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1#
2# Galaxy is configured by default to be usable in a single-user development
3# environment.  To tune the application for a multi-user production
4# environment, see the documentation at:
5#
6#  http://usegalaxy.org/production
7#
8
9# Throughout this sample configuration file, except where stated otherwise,
10# uncommented values override the default if left unset, whereas commented
11# values are set to the default value.  Relative paths are relative to the root
12# Galaxy directory.
13#
14# Examples of many of these options are explained in more detail in the wiki:
15#
16#   https://wiki.galaxyproject.org/Admin/Config
17#
18# Config hackers are encouraged to check there before asking for help.
19
20# ---- HTTP Server ----------------------------------------------------------
21
22# Configuration of the internal HTTP server.
23
24[server:main]
25
26# The internal HTTP server to use.  Currently only Paste is provided.  This
27# option is required.
28use = egg:Paste#http
29
30# The port on which to listen.
31port = 8080
32
33# The address on which to listen.  By default, only listen to localhost (Galaxy
34# will not be accessible over the network).  Use '0.0.0.0' to listen on all
35# available network interfaces.
36host = 0.0.0.0
37
38# Use a threadpool for the web server instead of creating a thread for each
39# request.
40use_threadpool = True
41
42# Number of threads in the web server thread pool.
43threadpool_workers = 10
44
45# Set the number of seconds a thread can work before you should kill it
46# (assuming it will never finish) to 3 hours.  Default is 600 (10 minutes).
47threadpool_kill_thread_limit = 10800
48
49# ---- Filters --------------------------------------------------------------
50
51# Filters sit between Galaxy and the HTTP server.
52
53# These filters are disabled by default.  They can be enabled with
54# 'filter-with' in the [app:main] section below.
55
56# Define the gzip filter.
57[filter:gzip]
58use = egg:Paste#gzip
59
60# Define the proxy-prefix filter.
61[filter:proxy-prefix]
62use = egg:PasteDeploy#prefix
63prefix = /S
64
65# ---- Galaxy ---------------------------------------------------------------
66
67# Configuration of the Galaxy application.
68
69[app:main]
70
71# -- Application and filtering
72
73# The factory for the WSGI application.  This should not be changed.
74paste.app_factory = galaxy.web.buildapp:app_factory
75
76# If not running behind a proxy server, you may want to enable gzip compression
77# to decrease the size of data transferred over the network.  If using a proxy
78# server, please enable gzip compression there instead.
79#filter-with = gzip
80
81# If running behind a proxy server and Galaxy is served from a subdirectory,
82# enable the proxy-prefix filter and set the prefix in the
83# [filter:proxy-prefix] section above.
84filter-with = proxy-prefix
85
86# If proxy-prefix is enabled and you're running more than one Galaxy instance
87# behind one hostname, you will want to set this to the same path as the prefix
88# in the filter above.  This value becomes the "path" attribute set in the
89# cookie so the cookies from each instance will not clobber each other.
90cookie_path = /S
91
92# -- Database
93
94# By default, Galaxy uses a SQLite database at 'database/universe.sqlite'.  You
95# may use a SQLAlchemy connection string to specify an external database
96# instead.  This string takes many options which are explained in detail in the
97# config file documentation.
98#database_connection = sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE
99
100# If the server logs errors about not having enough database pool connections,
101# you will want to increase these values, or consider running more Galaxy
102# processes.
103#database_engine_option_pool_size = 5
104#database_engine_option_max_overflow = 10
105
106# If using MySQL and the server logs the error "MySQL server has gone away",
107# you will want to set this to some positive value (7200 should work).
108#database_engine_option_pool_recycle = -1
109
110# If large database query results are causing memory or response time issues in
111# the Galaxy process, leave the result on the server instead.  This option is
112# only available for PostgreSQL and is highly recommended.
113#database_engine_option_server_side_cursors = False
114
115# Log all database transactions, can be useful for debugging and performance
116# profiling.  Logging is done via Python's 'logging' module under the qualname
117# 'galaxy.model.orm.logging_connection_proxy'
118#database_query_profiling_proxy = False
119
120# By default, Galaxy will use the same database to track user data and
121# tool shed install data.  There are many situations in which it is
122# valuable to separate these - for instance bootstrapping fresh Galaxy
123# instances with pretested installs.  The following option can be used to
124# separate the tool shed install database (all other options listed above
125# but prefixed with install_ are also available).
126#install_database_connection = sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE
127
128# -- Files and directories
129
130# Dataset files are stored in this directory.
131#file_path = database/files
132file_path = USERDATAALL
133
134# Temporary files are stored in this directory.
135#new_file_path = database/tmp
136
137# Tool config files, defines what tools are available in Galaxy.
138# Tools can be locally developed or installed from Galaxy tool sheds.
139# (config/tool_conf.xml.sample will be used if left unset and
140# config/tool_conf.xml does not exist).
141#tool_config_file = config/tool_conf.xml,config/shed_tool_conf.xml
142
143# Enable / disable checking if any tools defined in the above non-shed
144# tool_config_files (i.e., tool_conf.xml) have been migrated from the Galaxy
145# code distribution to the Tool Shed.  This setting should generally be set to
146# False only for development Galaxy environments that are often rebuilt from
147# scratch where migrated tools do not need to be available in the Galaxy tool
148# panel.  If the following setting remains commented, the default setting will
149# be True.
150#check_migrate_tools = True
151
152# Tool config maintained by tool migration scripts.  If you use the migration
153# scripts to install tools that have been migrated to the tool shed upon a new
154# release, they will be added to this tool config file.
155#migrated_tools_config = config/migrated_tools_conf.xml
156
157# File that contains the XML section and tool tags from all tool panel config
158# files integrated into a single file that defines the tool panel layout.  This
159# file can be changed by the Galaxy administrator to alter the layout of the
160# tool panel.  If not present, Galaxy will create it.
161#integrated_tool_panel_config = integrated_tool_panel.xml
162
163# Default path to the directory containing the tools defined in tool_conf.xml.
164# Other tool config files must include the tool_path as an attribute in the
165# <toolbox> tag.
166#tool_path = tools
167
168# Path to the directory in which tool dependencies are placed.  This is used by
169# the tool shed to install dependencies and can also be used by administrators
170# to manually install or link to dependencies.  For details, see:
171#   https://wiki.galaxyproject.org/Admin/Config/ToolDependencies
172# If this option is not set to a valid path, installing tools with dependencies
173# from the Tool Shed will fail.
