/universe_wsgi.ini.sample

Relevant Search: With Applications for Solr and Elasticsearch

For more in depth reading about search, ranking and generally everything you could ever want to know about how lucene, elasticsearch or solr work under the hood I highly suggest this book. Easily one of the most interesting technical books I have read in a long time. If you are tasked with solving search relevance problems even if not in Solr or Elasticsearch it should be your first reference. Amazon Affiliate Link

  1#
  2# Galaxy is configured by default to be useable 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.
 12# Examples of many of these options are explained in more detail in the wiki:
 13#
 14#   https://wiki.galaxyproject.org/Admin/Config
 15#
 16# Config hackers are encouraged to check there before asking for help.
 17
 18# ---- HTTP Server ----------------------------------------------------------
 19
 20# Configuration of the internal HTTP server.
 21
 22[server:main]
 23
 24# The internal HTTP server to use.  Currently only Paste is provided.  This
 25# option is required.
 26use = egg:Paste#http
 27
 28# The port on which to listen.
 29#port = 8080
 30
 31# The address on which to listen.  By default, only listen to localhost (Galaxy
 32# will not be accessible over the network).  Use '0.0.0.0' to listen on all
 33# available network interfaces.
 34#host = 127.0.0.1
 35
 36# Use a threadpool for the web server instead of creating a thread for each
 37# request.
 38use_threadpool = True
 39
 40# Number of threads in the web server thread pool.
 41#threadpool_workers = 10
 42
 43# Set the number of seconds a thread can work before you should kill it (assuming it will never finish) to 3 hours.
 44threadpool_kill_thread_limit = 10800
 45
 46# ---- Filters --------------------------------------------------------------
 47
 48# Filters sit between Galaxy and the HTTP server.
 49
 50# These filters are disabled by default.  They can be enabled with
 51# 'filter-with' in the [app:main] section below.
 52
 53# Define the gzip filter.
 54[filter:gzip]
 55use = egg:Paste#gzip
 56
 57# Define the proxy-prefix filter.
 58[filter:proxy-prefix]
 59use = egg:PasteDeploy#prefix
 60prefix = /galaxy
 61
 62# ---- Galaxy ---------------------------------------------------------------
 63
 64# Configuration of the Galaxy application.
 65
 66[app:main]
 67
 68# -- Application and filtering
 69
 70# The factory for the WSGI application.  This should not be changed.
 71paste.app_factory = galaxy.web.buildapp:app_factory
 72
 73# If not running behind a proxy server, you may want to enable gzip compression
 74# to decrease the size of data transferred over the network.  If using a proxy
 75# server, please enable gzip compression there instead.
 76#filter-with = gzip
 77
 78# If running behind a proxy server and Galaxy is served from a subdirectory,
 79# enable the proxy-prefix filter and set the prefix in the
 80# [filter:proxy-prefix] section above.
 81#filter-with = proxy-prefix
 82
 83# If proxy-prefix is enabled and you're running more than one Galaxy instance
 84# behind one hostname, you will want to set this to the same path as the prefix
 85# in the filter above.  This value becomes the "path" attribute set in the
 86# cookie so the cookies from each instance will not clobber each other.
 87#cookie_path = None
 88
 89# -- Database
 90
 91# By default, Galaxy uses a SQLite database at 'database/universe.sqlite'.  You
 92# may use a SQLAlchemy connection string to specify an external database
 93# instead.  This string takes many options which are explained in detail in the
 94# config file documentation.
 95#database_connection = sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE
 96
 97# If the server logs errors about not having enough database pool connections,
 98# you will want to increase these values, or consider running more Galaxy
 99# processes.
100#database_engine_option_pool_size = 5
101#database_engine_option_max_overflow = 10
102
103# If using MySQL and the server logs the error "MySQL server has gone away",
104# you will want to set this to some positive value (7200 should work).
105#database_engine_option_pool_recycle = -1
106
107# If large database query results are causing memory or response time issues in
108# the Galaxy process, leave the result on the server instead.  This option is
109# only available for PostgreSQL and is highly recommended.
