universe_wsgi.ini.sample

#
# Galaxy is configured by default to be useable in a single-user development
# environment.  To tune the application for a multi-user production
# environment, see the documentation at:
#
# http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Production%20Server
#

# Throughout this sample configuration file, except where stated otherwise,
# uncommented values override the default if left unset, whereas commented
# values are set to the default value.
# Examples of many of these options are explained in more detail in the wiki:
#
# http://wiki.g2.bx.psu.edu/Admin/Config
#
# Config hackers are encouraged to check there before asking for help.

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

# Configuration of the internal HTTP server.

[server:main]

# The internal HTTP server to use.  Currently only Paste is provided.  This
# option is required.
use = egg:Paste#http

# The port on which to listen.
#port = 8080

# The address on which to listen.  By default, only listen to localhost (Galaxy
# will not be accessible over the network).  Use '0.0.0.0' to listen on all
# available network interfaces.
#host = 127.0.0.1

# Use a threadpool for the web server instead of creating a thread for each
# request.
use_threadpool = True

# Number of threads in the web server thread pool.
#threadpool_workers = 10

# Set the number of seconds a thread can work before you should kill it (assuming it will never finish) to 3 hours.
threadpool_kill_thread_limit = 10800

# ---- Filters --------------------------------------------------------------

# Filters sit between Galaxy and the HTTP server.

# These filters are disabled by default.  They can be enabled with
# 'filter-with' in the [app:main] section below.

# Define the gzip filter.
[filter:gzip]
use = egg:Paste#gzip

# Define the proxy-prefix filter.
[filter:proxy-prefix]
use = egg:PasteDeploy#prefix
prefix = /galaxy

# ---- Galaxy ---------------------------------------------------------------

# Configuration of the Galaxy application.

[app:main]

# -- Application and filtering

# The factory for the WSGI application.  This should not be changed.
paste.app_factory = galaxy.web.buildapp:app_factory

# If not running behind a proxy server, you may want to enable gzip compression
# to decrease the size of data transferred over the network.  If using a proxy
# server, please enable gzip compression there instead.
#filter-with = gzip

# If running behind a proxy server and Galaxy is served from a subdirectory,
# enable the proxy-prefix filter and set the prefix in the
# [filter:proxy-prefix] section above.
#filter-with = proxy-prefix

# If proxy-prefix is enabled and you're running more than one Galaxy instance
# behind one hostname, you will want to set this to the same path as the prefix
# in the filter above.  This value becomes the "path" attribute set in the
# cookie so the cookies from each instance will not clobber each other.
#cookie_path = None

# -- Database

# By default, Galaxy uses a SQLite database at 'database/universe.sqlite'.  You
# may use a SQLAlchemy connection string to specify an external database
# instead.  This string takes many options which are explained in detail in the
# config file documentation.
#database_connection = sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE

# If the server logs errors about not having enough database pool connections,
# you will want to increase these values, or consider running more Galaxy
# processes.
#database_engine_option_pool_size = 5
#database_engine_option_max_overflow = 10

# If using MySQL and the server logs the error "MySQL server has gone away",
# you will want to set this to some positive value (7200 should work).
#database_engine_option_pool_recycle = -1

# If large database query results are causing memory or response time issues in
# the Galaxy process, leave the result on the server instead.  This option is
# 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

# -- 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

# Temporary files are stored in this directory.
#new_file_path = database/tmp

# Tool config files, defines what tools are available in Galaxy.
# Tools can be locally developed or installed from Galaxy tool sheds.
#tool_config_file = tool_conf.xml,shed_tool_conf.xml

# Default path to the directory containing the tools defined in tool_conf.xml.
# Other tool config files must include the tool_path as an attribute in the <toolbox> tag.
#tool_path = tools

# Path to the directory in which managed tool dependencies are placed.  To use
# the dependency system, see the documentation at:
# http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies
#tool_dependency_dir = None

# Enable automatic polling of relative tool sheds to see if any updates
# are available for installed repositories.  Ideally only one Galaxy 
# server process should be able to check for repository updates.  The
# setting for hours_between_check should be an integer between 1 and 24.
#enable_tool_shed_check = False
#hours_between_check = 12

