universe_wsgi.ini changes for August release.

gistfile1.txt

Summary of new options added to universe_wsgi.ini:

display_chunk_size - Size of chunks to use when incrementally loading tabular data in the web browser.

citation_cache_type, citation_cache_data_dir, citation_cache_lock_dir - Tool citation (add this release) information maybe fetched from external sources such as http://dx.doi.org/ by Galaxy - these parameters can be used to control the caching used to store this information.

job_resource_params_file - An experimental feature allowing deployers to inject extra parameters into the tool form that can be parsed and used when allocating resources via dynamic job destinations. This option describes the tool form elements.

Options that have been removed: rsync_url, genome_data_path.

While not a new option, documentation for install_database_connection has been added.

Full Diff:

hg diff -r stable:next-stable universe_wsgi.ini.sample 
diff -r 7a4d321c0e38 -r d85ae37476a1 universe_wsgi.ini.sample
--- a/universe_wsgi.ini.sample  Wed Jul 30 11:13:20 2014 -0400
+++ b/universe_wsgi.ini.sample  Sat Aug 09 15:38:33 2014 -0400
@@ -109,23 +109,21 @@
 # only available for PostgreSQL and is highly recommended.
 #database_engine_option_server_side_cursors = False
 
-# Create only one connection to the database per thread, to reduce the
-# connection overhead.  Recommended when not using SQLite:
-#database_engine_option_strategy = threadlocal
-
 # Log all database transactions, can be useful for debugging and performance
 # profiling.  Logging is done via Python's 'logging' module under the qualname
 # 'galaxy.model.orm.logging_connection_proxy'
 #database_query_profiling_proxy = False
 
+# By default, Galaxy will use the same database to track user data and
+# tool shed install data. There are many situtations in which it is
+# valuable to seperate these - for instance bootstrapping fresh Galaxy
+# instances with pretested installs. The following optin can be used to
+# separate the tool shed install database (all other options listed above 
+# but prefixed with install_ are also available).
+#install_database_connection = sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE
+
 # -- Files and directories
 
-# Path where genome builds are stored. This defaults to tool-data/genome
-#genome_data_path = tool-data/genome
-
-# URL for rsync server to download pre-built indexes.
-#rsync_url = rsync://datacache.galaxyproject.org/indexes
-
 # Dataset files are stored in this directory.
 #file_path = database/files
 
@@ -210,6 +208,13 @@
 # used for the cache
 #template_cache_path = database/compiled_templates
 
+# Citation related caching. Tool citations information maybe fetched from
+# external sources such as http://dx.doi.org/ by Galaxy - the following parameters
+# can be used to control the caching used to store this information.
+#citation_cache_type=file
+#citation_cache_data_dir=database/citations/data
+#citation_cache_lock_dir=database/citations/lock
+
 # External service types config file, defines what types of external_services configurations 
 # are available in Galaxy.
 #external_service_type_config_file = external_service_types_conf.xml
@@ -454,6 +459,10 @@
 #enable_cloud_launch = False
 #cloudlaunch_default_ami = ami-a7dbf6ce
 
+# Incremental Display Options
+
+#display_chunk_size = 65536
+
 # -- Advanced proxy features
 
 # For help on configuring the Advanced proxy features, see:
@@ -796,9 +805,15 @@
 # the cluster that should be sourced by the user to set up the environment
 # prior to running tools.  This can be especially useful for running jobs as
 # the actual user, to remove the need to configure each user's environment
-# individually.  This only affects cluster jobs, not local jobs.
+# individually.
 #environment_setup_file = None
 
+
+# Optional file containing job resource data entry fields definition.
+# These fields will be presented to users in the tool forms and allow them to
+# overwrite default job resources such as number of processors, memory, and walltime.
+#job_resource_params_file = job_resource_params_conf.xml
+
 # If using job concurrency limits (configured in job_config_file), several
 # extra database queries must be performed to determine the number of jobs a
 # user has dispatched to a given destination.  By default, these queries will
@@ -831,7 +846,7 @@
 # will automatically create and use a separate sqlite database located in your
 # <galaxy>/database folder (indicated in the commented out line below).
 
-#amqp_internal_connection = sqlite:///./database/control.sqlite?isolation_level=IMMEDIATE
+#amqp_internal_connection = sqlalchemy+sqlite:///./database/control.sqlite?isolation_level=IMMEDIATE