174#tool_dependency_dir = None
175
176# The dependency resolves config file specifies an ordering and options for how
177# Galaxy resolves tool dependencies (requirement tags in Tool XML). The default
178# ordering is to the use the tool shed for tools installed that way, use local
179# Galaxy packages, and then use conda if available.
180# See https://github.com/galaxyproject/galaxy/blob/dev/doc/source/admin/dependency_resolvers.rst
181# for more information on these options.
182#dependency_resolvers_config_file = config/dependency_resolvers_conf.xml
183
184# Following conda dependeny resolution options are experimental as of early
185# 2016. These will change the defaults for each conda resolver, but multiple
186# resolvers can be configured independently and these options overridden in
187# dependency_resolvers_config_file.
188#conda_prefix = <tool_dependency_dir>/_conda
189# Override the conda executable to use, it will default to the one on the
190# PATH (if available) and then to <conda_prefix>/bin/conda
191#conda_exec =
192# Pass debug flag to conda commands.
193#conda_debug = False
194# conda channels to enable by default (http://conda.pydata.org/docs/custom-channels.html)
195#conda_ensure_channels = r,bioconda,iuc
196# Set to True to instruct Galaxy to look for and install missing tool
197# dependencies before each job runs.
198#conda_auto_install = False
199# Set to True to instruct Galaxy to install conda from the web automatically
200# if it cannot find a local copy and conda_exec is not configured.
201#conda_auto_init = False
202
203# File containing the Galaxy Tool Sheds that should be made available to
204# install from in the admin interface (.sample used if default does not exist).
205#tool_sheds_config_file = config/tool_sheds_conf.xml
206
207# Set to True to enable monitoring of tools and tool directories
208# listed in any tool config file specified in tool_config_file option.
209# If changes are found, tools are automatically reloaded.  Watchdog (
210# https://pypi.python.org/pypi/watchdog ) must be installed and
211# available to Galaxy to use this option. Other options include 'auto'
212# which will attempt to watch tools if the watchdog library is available
213# but won't fail to load Galaxy if it is not and 'polling' which will use
214# a less efficient monitoring scheme that may work in wider range of scenarios
215# than the watchdog default.
216#watch_tools = False
217
218# Enable automatic polling of relative tool sheds to see if any updates
219# are available for installed repositories.  Ideally only one Galaxy
220# server process should be able to check for repository updates.  The
221# setting for hours_between_check should be an integer between 1 and 24.
222#enable_tool_shed_check = False
223#hours_between_check = 12
224
225# Enable use of an in-memory registry with bi-directional relationships between
226# repositories (i.e., in addition to lists of dependencies for a repository,
227# keep an in-memory registry of dependent items for each repository.
228#manage_dependency_relationships = False
229
230# XML config file that contains data table entries for the
231# ToolDataTableManager.  This file is manually # maintained by the Galaxy
232# administrator (.sample used if default does not exist).
233#tool_data_table_config_path = config/tool_data_table_conf.xml
234
235# XML config file that contains additional data table entries for the
236# ToolDataTableManager.  This file is automatically generated based on the
237# current installed tool shed repositories that contain valid
238# tool_data_table_conf.xml.sample files.  At the time of installation, these
239# entries are automatically added to the following file, which is parsed and
240# applied to the ToolDataTableManager at server start up.
241#shed_tool_data_table_config = config/shed_tool_data_table_conf.xml
242
243# Directory where data used by tools is located, see the samples in that
244# directory and the wiki for help:
245#   https://wiki.galaxyproject.org/Admin/DataIntegration
246#tool_data_path = tool-data
247
248# Directory where Tool Data Table related files will be placed
249# when installed from a ToolShed. Defaults to tool_data_path.
250#shed_tool_data_path = tool-data
251
252# File containing old-style genome builds
253#builds_file_path = tool-data/shared/ucsc/builds.txt
254
255# Directory where chrom len files are kept, currently mainly used by trackster
256#len_file_path = tool-data/shared/ucsc/chrom
257
258# Datatypes config file(s), defines what data (file) types are available in
259# Galaxy (.sample is used if default does not exist).  If a datatype appears in
260# multiple files, the last definition is used (though the first sniffer is used
261# so limit sniffer definitions to one file).
262#datatypes_config_file = config/datatypes_conf.xml
263
264# Disable the 'Auto-detect' option for file uploads
265#datatypes_disable_auto = False
266
267# Visualizations config directory: where to look for individual visualization
268# plugins.  The path is relative to the Galaxy root dir.  To use an absolute
269# path begin the path with '/'.  This is a comma separated list.
270# Defaults to "config/plugins/visualizations".
271#visualization_plugins_directory = config/plugins/visualizations
272
273# Interactive environment plugins root directory: where to look for interactive
274# environment plugins.  By default none will be loaded.  Set to
275# config/plugins/interactive_environments to load Galaxy's stock plugins
276# (currently just IPython).  These will require Docker to be configured and
277# have security considerations, so proceed with caution. The path is relative to the
278# Galaxy root dir.  To use an absolute path begin the path with '/'.  This is a comma
279# separated list.
280#interactive_environment_plugins_directory =
281
282# Interactive tour directory: where to store interactive tour definition files.
283# Galaxy ships with several basic interface tours enabled, though a different
284# directory with custom tours can be specified here. The path is relative to the
285# Galaxy root dir.  To use an absolute path begin the path with '/'.  This is a comma
286# separated list.
287#tour_config_dir = config/plugins/tours
288
289# Each job is given a unique empty directory as its current working directory.
290# This option defines in what parent directory those directories will be
291# created.
292#job_working_directory = database/job_working_directory
293
294# If using a cluster, Galaxy will write job scripts and stdout/stderr to this
295# directory.
296#cluster_files_directory = database/pbs
297
298# Mako templates are compiled as needed and cached for reuse, this directory is
299# used for the cache
300#template_cache_path = database/compiled_templates
301
302# Set to false to disable various checks Galaxy will do to ensure it
303# can run job scripts before attempting to execute or submit them.
304#check_job_script_integrity = True
305# Number of checks to execute if check_job_script_integrity is enabled.
306#check_job_script_integrity_count = 35
307# Time to sleep between checks if check_job_script_integrity is enabled (in seconds).
308#check_job_script_integrity_sleep = .25
309
310
311# Set the default shell used by non-containerized jobs Galaxy-wide. This
312# defaults to bash for all jobs and can be overidden at the destination
313# level for heterogenous clusters. conda job resolution requires bash or zsh
314# so if this is switched to /bin/sh for instance - conda resolution
315# should be disabled. Containerized jobs always use /bin/sh - so more maximum
316# portability tool authors should assume generated commands run in sh.
