/universe_wsgi.ini.sample

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