# XML config file that contains data table entries for the ToolDataTableManager. This file is manually
# maintained by the Galaxy administrator.
#tool_data_table_config_path = tool_data_table_conf.xml

# XML config file that contains additional data table entries for the ToolDataTableManager.  This file
# is automatically generated based on the current installed tool shed repositories that contain valid
# tool_data_table_conf.xml.sample files.  At the time of installation, these entries are automatically
# added to the following file, which is parsed and applied to the ToolDataTableManager at server start up.
#shed_tool_data_table_config = shed_tool_data_table_conf.xml

# Directory where data used by tools is located, see the samples in that
# directory and the wiki for help:
# http://wiki.g2.bx.psu.edu/Admin/Data%20Integration
#tool_data_path = tool-data

# Directory where chrom len files are kept, currently mainly used by trackster
#len_file_path = tool-data/shared/ucsc/chrom

# Datatypes config file, defines what data (file) types are available in
# Galaxy.
#datatypes_config_file = datatypes_conf.xml

# Visualizations config directory: where to look for individual visualization plugins.
# The path is relative to the Galaxy root dir. To use an absolute path begin the path
# with '/'.
visualization_plugins_directory = config/plugins/visualizations

# Each job is given a unique empty directory as its current working directory.
# This option defines in what parent directory those directories will be
# created.
#job_working_directory = database/job_working_directory

# If using a cluster, Galaxy will write job scripts and stdout/stderr to this
# directory.
#cluster_files_directory = database/pbs

# 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

# Path to the directory containing the external_service_types defined in the config.
#external_service_type_path = external_service_types

# Tools with a number of outputs not known until runtime can write these
# outputs to a directory for collection by Galaxy when the job is done.
# Previously, this directory was new_file_path, but using one global directory
# can cause performance problems, so using job_working_directory ('.' or cwd
# when a job is run) is encouraged.  By default, both are checked to avoid
# breaking existing tools.
#collect_outputs_from = new_file_path,job_working_directory

# -- Data Storage (Object Store)
#
# Configuration file for the object store
# If this is set and exists, it overrides any other objectstore settings.
# object_store_config_file = object_store_conf.xml

# Object store backend module (valid options are: disk, s3, swift, irods,
# distributed, hierarchical)
#object_store = disk

# *Extremely* old Galaxy instances created datasets at the root of the
# `file_path` defined above.  If your Galaxy instance has datasets at the root
# (instead of in directories composed by hashing the dataset id), you should
# enable this option to allow Galaxy to find them.
#object_store_check_old_style = False

# Credentials used by certain (s3, swift) object store backends
#os_access_key = <your cloud object store access key>
#os_secret_key = <your cloud object store secret key>
#os_bucket_name = <name of an existing object store bucket or container>

# If using 'swift' object store, you must specify the following connection
# properties
#os_host = swift.rc.nectar.org.au
#os_port = 8888
#os_is_secure = False
#os_conn_path = /

# Reduced redundancy can be used only with the 's3' object store
#os_use_reduced_redundancy = False

# Path to cache directory for object store backends that utilize a cache (s3,
# swift, irods)
#object_store_cache_path = database/files/

# Size (in GB) that the cache used by object store should be limited to.
# If the value is not specified, the cache size will be limited only by the
# file system size.
#object_store_cache_size = 100

# Configuration file for the distributed object store, if object_store =
# distributed.  See the sample at distributed_object_store_conf.xml.sample
#distributed_object_store_config_file = None


# -- Mail and notification

# Galaxy sends mail for various things: Subscribing users to the mailing list
# if they request it, emailing password resets, notification from the Galaxy
# Sample Tracking system, reporting dataset errors, and sending activation emails.
# To do this, it needs to send mail through an SMTP server, which you may define here (host:port).
# Galaxy will automatically try STARTTLS but will continue upon failure.
#smtp_server = None

# If your SMTP server requires a username and password, you can provide them
# here (password in cleartext here, but if your server supports STARTTLS it
# will be sent over the network encrypted).
#smtp_username = None
#smtp_password = None