110#database_engine_option_server_side_cursors = False
111
112# Create only one connection to the database per thread, to reduce the
113# connection overhead.  Recommended when not using SQLite:
114#database_engine_option_strategy = threadlocal
115
116# Log all database transactions, can be useful for debugging and performance
117# profiling.  Logging is done via Python's 'logging' module under the qualname
118# 'galaxy.model.orm.logging_connection_proxy'
119#database_query_profiling_proxy = False
120
121# -- Files and directories
122
123# Path where genome builds are stored. This defaults to tool-data/genome
124#genome_data_path = tool-data/genome
125
126# URL for rsync server to download pre-built indexes.
127#rsync_url = rsync://datacache.galaxyproject.org/indexes
128
129# Dataset files are stored in this directory.
130#file_path = database/files
131
132# Temporary files are stored in this directory.
133#new_file_path = database/tmp
134
135# Tool config files, defines what tools are available in Galaxy.
136# Tools can be locally developed or installed from Galaxy tool sheds.
137#tool_config_file = tool_conf.xml,shed_tool_conf.xml
138
139# Default path to the directory containing the tools defined in tool_conf.xml.
140# Other tool config files must include the tool_path as an attribute in the <toolbox> tag.
141#tool_path = tools
142
143# Path to the directory in which tool dependencies are placed.  This is used by
144# the tool shed to install dependencies and can also be used by administrators
145# to manually install or link to dependencies.  For details, see:
146#   https://wiki.galaxyproject.org/Admin/Config/ToolDependencies
147# If this option is not set to a valid path, installing tools with dependencies
148# from the Tool Shed will fail.
149#tool_dependency_dir = None
150
151# Enable automatic polling of relative tool sheds to see if any updates
152# are available for installed repositories.  Ideally only one Galaxy 
153# server process should be able to check for repository updates.  The
154# setting for hours_between_check should be an integer between 1 and 24.
155#enable_tool_shed_check = False
156#hours_between_check = 12
157
158# Enable use of an in-memory registry with bi-directional relationships
159# between repositories (i.e., in addition to lists of dependencies for a
160# repository, keep an in-memory registry of dependent items for each repository.
161#manage_dependency_relationships = False
162
163# XML config file that contains data table entries for the ToolDataTableManager. This file is manually
164# maintained by the Galaxy administrator.
165#tool_data_table_config_path = tool_data_table_conf.xml
166
167# XML config file that contains additional data table entries for the ToolDataTableManager.  This file
168# is automatically generated based on the current installed tool shed repositories that contain valid
169# tool_data_table_conf.xml.sample files.  At the time of installation, these entries are automatically
170# added to the following file, which is parsed and applied to the ToolDataTableManager at server start up.
171#shed_tool_data_table_config = shed_tool_data_table_conf.xml
172
173# Directory where data used by tools is located, see the samples in that
174# directory and the wiki for help:
175#   https://wiki.galaxyproject.org/Admin/DataIntegration
176#tool_data_path = tool-data
177
178# Directory where chrom len files are kept, currently mainly used by trackster
179#len_file_path = tool-data/shared/ucsc/chrom
180
181# Datatypes config file, defines what data (file) types are available in
182# Galaxy.
183#datatypes_config_file = datatypes_conf.xml
184
185# Disable the 'Auto-detect' option for file uploads
186#datatypes_disable_auto = False
187
188# Visualizations config directory: where to look for individual visualization plugins.
189# The path is relative to the Galaxy root dir. To use an absolute path begin the path
190# with '/'.
191visualization_plugins_directory = config/plugins/visualizations
192
193# Each job is given a unique empty directory as its current working directory.
194# This option defines in what parent directory those directories will be
195# created.
196#job_working_directory = database/job_working_directory
197
198# If using a cluster, Galaxy will write job scripts and stdout/stderr to this
199# directory.
200#cluster_files_directory = database/pbs
201
202# Mako templates are compiled as needed and cached for reuse, this directory is
203# used for the cache
204#template_cache_path = database/compiled_templates
205
206# External service types config file, defines what types of external_services configurations 
207# are available in Galaxy.
208#external_service_type_config_file = external_service_types_conf.xml
209
210# Path to the directory containing the external_service_types defined in the config.
211#external_service_type_path = external_service_types
212
213# Tools with a number of outputs not known until runtime can write these
214# outputs to a directory for collection by Galaxy when the job is done.
