/universe_wsgi.ini.cistrome

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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://wiki.g2.bx.psu.edu/Admin/Config/Performance/Production%20Server
  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. # http://wiki.g2.bx.psu.edu/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 = 10096
  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. # ---- Filters --------------------------------------------------------------
  34. # Filters sit between Galaxy and the HTTP server.
  35. # These filters are disabled by default. They can be enabled with
  36. # 'filter-with' in the [app:main] section below.
  37. # Define the gzip filter.
  38. [filter:gzip]
  39. use = egg:Paste#gzip
  40. # Define the proxy-prefix filter.
  41. [filter:proxy-prefix]
  42. use = egg:PasteDeploy#prefix
  43. prefix = /ap
  44. # ---- Galaxy ---------------------------------------------------------------
  45. # Configuration of the Galaxy application.
  46. [app:main]
  47. # -- Application and filtering
  48. # The factory for the WSGI application. This should not be changed.
  49. paste.app_factory = galaxy.web.buildapp:app_factory
  50. # If not running behind a proxy server, you may want to enable gzip compression
  51. # to decrease the size of data transferred over the network. If using a proxy
  52. # server, please enable gzip compression there instead.
  53. #filter-with = gzip
  54. # If running behind a proxy server and Galaxy is served from a subdirectory,
  55. # enable the proxy-prefix filter and set the prefix in the
  56. # [filter:proxy-prefix] section above.
  57. filter-with = proxy-prefix
  58. # If proxy-prefix is enabled and you're running more than one Galaxy instance
  59. # behind one hostname, you will want to set this to the same path as the prefix
  60. # in the filter above. This value becomes the "path" attribute set in the
  61. # cookie so the cookies from each instance will not clobber each other.
  62. cookie_path = /ap
  63. # -- Database
  64. # By default, Galaxy uses a SQLite database at 'database/universe.sqlite'. You
  65. # may use a SQLAlchemy connection string to specify an external database
  66. # instead. This string takes many options which are explained in detail in the
  67. # config file documentation.
  68. #database_connection = postgres://cistrome:cistrome@localhost/cistromeap
  69. database_connection = mysql://cistrome:cistrome@localhost/cistromeap
  70. # If the server logs errors about not having enough database pool connections,
  71. # you will want to increase these values, or consider running more Galaxy
  72. # processes.
  73. database_engine_option_pool_size = 10
  74. database_engine_option_max_overflow = 20
  75. # If using MySQL and the server logs the error "MySQL server has gone away",
  76. # you will want to set this to some positive value (7200 should work).
  77. #database_engine_option_pool_recycle = -1
  78. # If large database query results are causing memory or response time issues in
  79. # the Galaxy process, leave the result on the server instead. This option is
  80. # only available for PostgreSQL and is highly recommended.
  81. #database_engine_option_server_side_cursors = False
  82. # Create only one connection to the database per thread, to reduce the
  83. # connection overhead. Recommended when not using SQLite:
  84. #database_engine_option_strategy = threadlocal
  85. # Log all database transactions, can be useful for debugging and performance
  86. # profiling. Logging is done via Python's 'logging' module under the qualname
  87. # 'galaxy.model.orm.logging_connection_proxy'
  88. #database_query_profiling_proxy = False
  89. # -- Files and directories
  90. # Path where genome builds are stored. This defaults to tool-data/genome
  91. #genome_data_path = tool-data/genome
  92. # URL for rsync server to download pre-built indexes.
  93. #rsync_url = rsync://scofield.bx.psu.edu/indexes
  94. # Dataset files are stored in this directory.
  95. file_path = database/files
  96. # Temporary files are stored in this directory.
  97. new_file_path = database/tmp
  98. # Tool config files, defines what tools are available in Galaxy.
  99. # Tools can be locally developed or installed from Galaxy tool sheds.
  100. tool_config_file = tool_conf.xml,shed_tool_conf.xml
  101. # Default path to the directory containing the tools defined in tool_conf.xml.
  102. # Other tool config files must include the tool_path as an attribute in the <toolbox> tag.
  103. tool_path = tools
  104. # Path to the directory in which managed tool dependencies are placed. To use
  105. # the dependency system, see the documentation at:
  106. # http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies
  107. #tool_dependency_dir = None
  108. # Enable automatic polling of relative tool sheds to see if any updates
  109. # are available for installed repositories. Ideally only one Galaxy
  110. # server process should be able to check for repository updates. The
  111. # setting for hours_between_check should be an integer between 1 and 24.