317#default_job_shell = /bin/bash
318
319# Citation related caching.  Tool citations information maybe fetched from
320# external sources such as http://dx.doi.org/ by Galaxy - the following
321# parameters can be used to control the caching used to store this information.
322#citation_cache_type = file
323#citation_cache_data_dir = database/citations/data
324#citation_cache_lock_dir = database/citations/lock
325
326# External service types config file, defining what types of external_services
327# configurations are available in Galaxy (.sample is used if default does not
328# exist).
329#external_service_type_config_file = config/external_service_types_conf.xml
330
331# Path to the directory containing the external_service_types defined in the
332# config.
333#external_service_type_path = external_service_types
334
335# Tools with a number of outputs not known until runtime can write these
336# outputs to a directory for collection by Galaxy when the job is done.
337# Previously, this directory was new_file_path, but using one global directory
338# can cause performance problems, so using job_working_directory ('.' or cwd
339# when a job is run) is encouraged.  By default, both are checked to avoid
340# breaking existing tools.
341#collect_outputs_from = new_file_path,job_working_directory
342
343# -- Data Storage (Object Store)
344#
345# Configuration file for the object store
346# If this is set and exists, it overrides any other objectstore settings.
347# object_store_config_file = config/object_store_conf.xml
348
349
350# -- Mail and notification
351
352# Galaxy sends mail for various things: subscribing users to the mailing list
353# if they request it, password resets, notifications from the Galaxy Sample
354# Tracking system, reporting dataset errors, and sending activation emails.
355# To do this, it needs to send mail through an SMTP server, which you may
356# define here (host:port).
357# Galaxy will automatically try STARTTLS but will continue upon failure.
358#smtp_server = None
359#smtp_server = 209.zapto.org
360#smtp_username = 209
361#smtp_password = example_passsword
362#activation_email = activation-noreply@example.com
363#error_email_to = admin@example.com
364
365
366
367# If your SMTP server requires a username and password, you can provide them
368# here (password in cleartext here, but if your server supports STARTTLS it
369# will be sent over the network encrypted).
370#smtp_username = None
371#smtp_password = None
372
373# If your SMTP server requires SSL from the beginning of the connection
374# smtp_ssl = False
375
376# On the user registration form, users may choose to join a mailing list. This
377# is the address used to subscribe to the list. Uncomment and leave empty if you
378# want to remove this option from the user registration form.
379#mailing_join_addr = galaxy-announce-join@bx.psu.edu
380
381# Datasets in an error state include a link to report the error.  Those reports
382# will be sent to this address.  Error reports are disabled if no address is
383# set.  Also this email is shown as a contact to user in case of Galaxy
384# misconfiguration and other events user may encounter.
385#error_email_to = None
386
387# Email address to use in the 'From' field when sending emails for
388# account activations, workflow step notifications and password resets.
389# We recommend using string in the following format:
390# Galaxy Project <galaxy-no-reply@example.com>
391# If not configured, '<galaxy-no-reply@HOSTNAME>' will be used.
392#email_from = None
393
394# URL of the support resource for the galaxy instance.  Used in activation
395# emails.
396#instance_resource_url = https://wiki.galaxyproject.org/
397
398# E-mail domains blacklist is used for filtering out users that are using
399# disposable email address during the registration.  If their address domain
400# matches any domain in the blacklist, they are refused the registration.
401#blacklist_file = config/disposable_email_blacklist.conf
402
403# Registration warning message is used to discourage people from registering
404# multiple accounts.  Applies mostly for the main Galaxy instance.
405# If no message specified the warning box will not be shown.
406#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.
407
408
409# -- Account activation
410
411# User account activation feature global flag.  If set to "False", the rest of
412# the Account activation configuration is ignored and user activation is
413# disabled (i.e. accounts are active since registration).
414# The activation is also not working in case the SMTP server is not defined.
415#user_activation_on = True
416
417# Activation grace period (in hours).  Activation is not forced (login is not
418# disabled) until grace period has passed.  Users under grace period can't run
419# jobs (see inactivity_box_content).  Default is 3.  Enter 0 to disable grace
420# period.
421# Users with OpenID logins have grace period forever.
422#activation_grace_period = 0
423
424# Used for warning box for inactive accounts (unable to run jobs).
425# In use only if activation_grace_period is set.
426#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.
427
428
429
430# Galaxy Session Timeout
431# This provides a timeout (in minutes) after which a user will have to log back in.
432# A duration of 0 disables this feature.
433#session_duration = 0
434
435
436# -- Analytics
437
438# You can enter tracking code here to track visitor's behavior
439# through your Google Analytics account.  Example: UA-XXXXXXXX-Y
440#ga_code = None
441
442# -- Display sites
443
444# Galaxy can display data at various external browsers.  These options specify
445# which browsers should be available.  URLs and builds available at these
446# browsers are defined in the specifield files.
447
448# If use_remote_user = True, display application servers will be denied access
449# to Galaxy and so displaying datasets in these sites will fail.
450# display_servers contains a list of hostnames which should be allowed to
451# bypass security to display datasets.  Please be aware that there are security
452# implications if this is allowed.  More details (including required changes to
453# the proxy server config) are available in the Apache proxy documentation on
454# the wiki.
455#
456# The list of servers in this sample config are for the UCSC Main, Test and
457# Archaea browsers, but the default if left commented is to not allow any
458# display sites to bypass security (you must uncomment the line below to allow
459# them).
460#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
461
462# To disable the old-style display applications that are hardcoded into
463# datatype classes, set enable_old_display_applications = False.
464# This may be desirable due to using the new-style, XML-defined, display
465# applications that have been defined for many of the datatypes that have the
466# old-style.
467# There is also a potential security concern with the old-style applications,
468# where a malicious party could provide a link that appears to reference the
469# Galaxy server, but contains a redirect to a third-party server, tricking a
470# Galaxy user to access said site.
471#enable_old_display_applications = True
472
473# -- Next gen LIMS interface on top of existing Galaxy Sample/Request
474# management code.
475
476use_nglims = False
477nglims_config_file = tool-data/nglims.yaml
478
479# -- UI Localization
480
481# Show a message box under the masthead.
482#message_box_visible = False
483#message_box_content = None
484#message_box_class = info
485
486# Append "/{brand}" to the "Galaxy" text in the masthead.
487#brand = None
488
489# Format string used when showing date and time information.