215# Previously, this directory was new_file_path, but using one global directory
216# can cause performance problems, so using job_working_directory ('.' or cwd
217# when a job is run) is encouraged.  By default, both are checked to avoid
218# breaking existing tools.
219#collect_outputs_from = new_file_path,job_working_directory
220
221# -- Data Storage (Object Store)
222#
223# Configuration file for the object store
224# If this is set and exists, it overrides any other objectstore settings.
225# object_store_config_file = object_store_conf.xml
226
227# Object store backend module (valid options are: disk, s3, swift, irods,
228# distributed, hierarchical)
229#object_store = disk
230
231# *Extremely* old Galaxy instances created datasets at the root of the
232# `file_path` defined above.  If your Galaxy instance has datasets at the root
233# (instead of in directories composed by hashing the dataset id), you should
234# enable this option to allow Galaxy to find them.
235#object_store_check_old_style = False
236
237# Credentials used by certain (s3, swift) object store backends
238#os_access_key = <your cloud object store access key>
239#os_secret_key = <your cloud object store secret key>
240#os_bucket_name = <name of an existing object store bucket or container>
241
242# If using 'swift' object store, you must specify the following connection
243# properties
244#os_host = swift.rc.nectar.org.au
245#os_port = 8888
246#os_is_secure = False
247#os_conn_path = /
248
249# Reduced redundancy can be used only with the 's3' object store
250#os_use_reduced_redundancy = False
251
252# Path to cache directory for object store backends that utilize a cache (s3,
253# swift, irods)
254#object_store_cache_path = database/files/
255
256# Size (in GB) that the cache used by object store should be limited to.
257# If the value is not specified, the cache size will be limited only by the
258# file system size.
259#object_store_cache_size = 100
260
261# Configuration file for the distributed object store, if object_store =
262# distributed.  See the sample at distributed_object_store_conf.xml.sample
263#distributed_object_store_config_file = None
264
265
266# -- Mail and notification
267
268# Galaxy sends mail for various things: Subscribing users to the mailing list
269# if they request it, emailing password resets, notification from the Galaxy
270# Sample Tracking system, reporting dataset errors, and sending activation emails.
271# To do this, it needs to send mail through an SMTP server, which you may define here (host:port).
272# Galaxy will automatically try STARTTLS but will continue upon failure.
273#smtp_server = None
274
275# If your SMTP server requires a username and password, you can provide them
276# here (password in cleartext here, but if your server supports STARTTLS it
277# will be sent over the network encrypted).
278#smtp_username = None
279#smtp_password = None
280
281# If your SMTP server requires SSL from the beginning of the connection
282# smtp_ssl= False
283
284# On the user registration form, users may choose to join the mailing list.
285# This is the address of the list they'll be subscribed to.
286#mailing_join_addr = galaxy-announce-join@bx.psu.edu
287
288# Datasets in an error state include a link to report the error.  Those reports
289# will be sent to this address.  Error reports are disabled if no address is set.
290# Also this email is shown as a contact to user in case of Galaxy misconfiguration and other events user may encounter.
291#error_email_to = None
292
293# Activation email is used as a sender ('from' field) for the account activation mail.
294# We recommend using string in the following format: Galaxy Project <galaxy-no-reply@example.com>
295#activation_email = None
296
297# URL of the support resource for the galaxy instance. Used in activation emails.
298#instance_resource_url = http://wiki.galaxyproject.org/
299
300# E-mail domains blacklist is used for filtering out users that are using disposable email address
301# during the registration. If their address domain matches any domain in the BL they are refused the registration.
302#blacklist_file = config/disposable_email_blacklist.conf
303
304# Registration warning message is used to discourage people from registering multiple accounts. Applies mostly for the main Galaxy instance.
305# If no message specified the warning box will not be shown.
306#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.
307
308# When users opt to reset passwords, new ones are created, this option
309# specifies the length of these passwords.
310#reset_password_length = 15
311
312
313# -- Account activation
314
315# This is user account activation feature global flag. If set to "False" the rest of the Account 
316# activation configuration is ignored and user activation is disabled (a.k.a. accounts are active since registration).
317# Note the activation is also not working in case the smtp server is not defined.
318#user_activation_on = False
319
320# Activation grace period. Activation is not forced (login is not disabled) until 
321# grace period has passed. Users under grace period can't run jobs (see inactivity_box_content).