# If your SMTP server requires SSL from the beginning of the connection
# smtp_ssl= False

# On the user registration form, users may choose to join the mailing list.
# This is the address of the list they'll be subscribed to.
#mailing_join_addr = galaxy-announce-join@bx.psu.edu

# Datasets in an error state include a link to report the error.  Those reports
# will be sent to this address.  Error reports are disabled if no address is set.
# Also this email is shown as a contact to user in case of Galaxy misconfiguration and other events user may encounter.
#error_email_to = None

# Activation email is used as a sender ('from' field) for the account activation mail.
# We recommend using string in the following format: Galaxy Project <galaxy-no-reply@example.com>
#activation_email = None

# URL of the support resource for the galaxy instance. Used in activation emails.
#instance_resource_url = http://wiki.galaxyproject.org/

# E-mail domains blacklist is used for filtering out users that are using disposable email address
# during the registration. If their address domain matches any domain in the BL they are refused the registration.
#blacklist_file = config/disposable_email_blacklist.conf

# Registration warning message is used to discourage people from registering multiple accounts. Applies mostly for the main Galaxy instance.
# If no message specified the warning box will not be shown.
#registration_warning_message = Please register only one account - we provide this service free of charge and have limited computational resources. Multi-accounts are tracked and will be subjected to account termination and data deletion.

# When users opt to reset passwords, new ones are created, this option
# specifies the length of these passwords.
#reset_password_length = 15


# -- Account activation

# This is user account activation feature global flag. If set to "False" the rest of the Account 
# activation configuration is ignored and user activation is disabled (a.k.a. accounts are active since registration).
# Note the activation is also not working in case the smtp server is not defined.
#user_activation_on = False

# Activation grace period. Activation is not forced (login is not disabled) until 
# grace period has passed. Users under grace period can't run jobs (see inactivity_box_content).
# In hours. Default is 3. Enter 0 to disable grace period. 
# Users with OpenID logins have grace period forever. 
#activation_grace_period = 0

# Used for warning box for inactive accounts (unable to run jobs).
# In use only if activation_grace_period is set.
#inactivity_box_content = Your account has not been activated yet.  Feel free to browse around and see what's available, but you won't be able to upload data or run jobs until you have verified your email address.


# -- Display sites

# Galaxy can display data at various external browsers.  These options specify
# which browsers should be available.  URLs and builds available at these
# browsers are defined in the specifield files.

# UCSC browsers: tool-data/shared/ucsc/ucsc_build_sites.txt
#ucsc_display_sites = main,test,archaea,ucla

# GBrowse servers: tool-data/shared/gbrowse/gbrowse_build_sites.txt
#gbrowse_display_sites = modencode,sgd_yeast,tair,wormbase,wormbase_ws120,wormbase_ws140,wormbase_ws170,wormbase_ws180,wormbase_ws190,wormbase_ws200,wormbase_ws204,wormbase_ws210,wormbase_ws220,wormbase_ws225

# GeneTrack servers: tool-data/shared/genetrack/genetrack_sites.txt
#genetrack_display_sites = main,test

# If use_remote_user = True, display application servers will be denied access
# to Galaxy and so displaying datasets in these sites will fail.
# display_servers contains a list of hostnames which should be allowed to
# bypass security to display datasets.  Please be aware that there are security
# implications if this is allowed.  More details (including required changes to
# the proxy server config) are available in the Apache proxy documentation on
# the wiki.
#
# The list of servers in this sample config are for the UCSC Main, Test and
# Archaea browsers, but the default if left commented is to not allow any
# display sites to bypass security (you must uncomment the line below to allow
# them).
#display_servers = hgw1.cse.ucsc.edu,hgw2.cse.ucsc.edu,hgw3.cse.ucsc.edu,hgw4.cse.ucsc.edu,hgw5.cse.ucsc.edu,hgw6.cse.ucsc.edu,hgw7.cse.ucsc.edu,hgw8.cse.ucsc.edu,lowepub.cse.ucsc.edu