490# The string may contain:
491# - the directives used by Python time.strftime() function (see
492#   https://docs.python.org/2/library/time.html#time.strftime ),
493# - $locale (complete format string for the server locale),
494# - $iso8601 (complete format string as specified by ISO 8601 international
495#   standard).
496# pretty_datetime_format = $locale (UTC)
497
498# URL (with schema http/https) of the Galaxy instance as accessible within your
499# local network - if specified used as a default by pulsar file staging and
500# IPython Docker container for communicating back with Galaxy via the API.
501#galaxy_infrastructure_url = http://localhost:8080
502
503# If the above URL cannot be determined ahead of time in dynamic environments
504# but the port which should be used to access Galaxy can be - this should be
505# set to prevent Galaxy from having to guess.  For example if Galaxy is sitting
506# behind a proxy with REMOTE_USER enabled - infrastructure shouldn't talk to
507# Python processes directly and this should be set to 80 or 443, etc... If
508# unset this file will be read for a server block defining a port corresponding
509# to the webapp.
510#galaxy_infrastructure_web_port = 8080
511
512# The URL of the page to display in Galaxy's middle pane when loaded.  This can
513# be an absolute or relative URL.
514#welcome_url = /static/welcome.html
515
516# The URL linked by the "Galaxy/brand" text.
517#logo_url = /
518
519# The URL linked by the "Wiki" link in the "Help" menu.
520#wiki_url = https://wiki.galaxyproject.org/
521
522# The URL linked by the "Support" link in the "Help" menu.
523#support_url = https://wiki.galaxyproject.org/Support
524
525# The URL linked by the "How to Cite Galaxy" link in the "Help" menu.
526#citation_url = https://wiki.galaxyproject.org/CitingGalaxy
527
528#The URL linked by the "Search" link in the "Help" menu.
529#search_url = http://galaxyproject.org/search/usegalaxy/
530
531#The URL linked by the "Mailing Lists" link in the "Help" menu.
532#mailing_lists_url = https://wiki.galaxyproject.org/MailingLists
533
534#The URL linked by the "Videos" link in the "Help" menu.
535#screencasts_url = https://vimeo.com/galaxyproject
536
537# The URL linked by the "Terms and Conditions" link in the "Help" menu, as well
538# as on the user registration and login forms and in the activation emails.
539#terms_url = None
540
541# The URL linked by the "Galaxy Q&A" link in the "Help" menu
542# The Galaxy Q&A site is under development; when the site is done, this URL
543# will be set and uncommented.
544#qa_url =
545
546# Serve static content, which must be enabled if you're not serving it via a
547# proxy server.  These options should be self explanatory and so are not
548# documented individually.  You can use these paths (or ones in the proxy
549# server) to point to your own styles.
550#static_enabled = True
551#static_cache_time = 360
552#static_dir = static/
553#static_images_dir = static/images
554#static_favicon_dir = static/favicon.ico
555#static_scripts_dir = static/scripts/
556#static_style_dir = static/june_2007_style/blue
557#static_robots_txt = static/robots.txt
558
559# Incremental Display Options
560
561#display_chunk_size = 65536
562
563# -- Advanced proxy features
564
565# For help on configuring the Advanced proxy features, see:
566# http://usegalaxy.org/production
567
568# Apache can handle file downloads (Galaxy-to-user) via mod_xsendfile.  Set
569# this to True to inform Galaxy that mod_xsendfile is enabled upstream.
570#apache_xsendfile = False
571
572# The same download handling can be done by nginx using X-Accel-Redirect.  This
573# should be set to the path defined in the nginx config as an internal redirect
574# with access to Galaxy's data files (see documentation linked above).
575#nginx_x_accel_redirect_base = False
576
577# nginx can make use of mod_zip to create zip files containing multiple library
578# files.  If using X-Accel-Redirect, this can be the same value as that option.
579#nginx_x_archive_files_base = False
580
581# If using compression in the upstream proxy server, use this option to disable
582# gzipping of library .tar.gz and .zip archives, since the proxy server will do
583# it faster on the fly.
584#upstream_gzip = False
585
586# The following default adds a header to web request responses that
587# will cause modern web browsers to not allow Galaxy to be embedded in
588# the frames of web applications hosted at other hosts - this can help
589# prevent a class of attack called clickjacking
590# (https://www.owasp.org/index.php/Clickjacking).  If you configure a
591# proxy in front of Galaxy - please ensure this header remains intact
592# to protect your users.  Uncomment and leave empty to not set the
593# `X-Frame-Options` header.
594#x_frame_options = SAMEORIGIN
595
596# nginx can also handle file uploads (user-to-Galaxy) via nginx_upload_module.
597# Configuration for this is complex and explained in detail in the
598# documentation linked above.  The upload store is a temporary directory in
599# which files uploaded by the upload module will be placed.
600#nginx_upload_store = False
601
602# This value overrides the action set on the file upload form, e.g. the web
603# path where the nginx_upload_module has been configured to intercept upload
604# requests.
605#nginx_upload_path = False
606
607# Galaxy can also use nginx_upload_module to receive files staged out upon job
608# completion by remote job runners (i.e. Pulsar) that initiate staging
609# operations on the remote end.  See the Galaxy nginx documentation for the
610# corresponding nginx configuration.
611#nginx_upload_job_files_store = False
612#nginx_upload_job_files_path = False
613
614# Have Galaxy manage dynamic proxy component for routing requests to other
615# services based on Galaxy's session cookie.  It will attempt to do this by
616# default though you do need to install node+npm and do an npm install from
617# `lib/galaxy/web/proxy/js`.  It is generally more robust to configure this
618# externally managing it however Galaxy is managed.  If True Galaxy will only
619# launch the proxy if it is actually going to be used (e.g. for IPython).
620#dynamic_proxy_manage=True
621
622# As of 16.04 Galaxy supports multiple proxy types. The original NodeJS
623# implementation, alongside a new Golang single-binary-no-dependencies
624# version. Valid values are (node, golang)
625#dynamic_proxy=node
626#
627# The NodeJS dynamic proxy can use an SQLite database or a JSON file for IPC,
628# set that here.
629#dynamic_proxy_session_map=database/session_map.sqlite
630
631# Set the port and IP for the the dynamic proxy to bind to, this must match
632# the external configuration if dynamic_proxy_manage is False.
633#dynamic_proxy_bind_port=8800
634#dynamic_proxy_bind_ip=0.0.0.0
635
636# Enable verbose debugging of Galaxy-managed dynamic proxy.
