# ---- HTTP Server ----------------------------------------------------------

[server:main]

use = egg:Paste#http
port = 3216
host = xxxxx.dundee.ac.uk
use_threadpool = true
threadpool_workers = 10

# ---- HTTP gzip compression ----
# If planning to run Galaxy as a production service, we recommend running Galaxy 
# through a proxy and enabling gzip compression there (instructions at 
# http://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer )
# but you may also turn on Paste's built-in gzip compressor by uncommenting the following lines
# and also the 'filter-with = gzip' line under [app:main]. This will reduce network traffic
# and should speed up the interface, especially the visualization module.
# [filter:gzip]
# use = egg:Paste#gzip

# ---- Galaxy Web Interface -------------------------------------------------
[app:main]

# Uncomment following line to enable Paste gzip compression
# filter-with = gzip

# Uncomment following line below to enable visualization module
# enable_tracks = True

# Specifies the factory for the universe WSGI application
paste.app_factory = galaxy.web.buildapp:app_factory

# By default, Galaxy uses a SQLite database found here
#database_file = database/universe.sqlite

# You may use a SQLAlchemy connection string to specify an external database
# instead.  PostgreSQL and MySQL are supported.
database_connection = mysql://xxxxx:xxxxxxx@xxxxxxx.dundee.ac.uk/galaxy
database_engine_option_pool_size = 10
database_engine_option_max_overflow = 20
#database_engine_option_echo = true
#database_engine_option_echo_pool = true

# If using MySQL, see:
# http://rapd.wordpress.com/2008/03/02/sqlalchemy-sqlerror-operationalerror-2006-mysql-server-has-gone-away/
# To handle this issue, try the following setting:
database_engine_option_pool_recycle = 7200

# Where dataset files are saved
file_path = database/files
# Temporary storage for additional datasets, this should be shared through the cluster
new_file_path = database/tmp

# Tools
tool_config_file = tool_conf.xml
tool_path = tools
tool_data_path = tool-data

# Datatype converters
datatype_converters_config_file = datatype_converters_conf.xml
datatype_converters_path = %(here)s/lib/galaxy/datatypes/converters

# Datatype indexers
datatype_indexers_path = %(here)s/lib/galaxy/datatypes/indexers
# Metadata
set_metadata_externally = False

# Session support (beaker)
use_beaker_session = True
session_type = file
session_data_dir = %(here)s/database/beaker_sessions
session_key = galaxysessions
session_secret = changethisinproduction

# Galaxy session security
id_secret = changethisinproductiontoo

# Directories of files contained in the following directory can be uploaded to
# a library from the Admin view
library_import_dir = /homes/www-galaxy/data_import

# The following can be configured to allow non-admin users to upload a
# directory of files.  The configured directory must contain sub-directories
# named the same as the non-admin user's Galaxy login ( email ).  The non-admin
# user is restricted to uploading files or sub-directories of files contained
# in their directory.
#user_library_import_dir = /var/opt/galaxy/import/users

# The admin library upload tool may contain a box allowing admins to paste
# filesystem paths to files and directories to add to a library.  Set to True
# to enable.  Please note the security implication that this will give Galaxy
# Admins access to anything your Galaxy user has access to.
#allow_library_path_paste = False

# path to sendmail
sendmail_path = /usr/sbin/sendmail

# Address to join mailing list
mailing_join_addr = galaxy-user-join@bx.psu.edu

# For use by 'report this error' link on error-state datasets
smtp_server = smtp.lifesci.dundee.ac.uk
error_email_to = xxxxxxxxxxxxxxxxxxxxx

# Use the new iframe / javascript based layout
use_new_layout = true

# Comma separated list of UCSC / gbrowse / GeneTrack browsers to use for viewing
ucsc_display_sites = main,test,archaea,ucla
gbrowse_display_sites = main,test,tair
# Define your GeneTrack servers in tool-data/shared/genetrack/genetrack_sites.txt
#genetrack_display_sites =

# Serving static files (needed if running standalone)
static_enabled = True
static_cache_time = 360
static_dir = %(here)s/static/
static_images_dir = %(here)s/static/images
static_favicon_dir = %(here)s/static/favicon.ico
static_scripts_dir = %(here)s/static/scripts/
static_style_dir = %(here)s/static/june_2007_style/blue

## Leave these commented out for the defaults at the main galaxy site
## Uncomment and adjust these to change locally configurable items in the masthead
## for a local mirror where you are doing private software development
##
## Brand: appends "/[brand]" to the "Galaxy" text in the masthead
## wiki_url: replaces the default galaxy main wiki
## bugs_email: replaces the default galaxy bugs email list
brand = @Development
#wiki_url = /path/to/my/local/wiki
bugs_email = xxxxxxxxxxxxxxxxxxx