# To disable the old-style display applications that are hardcoded into datatype classes,
# set enable_old_display_applications = False.
# This may be desirable due to using the new-style, XML-defined, display applications that
# have been defined for many of the datatypes that have the old-style.
# There is also a potential security concern with the old-style applications,
# where a malicious party could provide a link that appears to reference the Galaxy server,
# but contains a redirect to a third-party server, tricking a Galaxy user to access said
# site.
#enable_old_display_applications = True

# -- Next gen LIMS interface on top of existing Galaxy Sample/Request management code.

use_nglims = False
nglims_config_file = tool-data/nglims.yaml

# -- UI Localization

# Show a message box under the masthead.
#message_box_visible = False
#message_box_content = None
#message_box_class = info

# Append "/{brand}" to the "Galaxy" text in the masthead.
#brand = None

# Format string used when showing date and time information.
# The string may contain:
# - the directives used by Python time.strftime() function (see http://docs.python.org/2/library/time.html#time.strftime ),
# - $locale (complete format string for the server locale),
# - $iso8601 (complete format string as specified by ISO 8601 international standard).
# pretty_datetime_format = $locale (UTC)

# The URL of the page to display in Galaxy's middle pane when loaded. This can be 
# an absolute or relative URL.
#welcome_url = /static/welcome.html

# The URL linked by the "Galaxy/brand" text.
#logo_url = /

# The URL linked by the "Wiki" link in the "Help" menu.
#wiki_url = http://wiki.galaxyproject.org/

# The URL linked by the "Support" link in the "Help" menu.
#support_url = http://wiki.galaxyproject.org/Support

# The URL linked by the "How to Cite Galaxy" link in the "Help" menu.
#citation_url = http://wiki.galaxyproject.org/CitingGalaxy

#The URL linked by the "Search" link in the "Help" menu.
#search_url = http://galaxyproject.org/search/usegalaxy/

#The URL linked by the "Mailing Lists" link in the "Help" menu.
#mailing_lists_url = http://wiki.galaxyproject.org/MailingLists

#The URL linked by the "Videos" link in the "Help" menu.
#videos_url = http://vimeo.com/galaxyproject

# The URL linked by the "Terms and Conditions" link in the "Help" menu, as well
# as on the user registration and login forms and in the activation emails.
#terms_url = None

# The URL linked by the "Galaxy Q&A" link in the "Help" menu
# The Galaxy Q&A site is under development; when the site is done, this URL
# will be set and uncommented.
# qa_url = 

# Serve static content, which must be enabled if you're not serving it via a
# proxy server.  These options should be self explanatory and so are not
# documented individually.  You can use these paths (or ones in the proxy
# server) to point to your own styles.
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
static_robots_txt = %(here)s/static/robots.txt

# Pack javascript at launch (/static/scripts/*.js)
# This only happens if the modified timestamp of the source .js is newer
# than the version (if it exists) in /static/scripts/packed/
# Note that this requires java > 1.4 for executing yuicompressor.jar
#pack_scripts = False

# Cloud Launch

#enable_cloud_launch = False
#cloudlaunch_default_ami = ami-a7dbf6ce

# -- Advanced proxy features

# For help on configuring the Advanced proxy features, see:
# http://usegalaxy.org/production

# Apache can handle file downloads (Galaxy-to-user) via mod_xsendfile.  Set
# this to True to inform Galaxy that mod_xsendfile is enabled upstream.
#apache_xsendfile = False

# The same download handling can be done by nginx using X-Accel-Redirect.  This
# should be set to the path defined in the nginx config as an internal redirect
# with access to Galaxy's data files (see documentation linked above).
#nginx_x_accel_redirect_base = False

# nginx can make use of mod_zip to create zip files containing multiple library
# files.  If using X-Accel-Redirect, this can be the same value as that option.
#nginx_x_archive_files_base = False

# If using compression in the upstream proxy server, use this option to disable
# gzipping of library .tar.gz and .zip archives, since the proxy server will do
# it faster on the fly.
#upstream_gzip = False

