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

[server:main]

use = egg:Paste#http
port = 3116
host = xxxxxxxx.lifesci.dundee.ac.uk
use_threadpool = true
threadpool_workers = 10

# ---- Galaxy Web Interface -------------------------------------------------

[app:main]

# 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://www-galaxy:abc123@mysql-rw.compbio.dundee.ac.uk/galaxy
database_engine_option_pool_size = 10
database_engine_option_max_overflow = 20

# 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 = /var/opt/galaxy/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

# 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 = www-galaxy@compbio.dundee.ac.uk

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

# Comma separated list of UCSC / gbrowse browsers to use for viewing
ucsc_display_sites = main,test,archaea
gbrowse_display_sites = main,test

# 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 = @Dundee
#wiki_url = /path/to/my/local/wiki
bugs_email = www-galaxy@compbio.dundee.ac.uk

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

# Verbosity of log messages
log_level = DEBUG

# Log memory usage
log_memory_usage = False

# Log events
log_events = 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

# this should be a comma-separated list of valid Galaxy users
admin_users = chris@compbio.dundee.ac.uk

# 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

# ---- 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 = True

# 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:///
encode_import_all_latest_datasets1 = local:///
encode_import_chromatin_and_chromosomes1 = local:///
encode_import_gencode1 = local:///
encode_import_genes_and_transcripts1 = local:///
encode_import_multi-species_sequence_analysis1 = local:///
encode_import_transcription_regulation1 = local:///
hbvar = local:///
microbial_import1 = local:///
ucsc_table_direct1 = local:///
ucsc_table_direct_archaea1 = local:///
ucsc_table_direct_test1 = local:///
upload1 = local:///