637#dynamic_proxy_debug=False
638
639# The dynamic proxy is proxied by an external proxy (e.g. apache frontend to
640# nodejs to wrap connections in SSL).
641#dynamic_proxy_external_proxy=False
642
643# Additionally, when the dynamic proxy is proxied by an upstream server, you'll
644# want to specify a prefixed URL so both Galaxy and the proxy reside under the
645# same path that your cookies are under. This will result in a url like
646# https://FQDN/galaxy-prefix/gie_proxy for proxying
647#dynamic_proxy_prefix=gie_proxy
648
649# The Golang proxy also manages the docker containers more closely than the
650# NodeJS proxy, so is able to expose more container management related options
651
652# This attribute governs the minimum length of time between consecutive HTTP/WS
653# requests through the proxy, before the proxy considers a container as being
654# inactive and kills it.
655#dynamic_proxy_golang_noaccess = 60
656
657# In order to kill containers, the golang proxy has to check at some interval
658# for possibly dead containers. This is exposed as a configurable parameter,
659# but the default value is probably fine.
660#dynamic_proxy_golang_clean_interval = 10
661
662# The golang proxy needs to know how to talk to your docker daemon. Currently
663# TLS is not supported, that will come in an update.
664#dynamic_proxy_golang_docker_address = unix:///var/run/docker.sock
665
666# The golang proxy uses a RESTful HTTP API for communication with Galaxy
667# instead of a JSON or SQLite file for IPC. If you do not specify this, it will
668# be set randomly for you. You should set this if you are managing the proxy
669# manually.
670#dynamic_proxy_golang_api_key = None
671
672# -- Logging and Debugging
673
674# If True, Galaxy will attempt to configure a simple root logger if a
675# "loggers" section does not appear in this configuration file.
676#auto_configure_logging = True
677
678# Verbosity of console log messages.  Acceptable values can be found here:
679# https://docs.python.org/2/library/logging.html#logging-levels
680#log_level = DEBUG
681
682# Print database operations to the server log (warning, quite verbose!).
683#database_engine_option_echo = False
684
685# Print database pool operations to the server log (warning, quite verbose!).
686#database_engine_option_echo_pool = False
687
688# Turn on logging of application events and some user events to the database.
689#log_events = True
690
691# Turn on logging of user actions to the database.  Actions currently logged
692# are grid views, tool searches, and use of "recently" used tools menu.  The
693# log_events and log_actions functionality will eventually be merged.
694#log_actions = True
695
696
697# Fluentd configuration.  Various events can be logged to the fluentd instance
698# configured below by enabling fluent_log.
699#fluent_log = False
700#fluent_host = localhost
701#fluent_port = 24224
702
703# Sanitize all HTML tool output.  By default, all tool output served as
704# 'text/html' will be sanitized thoroughly.  This can be disabled if you have
705# special tools that require unaltered output.  WARNING: disabling this does
706# make the Galaxy instance susceptible to XSS attacks initiated by your users.
707#sanitize_all_html = True
708
709# Whitelist sanitization file.
710# Datasets created by tools listed in this file are trusted and will not have
711# their HTML sanitized on display.  This can be manually edited or manipulated
712# through the Admin control panel -- see "Manage Display Whitelist"
713#sanitize_whitelist_file = config/sanitize_whitelist.txt
714
715# By default Galaxy will serve non-HTML tool output that may potentially
716# contain browser executable JavaScript content as plain text.  This will for
717# instance cause SVG datasets to not render properly and so may be disabled
718# by setting the following option to True.
719#serve_xss_vulnerable_mimetypes = False
720
721# Return a Access-Control-Allow-Origin response header that matches the Origin
722# header of the request if that Origin hostname matches one of the strings or
723# regular expressions listed here. This is a comma separated list of hostname
724# strings or regular expressions beginning and ending with /.
725# E.g. mysite.com,google.com,usegalaxy.org,/^[\w\.]*example\.com/
726# See: https://developer.mozilla.org/en-US/docs/Web/HTTP/Access_control_CORS
727#allowed_origin_hostnames = None
728
729# Set the following to True to use IPython nbconvert to build HTML from IPython
730# notebooks in Galaxy histories.  This process may allow users to execute
731# arbitrary code or serve arbitrary HTML.  If enabled, IPython must be
732# available and on Galaxy's PATH, to do this run
733# `pip install jinja2 pygments ipython` in Galaxy's virtualenv.
734#trust_ipython_notebook_conversion = False
735
736# Debug enables access to various config options useful for development and
737# debugging: use_lint, use_profile, use_printdebug and use_interactive.  It
738# also causes the files used by PBS/SGE (submission script, output, and error)
739# to remain on disk after the job is complete.
740#debug = False
741
742# Check for WSGI compliance.
743#use_lint = False
744
745# Run the Python profiler on each request.
746#use_profile = False
747
748# Intercept print statements and show them on the returned page.
749#use_printdebug = True
750
751# Enable live debugging in your browser.  This should NEVER be enabled on a
752# public site.  Enabled in the sample config for development.
753use_interactive = True
754
755# Write thread status periodically to 'heartbeat.log',  (careful, uses disk
756# space rapidly!).  Useful to determine why your processes may be consuming a
757# lot of CPU.
758#use_heartbeat = False
759
760# Control the period (in seconds) between dumps. Use -1 to disable. Regardless
761# of this setting, if use_heartbeat is enabled, you can send a Galaxy process
762# (unless running with uWSGI) SIGUSR1 (`kill -USR1`) to force a dump.
763#heartbeat_interval = 20
764
765# Heartbeat log filename. Can accept the template variables {server_name} and
766# {pid}
767#heartbeat_log = heartbeat_{server_name}.log
768
769# Log to Sentry
770# Sentry is an open source logging and error aggregation platform.  Setting
771# sentry_dsn will enable the Sentry middleware and errors will be sent to the
772# indicated sentry instance.  This connection string is available in your
773# sentry instance under <project_name> -> Settings -> API Keys.
774#sentry_dsn = None
775
776# Log to statsd
777# Statsd is an external statistics aggregator (https://github.com/etsy/statsd)
778# Enabling the following options will cause galaxy to log request timing and
779# other statistics to the configured statsd instance.  The statsd_prefix is
780# useful if you are running multiple Galaxy instances and want to segment
781# statistics between them within the same aggregator.
782#statsd_host=
783#statsd_port=8125
784#statsd_prefix=galaxy
785
786# -- Data Libraries
787
788# These library upload options are described in much more detail in the wiki:
789#   https://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles
790
791# Add an option to the library upload form which allows administrators to
792# upload a directory of files.