# nginx can also handle file uploads (user-to-Galaxy) via nginx_upload_module.
# Configuration for this is complex and explained in detail in the
# documentation linked above.  The upload store is a temporary directory in
# which files uploaded by the upload module will be placed.
#nginx_upload_store = False

# This value overrides the action set on the file upload form, e.g. the web
# path where the nginx_upload_module has been configured to intercept upload
# requests.
#nginx_upload_path = False

# -- Logging and Debugging

# Verbosity of console log messages.  Acceptable values can be found here:
# http://docs.python.org/library/logging.html#logging-levels
#log_level = DEBUG

# Print database operations to the server log (warning, quite verbose!).
#database_engine_option_echo = False

# Print database pool operations to the server log (warning, quite verbose!).
#database_engine_option_echo_pool = False

# Turn on logging of application events and some user events to the database.
#log_events = True

# Turn on logging of user actions to the database. Actions currently logged are
# grid views, tool searches, and use of "recently" used tools menu.  The
# log_events and log_actions functionality will eventually be merged.
#log_actions = True

# Sanitize All HTML Tool Output
# By default, all tool output served as 'text/html' will be sanitized
# thoroughly. This can be disabled if you have special tools that require
# unaltered output.
#sanitize_all_html = True

# Debug enables access to various config options useful for development and
# debugging: use_lint, use_profile, use_printdebug and use_interactive.  It
# also causes the files used by PBS/SGE (submission script, output, and error)
# to remain on disk after the job is complete.  Debug mode is disabled if
# commented, but is uncommented by default in the sample config.
debug = True

# Check for WSGI compliance.
#use_lint = False

# Run the Python profiler on each request.
#use_profile = False

# Intercept print statements and show them on the returned page.
#use_printdebug = True

# Enable live debugging in your browser.  This should NEVER be enabled on a
# public site.  Enabled in the sample config for development.
use_interactive = True

# Write thread status periodically to 'heartbeat.log',  (careful, uses disk
# space rapidly!).  Useful to determine why your processes may be consuming a
# lot of CPU.
#use_heartbeat = False

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

# -- Data Libraries

# These library upload options are described in much more detail in the wiki:
# http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files

# Add an option to the library upload form which allows administrators to
# upload a directory of files.
#library_import_dir = None

# Add an option to the library upload form which allows authorized
# non-administrators 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 = None

# Add an option to the admin library upload tool allowing admins to paste
# filesystem paths to files and directories in a box, and these paths will be
# added 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

# Users may choose to download multiple files from a library in an archive.  By
# default, Galaxy allows users to select from a few different archive formats
# if testing shows that Galaxy is able to create files using these formats.
# Specific formats can be disabled with this option, separate more than one
# format with commas.  Available formats are currently 'zip', 'gz', and 'bz2'.
#disable_library_comptypes = 

# Some sequencer integration features in beta allow you to automatically
# transfer datasets.  This is done using a lightweight transfer manager which
# runs outside of Galaxy (but is spawned by it automatically).  Galaxy will
# communicate with this manager over the port specified here.
#transfer_manager_port = 8163

# Search data libraries with whoosh
#enable_whoosh_library_search = True
# Whoosh indexes are stored in this directory.
#whoosh_index_dir = database/whoosh_indexes

# Search data libraries with lucene
#enable_lucene_library_search = False
# maxiumum file size to index for searching, in MB
#fulltext_max_size = 500
#fulltext_noindex_filetypes=bam,sam,wig,bigwig,fasta,fastq,fastqsolexa,fastqillumina,fastqsanger
# base URL of server providing search functionality using lucene
#fulltext_url = http://localhost:8081

# -- Users and Security

# Galaxy encodes various internal values when these values will be output in
# some format (for example, in a URL or cookie).  You should set a key to be
# used by the algorithm that encodes and decodes these values.  It can be any
# string.  If left unchanged, anyone could construct a cookie that would grant
# them access to others' sessions.
#id_secret = USING THE DEFAULT IS NOT SECURE!