  112. #enable_tool_shed_check = False
  113. #hours_between_check = 12
  114. # Directory where data used by tools is located, see the samples in that
  115. # directory and the wiki for help:
  116. # http://wiki.g2.bx.psu.edu/Admin/Data%20Integration
  117. tool_data_path = tool-data
  118. # Directory where chrom len files are kept, currently mainly used by trackster
  119. len_file_path = tool-data/shared/ucsc/chrom
  120. # Datatypes config file, defines what data (file) types are available in
  121. # Galaxy.
  122. datatypes_config_file = datatypes_conf.xml
  123. # Each job is given a unique empty directory as its current working directory.
  124. # This option defines in what parent directory those directories will be
  125. # created.
  126. job_working_directory = database/job_working_directory
  127. # If using a cluster, Galaxy will write job scripts and stdout/stderr to this
  128. # directory.
  129. #cluster_files_directory = database/pbs
  130. # External service types config file, defines what types of external_services configurations
  131. # are available in Galaxy.
  132. #external_service_type_config_file = external_service_types_conf.xml
  133. # Path to the directory containing the external_service_types defined in the config.
  134. #external_service_type_path = external_service_types
  135. # Tools with a number of outputs not known until runtime can write these
  136. # outputs to a directory for collection by Galaxy when the job is done.
  137. # Previously, this directory was new_file_path, but using one global directory
  138. # can cause performance problems, so using job_working_directory ('.' or cwd
  139. # when a job is run) is encouraged. By default, both are checked to avoid
  140. # breaking existing tools.
  141. #collect_outputs_from = new_file_path,job_working_directory
  142. # -- Mail and notification
  143. # Galaxy sends mail for various things: Subscribing users to the mailing list
  144. # if they request it, emailing password resets, notification from the Galaxy
  145. # Sample Tracking system, and reporting dataset errors. To do this, it needs
  146. # to send mail through an SMTP server, which you may define here (host:port).
  147. # Galaxy will automatically try STARTTLS but will continue upon failure.
  148. smtp_server = localhost
  149. # If your SMTP server requires a username and password, you can provide them
  150. # here (password in cleartext here, but if your server supports STARTTLS it
  151. # will be sent over the network encrypted).
  152. #smtp_username = None
  153. #smtp_password = None
  154. # On the user registration form, users may choose to join the mailing list.
  155. # This is the address of the list they'll be subscribed to.
  156. #mailing_join_addr = galaxy-announce-join@bx.psu.edu
  157. # Datasets in an error state include a link to report the error. Those reports
  158. # will be sent to this address. Error reports are disabled if no address is set.
  159. error_email_to = cistrome-bugs@jimmy.harvard.edu
  160. # -- Display sites
  161. # Galaxy can display data at various external browsers. These options specify
  162. # which browsers should be available. URLs and builds available at these
  163. # browsers are defined in the specifield files.
  164. # UCSC browsers: tool-data/shared/ucsc/ucsc_build_sites.txt
  165. ucsc_display_sites = main,test,archaea,ucla
  166. # GBrowse servers: tool-data/shared/gbrowse/gbrowse_build_sites.txt
  167. #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
  168. # GeneTrack servers: tool-data/shared/genetrack/genetrack_sites.txt
  169. #genetrack_display_sites = main,test
  170. # If use_remote_user = True, display application servers will be denied access
  171. # to Galaxy and so displaying datasets in these sites will fail.
  172. # display_servers contains a list of hostnames which should be allowed to
  173. # bypass security to display datasets. Please be aware that there are security
  174. # implications if this is allowed. More details (including required changes to
  175. # the proxy server config) are available in the Apache proxy documentation on
  176. # the wiki.
  177. #
  178. # The list of servers in this sample config are for the UCSC Main, Test and
  179. # Archaea browsers, but the default if left commented is to not allow any
  180. # display sites to bypass security (you must uncomment the line below to allow
  181. # them).
  182. #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
  183. # -- Next gen LIMS interface on top of existing Galaxy Sample/Request management code.
  184. use_nglims = False
  185. nglims_config_file = tool-data/nglims.yaml
  186. # -- UI Localization
  187. # Append "/{brand}" to the "Galaxy" text in the masthead.
  188. brand = Cistrome
  189. # The URL linked by the "Galaxy/brand" text.
  190. logo_url = http://cistrome.org/ap/
  191. # The URL linked by the "Galaxy Wiki" link in the "Help" menu.
  192. wiki_url = http://bitbucket.org/cistrome/cistrome-harvard/wiki
  193. # The URL linked by the "Email comments..." link in the "Help" menu.