# ---- Logging and Debugging ------------------------------------------------

# Verbosity of log messages
log_level = DEBUG

# Log memory usage
log_memory_usage = False

# Log events
log_events = True

# Log user actions
log_actions = True

# Configuration for debugging middleware
debug = True
use_lint = False

# Interactive debugging - NEVER enable this on a public site
use_interactive = False

# Write thread status periodically to 'heartbeat.log' (careful, uses disk space rapidly!)
#use_heartbeat = False

# Enable the memory debugging interface (careful, negatively impacts server performance)
#use_memdump = False

# Profiling middleware (cProfile based)
#use_profile = False

# ---- Users and Security ---------------------------------------------------

# User authentication can be delegated to an upstream proxy server (usually
# Apache).  This is explained on the Galaxy wiki:
#
# http://g2.trac.bx.psu.edu/wiki/HowToInstall/ApacheProxy

# Use user provided in an upstream server's $REMOTE_USER variable
#use_remote_user = False

# If use_remote_user is enabled and your external authentication
# method just returns bare usernames, set a default mail domain
#remote_user_maildomain = example.org

# If use_remote_user is enabled, set a logout anchor href option
#remote_user_logout_href = /logout

# this should be a comma-separated list of valid Galaxy users
admin_users = xxxxxxxxxxxxxxxxxxxxxxxxx

# Force everyone to log in (disable anonymous access)
#require_login = False

# Can users register new accounts?
allow_user_creation = True

# Can an admin user delete user accounts?
allow_user_deletion = False

# Should default dataset access permissions be private for new users; default is False (datasets are public)
new_user_dataset_access_role_default_private = False

# ---- Cloud Management --------------------------------------------------------

# Uncomment following line to enable cloud management mode (only leaves the Cloud, Help and User tabs on)
# cloud_controller_instance = True

# ---- Job Execution --------------------------------------------------------

# Number of concurrent jobs to run (local job runner)
local_job_queue_workers = 3

# Should jobs be tracked through the database, rather than in memory
#track_jobs_in_database = False

# Enable job recovery (if Galaxy is restarted while cluster jobs are running,
# it can "recover" them when it starts).  This is not safe to use if you are
# running more than one Galaxy server using the same database.
enable_job_recovery = False

# Job scheduling policy to be used. 
# module/package name and classname should be in "module:classname" format.
# Comment / uncomment the following policies depending upon which is to be used.
#job_scheduler_policy = FIFO
job_scheduler_policy = galaxy.jobs.schedulingpolicy.roundrobin:UserRoundRobin

# Job queue cleanup interval in minutes. Currently only used by RoundRobin
job_queue_cleanup_interval = 30

# Jobs can be killed after a certain amount of execution time.  Format is in
# hh:mm:ss.  Currently only implemented for PBS.  Leave commented for
# unlimited.
#job_walltime = 10:00:00

# 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:
#
# http://g2.trac.bx.psu.edu/wiki/ClusteringGalaxy
#
# If running normally (without a cluster), do not change anything in this
# section.

# 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 runners
# currently available are 'pbs' and 'sge'.
start_job_runners = sge

# 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.
default_cluster_job_runner = sge:///

# The cluster runners have their own thread pools used to prepare and finish
# jobs (so that these operations do not block normal queue operation).  The
# value here is the number of worker threads available to each runner.
cluster_job_queue_workers = 3

# Individual per-tool job runner overrides.  If not listed here, a tool will
# run with the runner defined with default_cluster_job_runner.
[galaxy:tool_runners]

biomart = local:///
encode_db1 = local:///
hbvar = local:///
microbial_import1 = local:///
ucsc_table_direct1 = local:///
ucsc_table_direct_archaea1 = local:///
ucsc_table_direct_test1 = local:///
upload1 = local:///
#detag_reads = sge://///-q 64bit-pri.q -l ram=3G -R y/
#quality_clip_reads = sge://///-q 64bit-pri.q -l ram=3G -R y/
#collate_reads = sge://///-q 64bit-pri.q -l ram=4G -R y/
#run_vmatch = sge://///-q 64bit-pri.q -l ram=2G/


# Galaxy Message Queue
# Galaxy uses AMQ protocol to receive messages from external sources like 
# bar code scanners. Galaxy has been tested against RabbitMQ AMQP implementation.
# For Galaxy to receive messages from a message queue the RabbitMQ server has 
# to be set up with a user account and other parameters listed below. The 'host'
# and 'port' fields should point to where the RabbitMQ server is running. 

#[galaxy:amqp]
#host = 127.0.0.1
#port = 5672
#userid = galaxy
#password = galaxy
#virtual_host = galaxy_messaging_engine
#queue = galaxy_queue
#exchange = galaxy_exchange
#routing_key = bar_code_scanner