# User authentication can be delegated to an upstream proxy server (usually
# Apache).  The upstream proxy should set a REMOTE_USER header in the request.
# Enabling remote user disables regular logins.  For more information, see:
# http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy
#use_remote_user = False

# If use_remote_user is enabled and your external authentication
# method just returns bare usernames, set a default mail domain to be appended
# to usernames, to become your Galaxy usernames (email addresses).
#remote_user_maildomain = None

# If use_remote_user is enabled, the header that the upstream proxy provides
# the remote username in defaults to HTTP_REMOTE_USER (the 'HTTP_' is prepended
# by WSGI).  This option allows you to change the header.  Note, you still need
# to prepend 'HTTP_' to the header in this option, but your proxy server should
# *not* include 'HTTP_' at the beginning of the header name.
#remote_user_header = 'HTTP_REMOTE_USER'

# If use_remote_user is enabled, you can set this to a URL that will log your
# users out.
#remote_user_logout_href = None

# If your proxy and/or authentication source does not normalize e-mail
# addresses or user names being passed to Galaxy - enable the following option
# to force these to lower case.
#normalize_remote_user_email = True  

# Administrative users - set this to a comma-separated list of valid Galaxy
# users (email addresses).  These users will have access to the Admin section
# of the server, and will have access to create users, groups, roles,
# libraries, and more.  For more information, see:
# http://wiki.g2.bx.psu.edu/Admin/Interface
#admin_users = None

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

# Allow unregistered users to create new accounts (otherwise, they will have to
# be created by an admin).
#allow_user_creation = True

# Allow administrators to delete accounts.
#allow_user_deletion = False

# Allow administrators to log in as other users (useful for debugging)
#allow_user_impersonation = False

# Allow users to remove their datasets from disk immediately (otherwise,
# datasets will be removed after a time period specified by an administrator in
# the cleanup scripts run via cron)
#allow_user_dataset_purge = False

# By default, users' data will be public, but setting this to True will cause
# it to be private.  Does not affect existing users and data, only ones created
# after this option is set.  Users may still change their default back to
# public.
#new_user_dataset_access_role_default_private = False

# -- Beta features

# Enable Galaxy to communicate directly with a sequencer
#enable_sequencer_communication = False

# Enable authentication via OpenID.  Allows users to log in to their Galaxy
# account by authenticating with an OpenID provider.
#enable_openid = False
#openid_config_file = openid_conf.xml

# Optional list of email addresses of API users who can make calls on behalf of
# other users
#api_allow_run_as = None

# Master key that allows many API admin actions to be used without actually
# having a defined admin user in the database/config. Only set this if you need
# to bootstrap Galaxy, you probably do not want to set this on public servers.
#master_api_key=changethis

# Enable tool tags (associating tools with tags).  This has its own option
# since its implementation has a few performance implications on startup for
# large servers.
#enable_tool_tags = False

# Enable a feature when running workflows. When enabled, default datasets
# are selected for "Set at Runtime" inputs from the history such that the
# same input will not be selected twice, unless there are more inputs than
# compatible datasets in the history.
# When False, the most recently added compatible item in the history will
# be used for each "Set at Runtime" input, independent of others in the Workflow
#enable_unique_workflow_defaults = False

# The URL to the myExperiment instance being used (omit scheme but include port)
#myexperiment_url = www.myexperiment.org:80

# Enable Galaxy's "Upload via FTP" interface.  You'll need to install and
# configure an FTP server (we've used ProFTPd since it can use Galaxy's
# database for authentication) and set the following two options.

# This should point to a directory containing subdirectories matching users'
# email addresses, where Galaxy will look for files.
#ftp_upload_dir = None

# This should be the hostname of your FTP server, which will be provided to
# users in the help text.
#ftp_upload_site = None

# Enable enforcement of quotas.  Quotas can be set from the Admin interface.
#enable_quotas = False

# Enable a feature when running workflows. When enabled, default datasets
# are selected for "Set at Runtime" inputs from the history such that the
# same input will not be selected twice, unless there are more inputs than
# compatible datasets in the history.
# When False, the most recently added compatible item in the history will
# be used for each "Set at Runtime" input, independent of others in the Workflow
#enable_unique_workflow_defaults = False