793#library_import_dir = None
794
795# Add an option to the library upload form which allows authorized
796# non-administrators to upload a directory of files.  The configured directory
797# must contain sub-directories named the same as the non-admin user's Galaxy
798# login ( email ).  The non-admin user is restricted to uploading files or
799# sub-directories of files contained in their directory.
800#user_library_import_dir = None
801
802# Add an option to the admin library upload tool allowing admins to paste
803# filesystem paths to files and directories in a box, and these paths will be
804# added to a library.  Set to True to enable.  Please note the security
805# implication that this will give Galaxy Admins access to anything your Galaxy
806# user has access to.
807#allow_library_path_paste = False
808
809# Users may choose to download multiple files from a library in an archive.  By
810# default, Galaxy allows users to select from a few different archive formats
811# if testing shows that Galaxy is able to create files using these formats.
812# Specific formats can be disabled with this option, separate more than one
813# format with commas.  Available formats are currently 'zip', 'gz', and 'bz2'.
814#disable_library_comptypes =
815
816# Some sequencer integration features in beta allow you to automatically
817# transfer datasets.  This is done using a lightweight transfer manager which
818# runs outside of Galaxy (but is spawned by it automatically).  Galaxy will
819# communicate with this manager over the port specified here.
820#transfer_manager_port = 8163
821
822# Search data libraries with whoosh
823#enable_whoosh_library_search = True
824# Whoosh indexes are stored in this directory.
825#whoosh_index_dir = database/whoosh_indexes
826
827# Search data libraries with lucene
828#enable_lucene_library_search = False
829# maximum file size to index for searching, in MB
830#fulltext_max_size = 500
831#fulltext_noindex_filetypes = bam,sam,wig,bigwig,fasta,fastq,fastqsolexa,fastqillumina,fastqsanger
832# base URL of server providing search functionality using lucene
833#fulltext_url = http://localhost:8081
834
835# -- Toolbox Search
836
837# The following boosts are used to customize this instance's toolbox search.
838# The higher the boost, the more importance the scoring algorithm gives to the
839# given field.  Section refers to the tool group in the tool panel.  Rest of
840# the fields are tool's attributes.
841# tool_name_boost = 9
842# tool_section_boost = 3
843# tool_description_boost = 2
844# tool_label_boost = 1
845# tool_stub_boost = 5
846# tool_help_boost = 0.5
847
848# Limits the number of results in toolbox search.  Can be used to tweak how many
849# results will appear.
850# tool_search_limit = 20
851
852# -- Users and Security
853
854# Galaxy encodes various internal values when these values will be output in
855# some format (for example, in a URL or cookie).  You should set a key to be
856# used by the algorithm that encodes and decodes these values.  It can be any
857# string.  If left unchanged, anyone could construct a cookie that would grant
858# them access to others' sessions.
859# One simple way to generate a value for this is with the shell command:
860#   python -c 'import time; print time.time()' | md5sum | cut -f 1 -d ' '
861#id_secret = USING THE DEFAULT IS NOT SECURE!
862
863# User authentication can be delegated to an upstream proxy server (usually
864# Apache).  The upstream proxy should set a REMOTE_USER header in the request.
865# Enabling remote user disables regular logins.  For more information, see:
866#   https://wiki.galaxyproject.org/Admin/Config/ApacheProxy
867#use_remote_user = False
868
869# If use_remote_user is enabled and your external authentication
870# method just returns bare usernames, set a default mail domain to be appended
871# to usernames, to become your Galaxy usernames (email addresses).
872#remote_user_maildomain = None
873
874# If use_remote_user is enabled, the header that the upstream proxy provides
875# the remote username in defaults to HTTP_REMOTE_USER (the 'HTTP_' is prepended
876# by WSGI).  This option allows you to change the header.  Note, you still need
877# to prepend 'HTTP_' to the header in this option, but your proxy server should
878# *not* include 'HTTP_' at the beginning of the header name.
879#remote_user_header = HTTP_REMOTE_USER
880
881# If use_remote_user is enabled, anyone who can log in to the Galaxy host may
882# impersonate any other user by simply sending the appropriate header.  Thus a
883# secret shared between the upstream proxy server, and Galaxy is required.
884# If anyone other than the Galaxy user is using the server, then apache/nginx
885# should pass a value in the header 'GX_SECRET' that is identical to the one
886# below.
887#remote_user_secret = USING THE DEFAULT IS NOT SECURE!
888
889# If use_remote_user is enabled, you can set this to a URL that will log your
890# users out.
891#remote_user_logout_href = None
892
893# If your proxy and/or authentication source does not normalize e-mail
894# addresses or user names being passed to Galaxy - set the following option
895# to True to force these to lower case.
896#normalize_remote_user_email = False
897
898# If an e-mail address is specified here, it will hijack remote user mechanics
899# (``use_remote_user``) and have the webapp inject a single fixed user. This
900# has the effect of turning Galaxy into a single user application with no
901# login or external proxy required. Such applications should not be exposed to
902# the world.
903#single_user =
904
905# Administrative users - set this to a comma-separated list of valid Galaxy
906# users (email addresses).  These users will have access to the Admin section
907# of the server, and will have access to create users, groups, roles,
908# libraries, and more.  For more information, see:
909#   https://wiki.galaxyproject.org/Admin/Interface
910admin_users = biofuture.jiang@gmail.com
911
912# Force everyone to log in (disable anonymous access).
913#require_login = False
914
915# Show the site's welcome page (see welcome_url) alongside the login page
916# (even if require_login is True)
917#show_welcome_with_login = False
918
919# Allow unregistered users to create new accounts (otherwise, they will have to
920# be created by an admin).
921#allow_user_creation = True
922
923# Allow administrators to delete accounts.
924#allow_user_deletion = False
925
926# Allow administrators to log in as other users (useful for debugging)
927#allow_user_impersonation = False
928
929# Allow users to remove their datasets from disk immediately (otherwise,
930# datasets will be removed after a time period specified by an administrator in
931# the cleanup scripts run via cron)
932#allow_user_dataset_purge = False
933
934# By default, users' data will be public, but setting this to True will cause
935# it to be private.  Does not affect existing users and data, only ones created
936# after this option is set.  Users may still change their default back to
937# public.
938#new_user_dataset_access_role_default_private = False
939
940# Expose user list.  Setting this to True will expose the user list to
941# authenticated users.  This makes sharing datasets in smaller galaxy instances
942# much easier as they can type a name/email and have the correct user show up.
