parser = pbs:///blast
 microbial_import1 = local:///
-quality_score_distribution = pbs:///blast
 ucsc_table_direct1 = local:///
 ucsc_table_direct_archaea1 = local:///
 ucsc_table_direct_test1 = local:///