# This option allows users to see the full path of datasets via the "View
# Details" option in the history.  Administrators can always see this.
#expose_dataset_path = False

# Data manager configuration options
# Allow non-admin users to view available Data Manager options
#enable_data_manager_user_view = False
# File where Data Managers are configured
#data_manager_config_file = data_manager_conf.xml
# File where Tool Shed based Data Managers are configured 
#shed_data_manager_config_file = shed_data_manager_conf.xml
# Directory to store Data Manager based tool-data; defaults to tool_data_path
#galaxy_data_manager_data_path = tool-data

# -- Job Execution

# To increase performance of job execution and the web interface, you can
# separate Galaxy into multiple processes.  There are more than one way to do
# this, and they are explained in detail in the documentation:
#
#   http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Web%20Application%20Scaling
#
# By default, Galaxy manages and executes jobs from within a single process and
# notifies itself of new jobs via in-memory queues.  Jobs are run locally on
# the system on which Galaxy is started.  Advanced job running capabilities can
# be configured through the job configuration file.
#job_config_file = job_conf.xml

# In multiprocess configurations, notification between processes about new jobs
# is done via the database.  In single process configurations, this is done in
# memory, which is a bit quicker.  Galaxy tries to automatically determine
# which method it should used based on your handler configuration in the job
# config file, but you can explicitly override this behavior by setting the
# following option to True or False.
#track_jobs_in_database = None

# This enables splitting of jobs into tasks, if specified by the particular tool config.
# This is a new feature and not recommended for production servers yet.
#use_tasked_jobs = False
#local_task_queue_workers = 2

# 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

# Although it is fairly reliable, setting metadata can occasionally fail.  In
# these instances, you can choose to retry setting it internally or leave it in
# a failed state (since retrying internally may cause the Galaxy process to be
# unresponsive).  If this option is set to False, the user will be given the
# option to retry externally, or set metadata manually (when possible).
#retry_metadata_internally = True

# If (for example) you run on a cluster and your datasets (by default,
# database/files/) are mounted read-only, this option will override tool output
# paths to write outputs to the working directory instead, and the job manager
# will move the outputs to their proper place in the dataset directory on the
# Galaxy server after the job completes.
#outputs_to_working_directory = False

# If your network filesystem's caching prevents the Galaxy server from seeing
# the job's stdout and stderr files when it completes, you can retry reading
# these files.  The job runner will retry the number of times specified below,
# waiting 1 second between tries.  For NFS, you may want to try the -noac mount
# option (Linux) or -actimeo=0 (Solaris).
#retry_job_output_collection = 0

# Clean up various bits of jobs left on the filesystem after completion.  These
# bits include the job working directory, external metadata temporary files,
# and DRM stdout and stderr files (if using a DRM).  Possible values are:
# always, onsuccess, never
#cleanup_job = always

# File to source to set up the environment when running jobs.  By default, the
# environment in which the Galaxy server starts is used when running jobs
# locally, and the environment set up per the DRM's submission method and
# policy is used when running jobs on a cluster (try testing with `qsub` on the
# command line).  environment_setup_file can be set to the path of a file on
# 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.
#environment_setup_file = None

# 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
# happen for every job that is waiting to run, but if cache_user_job_count is
# set to True, it will only happen once per iteration of the handler queue.
# Although better for performance due to reduced queries, the tradeoff is a
# greater possibility that jobs will be dispatched past the configured limits
# if running many handlers.
#cache_user_job_count = False

# ToolBox filtering
# Modules from lib/galaxy/tools/filters/ can be specified in the following lines.
# tool_* filters will be applied for all users and can not be changed by them.
# user_tool_* filters will be shown under user preferences and can be toogled
# on and off by runtime
#tool_filters
#tool_label_filters
#tool_section_filters
#user_tool_filters = examples:restrict_upload_to_admins, examples:restrict_encode
#user_tool_section_filters = examples:restrict_text
#user_tool_label_filters = examples:restrict_upload_to_admins, examples:restrict_encode

# ---- 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
#rabbitmqctl_path = /path/to/rabbitmqctl