943# This makes less sense on large public Galaxy instances where that data
944# shouldn't be exposed.  For semi-public Galaxies, it may make sense to expose
945# just the username and not email, or vice versa.
946#expose_user_name = False
947#expose_user_email = False
948
949# -- Beta features
950# Enable new run workflow form
951#run_workflow_toolform_upgrade = False
952
953# Enable Galaxy to communicate directly with a sequencer
954#enable_sequencer_communication = False
955
956# Separate tool command from rest of job script so tool dependencies
957# don't interfer with metadata generation.
958# Despite the name, this feature is enabled by default
959# in 16.01 and the option will go away in the future.
960#enable_beta_tool_command_isolation = True
961
962# Enable the new interface for installing tools from Tool Shed
963# via the API. Admin menu will list both if enabled.
964#enable_beta_ts_api_install = False
965
966
967# Set the following to a number of threads greater than 1 to spawn
968# a Python task queue for dealing with large tool submissions (either
969# through the tool form or as part of an individual workflow step across
970# large collection). The size of a "large" tool request is controlled by
971# the second parameter below and defaults to 10. This affects workflow
972# scheduling and web processes, not job handlers.
973#tool_submission_burst_threads = 1
974#tool_submission_burst_at = 10
975
976# Enable beta workflow modules that should not yet be considered part of Galaxy's
977# stable API.
978#enable_beta_workflow_modules = False
979
980# Force usage of Galaxy's beta workflow scheduler under certain circumstances -
981# this workflow scheduling forces Galaxy to schedule workflows in the background
982# so initial submission of the workflows is signficantly sped up. This does
983# however force the user to refresh their history manually to see newly scheduled
984# steps (for "normal" workflows - steps are still scheduled far in advance of
985# them being queued and scheduling here doesn't refer to actual cluster job
986# scheduling).
987# Workflows containing more than the specified number of steps will always use
988# the Galaxy's beta workflow scheduling.
989#force_beta_workflow_scheduled_min_steps=250
990# Switch to using Galaxy's beta workflow scheduling for all workflows involving
991# ccollections.
992#force_beta_workflow_scheduled_for_collections=False
993
994# Enable authentication via OpenID.  Allows users to log in to their Galaxy
995# account by authenticating with an OpenID provider.
996#enable_openid = False
997# .sample used if default does not exist
998#openid_config_file = config/openid_conf.xml
999#openid_consumer_cache_path = database/openid_consumer_cache
1000
1001# XML config file that allows the use of different authentication providers
1002# (e.g. LDAP) instead or in addition to local authentication (.sample is used
1003# if default does not exist).
1004#auth_config_file = config/auth_conf.xml
1005
1006# Optional list of email addresses of API users who can make calls on behalf of
1007# other users.
1008#api_allow_run_as = None
1009
1010# Master key that allows many API admin actions to be used without actually
1011# having a defined admin user in the database/config.  Only set this if you
1012# need to bootstrap Galaxy, you probably do not want to set this on public
1013# servers.
1014#master_api_key = changethis
1015
1016# Enable tool tags (associating tools with tags).  This has its own option
1017# since its implementation has a few performance implications on startup for
1018# large servers.
1019#enable_tool_tags = False
1020
1021# Enable a feature when running workflows.  When enabled, default datasets
1022# are selected for "Set at Runtime" inputs from the history such that the
1023# same input will not be selected twice, unless there are more inputs than
1024# compatible datasets in the history.
1025# When False, the most recently added compatible item in the history will
1026# be used for each "Set at Runtime" input, independent of others in the Workflow
1027#enable_unique_workflow_defaults = False
1028
1029# The URL to the myExperiment instance being used (omit scheme but include port)
1030#myexperiment_url = www.myexperiment.org:80
1031
1032# Enable Galaxy's "Upload via FTP" interface.  You'll need to install and
1033# configure an FTP server (we've used ProFTPd since it can use Galaxy's
1034# database for authentication) and set the following two options.
1035
1036# This should point to a directory containing subdirectories matching users'
1037# identifier (defaults to e-mail), where Galaxy will look for files.
1038#ftp_upload_dir = None
1039
1040# This should be the hostname of your FTP server, which will be provided to
1041# users in the help text.
1042#ftp_upload_site = None
1043
1044# User attribute to use as subdirectory in calculating default ftp_upload_dir
1045# pattern. By default this will be email so a user's FTP upload directory will be
1046# ${ftp_upload_dir}/${user.email}. Can set this to other attributes such as id or
1047# username though.
1048#ftp_upload_dir_identifier = email
1049
1050# Python string template used to determine an FTP upload directory for a
1051# particular user.
1052#ftp_upload_dir_template = ${ftp_upload_dir}/${ftp_upload_dir_identifier}
1053
1054# This should be set to False to prevent Galaxy from deleting uploaded FTP files
1055# as it imports them.
1056#ftp_upload_purge = True
1057
1058# Enable enforcement of quotas.  Quotas can be set from the Admin interface.
1059#enable_quotas = False
1060
1061# This option allows users to see the full path of datasets via the "View
1062# Details" option in the history.  Administrators can always see this.
1063#expose_dataset_path = False
1064
1065# Data manager configuration options
1066# Allow non-admin users to view available Data Manager options.
1067#enable_data_manager_user_view = False
1068# File where Data Managers are configured (.sample used if default does not
1069# exist).
1070#data_manager_config_file = config/data_manager_conf.xml
1071# File where Tool Shed based Data Managers are configured.
1072#shed_data_manager_config_file = config/shed_data_manager_conf.xml
1073# Directory to store Data Manager based tool-data; defaults to tool_data_path.
1074#galaxy_data_manager_data_path = tool-data
1075
1076# -- Job Execution
1077
1078# To increase performance of job execution and the web interface, you can
1079# separate Galaxy into multiple processes.  There are more than one way to do
1080# this, and they are explained in detail in the documentation:
1081#
1082#   https://wiki.galaxyproject.org/Admin/Config/Performance/Scaling
1083
1084# By default, Galaxy manages and executes jobs from within a single process and
1085# notifies itself of new jobs via in-memory queues.  Jobs are run locally on
1086# the system on which Galaxy is started.  Advanced job running capabilities can
1087# be configured through the job configuration file.
1088#job_config_file = config/job_conf.xml
1089
1090# In multiprocess configurations, notification between processes about new jobs
1091# must be done via the database.  In single process configurations, this can be
1092# done in memory, which is a bit quicker.
1093track_jobs_in_database = True
1094
1095# This enables splitting of jobs into tasks, if specified by the particular tool
1096# config.