322# In hours. Default is 3. Enter 0 to disable grace period. 
323# Users with OpenID logins have grace period forever. 
324#activation_grace_period = 0
325
326# Used for warning box for inactive accounts (unable to run jobs).
327# In use only if activation_grace_period is set.
328#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.
329
330
331# -- Display sites
332
333# Galaxy can display data at various external browsers.  These options specify
334# which browsers should be available.  URLs and builds available at these
335# browsers are defined in the specifield files.
336
337# UCSC browsers: tool-data/shared/ucsc/ucsc_build_sites.txt
338#ucsc_display_sites = main,test,archaea,ucla
339
340# GBrowse servers: tool-data/shared/gbrowse/gbrowse_build_sites.txt
341#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
342
343# GeneTrack servers: tool-data/shared/genetrack/genetrack_sites.txt
344#genetrack_display_sites = main,test
345
346# If use_remote_user = True, display application servers will be denied access
347# to Galaxy and so displaying datasets in these sites will fail.
348# display_servers contains a list of hostnames which should be allowed to
349# bypass security to display datasets.  Please be aware that there are security
350# implications if this is allowed.  More details (including required changes to
351# the proxy server config) are available in the Apache proxy documentation on
352# the wiki.
353#
354# The list of servers in this sample config are for the UCSC Main, Test and
355# Archaea browsers, but the default if left commented is to not allow any
356# display sites to bypass security (you must uncomment the line below to allow
357# them).
358#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
359
360# To disable the old-style display applications that are hardcoded into datatype classes,
361# set enable_old_display_applications = False.
362# This may be desirable due to using the new-style, XML-defined, display applications that
363# have been defined for many of the datatypes that have the old-style.
364# There is also a potential security concern with the old-style applications,
365# where a malicious party could provide a link that appears to reference the Galaxy server,
366# but contains a redirect to a third-party server, tricking a Galaxy user to access said
367# site.
368#enable_old_display_applications = True
369
370# -- Next gen LIMS interface on top of existing Galaxy Sample/Request management code.
371
372use_nglims = False
373nglims_config_file = tool-data/nglims.yaml
374
375# -- UI Localization
376
377# Show a message box under the masthead.
378#message_box_visible = False
379#message_box_content = None
380#message_box_class = info
381
382# Append "/{brand}" to the "Galaxy" text in the masthead.
383#brand = None
384
385# Format string used when showing date and time information.
386# The string may contain:
387# - the directives used by Python time.strftime() function (see http://docs.python.org/2/library/time.html#time.strftime ),
388# - $locale (complete format string for the server locale),
389# - $iso8601 (complete format string as specified by ISO 8601 international standard).
390# pretty_datetime_format = $locale (UTC)
391
392# The URL of the page to display in Galaxy's middle pane when loaded. This can be 
393# an absolute or relative URL.
394#welcome_url = /static/welcome.html
395
396# The URL linked by the "Galaxy/brand" text.
397#logo_url = /
398
399# The URL linked by the "Wiki" link in the "Help" menu.
400#wiki_url = http://wiki.galaxyproject.org/
401
402# The URL linked by the "Support" link in the "Help" menu.
403#support_url = http://wiki.galaxyproject.org/Support
404
405# The URL linked by the "How to Cite Galaxy" link in the "Help" menu.
406#citation_url = http://wiki.galaxyproject.org/CitingGalaxy
407
408#The URL linked by the "Search" link in the "Help" menu.
409#search_url = http://galaxyproject.org/search/usegalaxy/
410
411#The URL linked by the "Mailing Lists" link in the "Help" menu.
412#mailing_lists_url = http://wiki.galaxyproject.org/MailingLists
413
414#The URL linked by the "Videos" link in the "Help" menu.
415#videos_url = http://vimeo.com/galaxyproject
416
417# The URL linked by the "Terms and Conditions" link in the "Help" menu, as well
418# as on the user registration and login forms and in the activation emails.
419#terms_url = None
420
421# The URL linked by the "Galaxy Q&A" link in the "Help" menu
422# The Galaxy Q&A site is under development; when the site is done, this URL
423# will be set and uncommented.
424# qa_url = 
425
426# Serve static content, which must be enabled if you're not serving it via a
427# proxy server.  These options should be self explanatory and so are not
428# documented individually.  You can use these paths (or ones in the proxy
429# server) to point to your own styles.
430static_enabled = True
431static_cache_time = 360
432static_dir = %(here)s/static/
433static_images_dir = %(here)s/static/images
434static_favicon_dir = %(here)s/static/favicon.ico
435static_scripts_dir = %(here)s/static/scripts/
436static_style_dir = %(here)s/static/june_2007_style/blue
437static_robots_txt = %(here)s/static/robots.txt
438
439# Pack javascript at launch (/static/scripts/*.js)
440# This only happens if the modified timestamp of the source .js is newer
441# than the version (if it exists) in /static/scripts/packed/
442# Note that this requires java > 1.4 for executing yuicompressor.jar
443#pack_scripts = False
444
445# Cloud Launch
446
447#enable_cloud_launch = False
448#cloudlaunch_default_ami = ami-a7dbf6ce
449
450# -- Advanced proxy features
451
452# For help on configuring the Advanced proxy features, see:
453# http://usegalaxy.org/production
454
455# Apache can handle file downloads (Galaxy-to-user) via mod_xsendfile.  Set
456# this to True to inform Galaxy that mod_xsendfile is enabled upstream.
457#apache_xsendfile = False
458
459# The same download handling can be done by nginx using X-Accel-Redirect.  This
460# should be set to the path defined in the nginx config as an internal redirect
461# with access to Galaxy's data files (see documentation linked above).
462#nginx_x_accel_redirect_base = False
463
464# nginx can make use of mod_zip to create zip files containing multiple library
465# files.  If using X-Accel-Redirect, this can be the same value as that option.
466#nginx_x_archive_files_base = False
467
468# If using compression in the upstream proxy server, use this option to disable
469# gzipping of library .tar.gz and .zip archives, since the proxy server will do
470# it faster on the fly.
471#upstream_gzip = False
472
473# nginx can also handle file uploads (user-to-Galaxy) via nginx_upload_module.
474# Configuration for this is complex and explained in detail in the
475# documentation linked above.  The upload store is a temporary directory in
476# which files uploaded by the upload module will be placed.
477#nginx_upload_store = False
478
479# This value overrides the action set on the file upload form, e.g. the web
480# path where the nginx_upload_module has been configured to intercept upload
481# requests.
482#nginx_upload_path = False
483
484# -- Logging and Debugging
485
486# Verbosity of console log messages.  Acceptable values can be found here:
487# http://docs.python.org/library/logging.html#logging-levels
488#log_level = DEBUG
489
490# Print database operations to the server log (warning, quite verbose!).
491#database_engine_option_echo = False
492
493# Print database pool operations to the server log (warning, quite verbose!).
494#database_engine_option_echo_pool = False
495
496# Turn on logging of application events and some user events to the database.
497#log_events = True
498
499# Turn on logging of user actions to the database. Actions currently logged are
500# grid views, tool searches, and use of "recently" used tools menu.  The
501# log_events and log_actions functionality will eventually be merged.
502#log_actions = True
503
504# Sanitize All HTML Tool Output
505# By default, all tool output served as 'text/html' will be sanitized
506# thoroughly. This can be disabled if you have special tools that require
507# unaltered output.
508#sanitize_all_html = True
509
510# By default Galaxy will serve non-HTML tool output that may potentially
511# contain browser executable JavaScript content as plain text. This will for
512# instance cause SVG datasets to not render properly and so may be disabled
513# by setting the following option to True.
514#serve_xss_vulnerable_mimetypes = False
515
516# Debug enables access to various config options useful for development and
517# debugging: use_lint, use_profile, use_printdebug and use_interactive.  It
518# also causes the files used by PBS/SGE (submission script, output, and error)
519# to remain on disk after the job is complete.  Debug mode is disabled if
520# commented, but is uncommented by default in the sample config.
521debug = True
522
523# Check for WSGI compliance.
524#use_lint = False
525
526# Run the Python profiler on each request.
527#use_profile = False
528
529# Intercept print statements and show them on the returned page.
530#use_printdebug = True
531
532# Enable live debugging in your browser.  This should NEVER be enabled on a
533# public site.  Enabled in the sample config for development.