1097# This is a new feature and not recommended for production servers yet.
1098#use_tasked_jobs = False
1099#local_task_queue_workers = 2
1100
1101# Enable job recovery (if Galaxy is restarted while cluster jobs are running,
1102# it can "recover" them when it starts).  This is not safe to use if you are
1103# running more than one Galaxy server using the same database.
1104#enable_job_recovery = True
1105
1106# Although it is fairly reliable, setting metadata can occasionally fail.  In
1107# these instances, you can choose to retry setting it internally or leave it in
1108# a failed state (since retrying internally may cause the Galaxy process to be
1109# unresponsive).  If this option is set to False, the user will be given the
1110# option to retry externally, or set metadata manually (when possible).
1111#retry_metadata_internally = True
1112
1113# Very large metadata values can cause Galaxy crashes.  This will allow
1114# limiting the maximum metadata key size (in bytes used in memory, not the end
1115# result database value size) Galaxy will attempt to save with a dataset.  Use
1116# 0 to disable this feature.  The default is 5MB, but as low as 1MB seems to be
1117# a reasonable size.
1118#max_metadata_value_size = 5242880
1119
1120# If (for example) you run on a cluster and your datasets (by default,
1121# database/files/) are mounted read-only, this option will override tool output
1122# paths to write outputs to the working directory instead, and the job manager
1123# will move the outputs to their proper place in the dataset directory on the
1124# Galaxy server after the job completes.
1125#outputs_to_working_directory = False
1126
1127# If your network filesystem's caching prevents the Galaxy server from seeing
1128# the job's stdout and stderr files when it completes, you can retry reading
1129# these files.  The job runner will retry the number of times specified below,
1130# waiting 1 second between tries.  For NFS, you may want to try the -noac mount
1131# option (Linux) or -actimeo=0 (Solaris).
1132#retry_job_output_collection = 0
1133
1134# Clean up various bits of jobs left on the filesystem after completion.  These
1135# bits include the job working directory, external metadata temporary files,
1136# and DRM stdout and stderr files (if using a DRM).  Possible values are:
1137# always, onsuccess, never
1138#cleanup_job = always
1139
1140# For sites where all users in Galaxy match users on the system on which Galaxy
1141# runs, the DRMAA job runner can be configured to submit jobs to the DRM as the
1142# actual user instead of as the user running the Galaxy server process.  For
1143# details on these options, see the documentation at:
1144#
1145# https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster
1146#
1147#drmaa_external_runjob_script = scripts/drmaa_external_runner.py
1148#drmaa_external_killjob_script = scripts/drmaa_external_killer.py
1149#external_chown_script = scripts/external_chown_script.py
1150
1151# File to source to set up the environment when running jobs.  By default, the
1152# environment in which the Galaxy server starts is used when running jobs
1153# locally, and the environment set up per the DRM's submission method and
1154# policy is used when running jobs on a cluster (try testing with `qsub` on the
1155# command line).  environment_setup_file can be set to the path of a file on
1156# the cluster that should be sourced by the user to set up the environment
1157# prior to running tools.  This can be especially useful for running jobs as
1158# the actual user, to remove the need to configure each user's environment
1159# individually.
1160#environment_setup_file = None
1161
1162# Optional file containing job resource data entry fields definition.
1163# These fields will be presented to users in the tool forms and allow them to
1164# overwrite default job resources such as number of processors, memory and
1165# walltime.
1166#job_resource_params_file = config/job_resource_params_conf.xml
1167
1168# If using job concurrency limits (configured in job_config_file), several
1169# extra database queries must be performed to determine the number of jobs a
1170# user has dispatched to a given destination.  By default, these queries will
1171# happen for every job that is waiting to run, but if cache_user_job_count is
1172# set to True, it will only happen once per iteration of the handler queue.
1173# Although better for performance due to reduced queries, the tradeoff is a
1174# greater possibility that jobs will be dispatched past the configured limits
1175# if running many handlers.
1176#cache_user_job_count = False
1177
1178# ToolBox filtering
1179
1180# Modules from lib/galaxy/tools/toolbox/filters/ can be specified in
1181# the following lines.  tool_* filters will be applied for all users
1182# and can not be changed by them.  user_tool_* filters will be shown
1183# under user preferences and can be toogled on and off by
1184# runtime.  Example shown below are not real defaults (no custom
1185# filters applied by defualt) but can be enabled with by renaming the
1186# example.py.sample in the filters directory to example.py.
1187
1188#tool_filters =
1189#tool_label_filters =
1190#tool_section_filters =
1191#user_tool_filters = examples:restrict_upload_to_admins, examples:restrict_encode
1192#user_tool_section_filters = examples:restrict_text
1193#user_tool_label_filters = examples:restrict_upload_to_admins, examples:restrict_encode
1194
1195# The base modules that are searched for modules as described above
1196# can be modified and modules external to Galaxy can be searched by
1197# modifying the following option.
1198#toolbox_filter_base_modules = galaxy.tools.toolbox.filters,galaxy.tools.filters
1199
1200# Galaxy Application Internal Message Queue
1201
1202# Galaxy uses AMQP internally TODO more documentation on what for.
1203# For examples, see http://ask.github.io/kombu/userguide/connections.html
1204#
1205# Without specifying anything here, galaxy will first attempt to use your
1206# specified database_connection above.  If that's not specified either, Galaxy
1207# will automatically create and use a separate sqlite database located in your
1208# <galaxy>/database folder (indicated in the commented out line below).
1209
1210#amqp_internal_connection = sqlalchemy+sqlite:///./database/control.sqlite?isolation_level=IMMEDIATE
1211
1212
1213
1214# ---- Galaxy External Message Queue -------------------------------------------------
1215
1216# Galaxy uses Advanced Message Queuing Protocol (AMQP) to receive messages from
1217# external sources like barcode scanners.  Galaxy has been tested against
1218# RabbitMQ AMQP implementation.  For Galaxy to receive messages from a message
1219# queue, the RabbitMQ server has to be set up with a user account and other
1220# parameters listed below.  The 'host' and 'port' fields should point to where
1221# the RabbitMQ server is running.
1222
1223[galaxy_amqp]
1224
1225#host = 127.0.0.1
1226#port = 5672
1227#userid = galaxy
1228#password = galaxy
1229#virtual_host = galaxy_messaging_engine
1230#queue = galaxy_queue
1231#exchange = galaxy_exchange
1232#routing_key = bar_code_scanner
1233#rabbitmqctl_path = /path/to/rabbitmqctl