534use_interactive = True
535
536# Write thread status periodically to 'heartbeat.log',  (careful, uses disk
537# space rapidly!).  Useful to determine why your processes may be consuming a
538# lot of CPU.
539#use_heartbeat = False
540
541# Enable the memory debugging interface (careful, negatively impacts server
542# performance).
543#use_memdump = False
544
545# -- Data Libraries
546
547# These library upload options are described in much more detail in the wiki:
548#   https://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles
549
550# Add an option to the library upload form which allows administrators to
551# upload a directory of files.
552#library_import_dir = None
553
554# Add an option to the library upload form which allows authorized
555# non-administrators to upload a directory of files.  The configured directory
556# must contain sub-directories named the same as the non-admin user's Galaxy
557# login ( email ).  The non-admin user is restricted to uploading files or
558# sub-directories of files contained in their directory.
559#user_library_import_dir = None
560
561# Add an option to the admin library upload tool allowing admins to paste
562# filesystem paths to files and directories in a box, and these paths will be
563# added to a library.  Set to True to enable.  Please note the security
564# implication that this will give Galaxy Admins access to anything your Galaxy
565# user has access to.
566#allow_library_path_paste = False
567
568# Users may choose to download multiple files from a library in an archive.  By
569# default, Galaxy allows users to select from a few different archive formats
570# if testing shows that Galaxy is able to create files using these formats.
571# Specific formats can be disabled with this option, separate more than one
572# format with commas.  Available formats are currently 'zip', 'gz', and 'bz2'.
573#disable_library_comptypes = 
574
575# Some sequencer integration features in beta allow you to automatically
576# transfer datasets.  This is done using a lightweight transfer manager which
577# runs outside of Galaxy (but is spawned by it automatically).  Galaxy will
578# communicate with this manager over the port specified here.
579#transfer_manager_port = 8163
580
581# Search data libraries with whoosh
582#enable_whoosh_library_search = True
583# Whoosh indexes are stored in this directory.
584#whoosh_index_dir = database/whoosh_indexes
585
586# Search data libraries with lucene
587#enable_lucene_library_search = False
588# maxiumum file size to index for searching, in MB
589#fulltext_max_size = 500
590#fulltext_noindex_filetypes=bam,sam,wig,bigwig,fasta,fastq,fastqsolexa,fastqillumina,fastqsanger
591# base URL of server providing search functionality using lucene
592#fulltext_url = http://localhost:8081
593
594# -- Users and Security
595
596# Galaxy encodes various internal values when these values will be output in
597# some format (for example, in a URL or cookie).  You should set a key to be
598# used by the algorithm that encodes and decodes these values.  It can be any
599# string.  If left unchanged, anyone could construct a cookie that would grant
600# them access to others' sessions.
601#id_secret = USING THE DEFAULT IS NOT SECURE!
602
603# User authentication can be delegated to an upstream proxy server (usually
604# Apache).  The upstream proxy should set a REMOTE_USER header in the request.
605# Enabling remote user disables regular logins.  For more information, see:
606#   https://wiki.galaxyproject.org/Admin/Config/ApacheProxy
607#use_remote_user = False
608
609# If use_remote_user is enabled and your external authentication
610# method just returns bare usernames, set a default mail domain to be appended
611# to usernames, to become your Galaxy usernames (email addresses).
612#remote_user_maildomain = None
613
614# If use_remote_user is enabled, the header that the upstream proxy provides
615# the remote username in defaults to HTTP_REMOTE_USER (the 'HTTP_' is prepended
616# by WSGI).  This option allows you to change the header.  Note, you still need
617# to prepend 'HTTP_' to the header in this option, but your proxy server should
618# *not* include 'HTTP_' at the beginning of the header name.
619#remote_user_header = HTTP_REMOTE_USER
620
621# If use_remote_user is enabled, you can set this to a URL that will log your
622# users out.
623#remote_user_logout_href = None
624
625# If your proxy and/or authentication source does not normalize e-mail
626# addresses or user names being passed to Galaxy - set the following option
627# to True to force these to lower case.
628#normalize_remote_user_email = False
629
630# Administrative users - set this to a comma-separated list of valid Galaxy
631# users (email addresses).  These users will have access to the Admin section
632# of the server, and will have access to create users, groups, roles,
633# libraries, and more.  For more information, see:
634#   https://wiki.galaxyproject.org/Admin/Interface
635#admin_users = None
636
637# Force everyone to log in (disable anonymous access).
638#require_login = False
639
640# Allow unregistered users to create new accounts (otherwise, they will have to
641# be created by an admin).
642#allow_user_creation = True
643
644# Allow administrators to delete accounts.
645#allow_user_deletion = False
646
647# Allow administrators to log in as other users (useful for debugging)
648#allow_user_impersonation = False
649
650# Allow users to remove their datasets from disk immediately (otherwise,
651# datasets will be removed after a time period specified by an administrator in
652# the cleanup scripts run via cron)
653#allow_user_dataset_purge = False
654
655# By default, users' data will be public, but setting this to True will cause
656# it to be private.  Does not affect existing users and data, only ones created
657# after this option is set.  Users may still change their default back to
658# public.
659#new_user_dataset_access_role_default_private = False
660
661# -- Beta features
662
663# Enable Galaxy to communicate directly with a sequencer
664#enable_sequencer_communication = False
665
666# Enable authentication via OpenID.  Allows users to log in to their Galaxy
667# account by authenticating with an OpenID provider.
668#enable_openid = False
669#openid_config_file = openid_conf.xml
670
671# Optional list of email addresses of API users who can make calls on behalf of
672# other users
673#api_allow_run_as = None
674
675# Master key that allows many API admin actions to be used without actually
676# having a defined admin user in the database/config. Only set this if you need
677# to bootstrap Galaxy, you probably do not want to set this on public servers.
678#master_api_key=changethis
679
680# Enable tool tags (associating tools with tags).  This has its own option
681# since its implementation has a few performance implications on startup for
682# large servers.
683#enable_tool_tags = False
684
685# Enable a feature when running workflows. When enabled, default datasets
686# are selected for "Set at Runtime" inputs from the history such that the
687# same input will not be selected twice, unless there are more inputs than
688# compatible datasets in the history.
689# When False, the most recently added compatible item in the history will
690# be used for each "Set at Runtime" input, independent of others in the Workflow
691#enable_unique_workflow_defaults = False
692
693# The URL to the myExperiment instance being used (omit scheme but include port)
694#myexperiment_url = www.myexperiment.org:80
695
696# Enable Galaxy's "Upload via FTP" interface.  You'll need to install and
697# configure an FTP server (we've used ProFTPd since it can use Galaxy's
698# database for authentication) and set the following two options.
699
700# This should point to a directory containing subdirectories matching users'
701# email addresses, where Galaxy will look for files.
702#ftp_upload_dir = None
703
704# This should be the hostname of your FTP server, which will be provided to
705# users in the help text.
706#ftp_upload_site = None
707
708# Enable enforcement of quotas.  Quotas can be set from the Admin interface.
709#enable_quotas = False
710
711# This option allows users to see the full path of datasets via the "View
712# Details" option in the history.  Administrators can always see this.
713#expose_dataset_path = False
714
715# Data manager configuration options
716# Allow non-admin users to view available Data Manager options
717#enable_data_manager_user_view = False
718# File where Data Managers are configured
719#data_manager_config_file = data_manager_conf.xml
720# File where Tool Shed based Data Managers are configured 
721#shed_data_manager_config_file = shed_data_manager_conf.xml
722# Directory to store Data Manager based tool-data; defaults to tool_data_path
723#galaxy_data_manager_data_path = tool-data
724
725# -- Job Execution
726
727# To increase performance of job execution and the web interface, you can
728# separate Galaxy into multiple processes.  There are more than one way to do
729# this, and they are explained in detail in the documentation:
730#
731#   https://wiki.galaxyproject.org/Admin/Config/Performance/Scaling
732
733# By default, Galaxy manages and executes jobs from within a single process and
734# notifies itself of new jobs via in-memory queues.  Jobs are run locally on
735# the system on which Galaxy is started.  Advanced job running capabilities can
736# be configured through the job configuration file.
737#job_config_file = job_conf.xml
738
739# In multiprocess configurations, notification between processes about new jobs
740# is done via the database.  In single process configurations, this is done in
741# memory, which is a bit quicker.  Galaxy tries to automatically determine
742# which method it should used based on your handler configuration in the job
743# config file, but you can explicitly override this behavior by setting the
744# following option to True or False.
745#track_jobs_in_database = None
746
747# This enables splitting of jobs into tasks, if specified by the particular tool config.
748# This is a new feature and not recommended for production servers yet.
749#use_tasked_jobs = False
750#local_task_queue_workers = 2
751
752# Enable job recovery (if Galaxy is restarted while cluster jobs are running,
753# it can "recover" them when it starts).  This is not safe to use if you are
754# running more than one Galaxy server using the same database.
755#enable_job_recovery = True
756
757# Although it is fairly reliable, setting metadata can occasionally fail.  In
758# these instances, you can choose to retry setting it internally or leave it in
759# a failed state (since retrying internally may cause the Galaxy process to be
760# unresponsive).  If this option is set to False, the user will be given the
761# option to retry externally, or set metadata manually (when possible).
762#retry_metadata_internally = True
763
764# If (for example) you run on a cluster and your datasets (by default,
765# database/files/) are mounted read-only, this option will override tool output
766# paths to write outputs to the working directory instead, and the job manager
767# will move the outputs to their proper place in the dataset directory on the
768# Galaxy server after the job completes.
769#outputs_to_working_directory = False
770
771# If your network filesystem's caching prevents the Galaxy server from seeing
772# the job's stdout and stderr files when it completes, you can retry reading
773# these files.  The job runner will retry the number of times specified below,
774# waiting 1 second between tries.  For NFS, you may want to try the -noac mount
775# option (Linux) or -actimeo=0 (Solaris).
776#retry_job_output_collection = 0
777
778# Clean up various bits of jobs left on the filesystem after completion.  These
779# bits include the job working directory, external metadata temporary files,
780# and DRM stdout and stderr files (if using a DRM).  Possible values are:
781# always, onsuccess, never
782#cleanup_job = always
783
784# File to source to set up the environment when running jobs.  By default, the
785# environment in which the Galaxy server starts is used when running jobs
786# locally, and the environment set up per the DRM's submission method and
787# policy is used when running jobs on a cluster (try testing with `qsub` on the
788# command line).  environment_setup_file can be set to the path of a file on
789# the cluster that should be sourced by the user to set up the environment
790# prior to running tools.  This can be especially useful for running jobs as
791# the actual user, to remove the need to configure each user's environment
792# individually.  This only affects cluster jobs, not local jobs.
793#environment_setup_file = None
794
795# If using job concurrency limits (configured in job_config_file), several
796# extra database queries must be performed to determine the number of jobs a
797# user has dispatched to a given destination.  By default, these queries will
798# happen for every job that is waiting to run, but if cache_user_job_count is
799# set to True, it will only happen once per iteration of the handler queue.
800# Although better for performance due to reduced queries, the tradeoff is a
801# greater possibility that jobs will be dispatched past the configured limits
802# if running many handlers.
803#cache_user_job_count = False
804
805# ToolBox filtering
806# Modules from lib/galaxy/tools/filters/ can be specified in the following lines.
807# tool_* filters will be applied for all users and can not be changed by them.
808# user_tool_* filters will be shown under user preferences and can be toogled
809# on and off by runtime
810#tool_filters
811#tool_label_filters
812#tool_section_filters
813#user_tool_filters = examples:restrict_upload_to_admins, examples:restrict_encode
814#user_tool_section_filters = examples:restrict_text
815#user_tool_label_filters = examples:restrict_upload_to_admins, examples:restrict_encode
816
817# ---- Galaxy Message Queue -------------------------------------------------
818
819# Galaxy uses AMQ protocol to receive messages from external sources like 
820# bar code scanners. Galaxy has been tested against RabbitMQ AMQP implementation.
821# For Galaxy to receive messages from a message queue the RabbitMQ server has 
822# to be set up with a user account and other parameters listed below. The 'host'
823# and 'port' fields should point to where the RabbitMQ server is running. 
824
825[galaxy_amqp]
826
827#host = 127.0.0.1
828#port = 5672
829#userid = galaxy
830#password = galaxy
831#virtual_host = galaxy_messaging_engine
832#queue = galaxy_queue
833#exchange = galaxy_exchange
834#routing_key = bar_code_scanner
835#rabbitmqctl_path = /path/to/rabbitmqctl
836