  194. bugs_email = mailto:cistrome-bugs@jimmy.harvard.edu
  195. # The URL linked by the "How to Cite..." link in the "Help" menu.
  196. citation_url = http://bitbucket.org/cistrome/cistrome-harvard/wiki/Citation
  197. # The URL linked by the "Terms and Conditions" link in the "Help" menu, as well
  198. # as on the user registration and login forms.
  199. #terms_url = None
  200. # Serve static content, which must be enabled if you're not serving it via a
  201. # proxy server. These options should be self explanatory and so are not
  202. # documented individually. You can use these paths (or ones in the proxy
  203. # server) to point to your own styles.
  204. static_enabled = True
  205. static_cache_time = 360
  206. static_dir = %(here)s/static/
  207. static_images_dir = %(here)s/static/images
  208. static_favicon_dir = %(here)s/static/favicon.ico
  209. static_scripts_dir = %(here)s/static/scripts/
  210. static_style_dir = %(here)s/static/june_2007_style/blue
  211. static_robots_txt = %(here)s/static/robots.txt
  212. # Pack javascript at launch (/static/scripts/*.js)
  213. # This only happens if the modified timestamp of the source .js is newer
  214. # than the version (if it exists) in /static/scripts/packed/
  215. # Note that this requires java > 1.4 for executing yuicompressor.jar
  216. #pack_scripts = False
  217. # Enable Cloud Launch
  218. #enable_cloud_launch = False
  219. # -- Advanced proxy features
  220. # For help on configuring the Advanced proxy features, see:
  221. # http://usegalaxy.org/production
  222. # Apache can handle file downloads (Galaxy-to-user) via mod_xsendfile. Set
  223. # this to True to inform Galaxy that mod_xsendfile is enabled upstream.
  224. #apache_xsendfile = False
  225. # The same download handling can be done by nginx using X-Accel-Redirect. This
  226. # should be set to the path defined in the nginx config as an internal redirect
  227. # with access to Galaxy's data files (see documentation linked above).
  228. #nginx_x_accel_redirect_base = False
  229. # nginx can make use of mod_zip to create zip files containing multiple library
  230. # files. If using X-Accel-Redirect, this can be the same value as that option.
  231. #nginx_x_archive_files_base = False
  232. # If using compression in the upstream proxy server, use this option to disable
  233. # gzipping of library .tar.gz and .zip archives, since the proxy server will do
  234. # it faster on the fly.
  235. upstream_gzip = False
  236. # nginx can also handle file uploads (user-to-Galaxy) via nginx_upload_module.
  237. # Configuration for this is complex and explained in detail in the
  238. # documentation linked above. The upload store is a temporary directory in
  239. # which files uploaded by the upload module will be placed.
  240. #nginx_upload_store = False
  241. # This value overrides the action set on the file upload form, e.g. the web
  242. # path where the nginx_upload_module has been configured to intercept upload
  243. # requests.
  244. #nginx_upload_path = False
  245. # -- Logging and Debugging
  246. # Verbosity of console log messages. Acceptable values can be found here:
  247. # http://docs.python.org/library/logging.html#logging-levels
  248. log_level = DEBUG
  249. # Print database operations to the server log (warning, quite verbose!).
  250. #database_engine_option_echo = False
  251. # Print database pool operations to the server log (warning, quite verbose!).
  252. #database_engine_option_echo_pool = False
  253. # Turn on logging of application events and some user events to the database.
  254. log_events = True
  255. # Turn on logging of user actions to the database. Actions currently logged are
  256. # grid views, tool searches, and use of "recently" used tools menu. The
  257. # log_events and log_actions functionality will eventually be merged.
  258. log_actions = True
  259. # Sanitize All HTML Tool Output
  260. # By default, all tool output served as 'text/html' will be sanitized
  261. # thoroughly. This can be disabled if you have special tools that require
  262. # unaltered output.
  263. #sanitize_all_html = True
  264. # Debug enables access to various config options useful for development and
  265. # debugging: use_lint, use_profile, use_printdebug and use_interactive. It
  266. # also causes the files used by PBS/SGE (submission script, output, and error)
  267. # to remain on disk after the job is complete. Debug mode is disabled if
  268. # commented, but is uncommented by default in the sample config.
  269. debug = True
  270. # Check for WSGI compliance.
  271. use_lint = False
  272. # Run the Python profiler on each request.
  273. use_profile = False
  274. # Intercept print statements and show them on the returned page.
  275. #use_printdebug = True
  276. # Enable live debugging in your browser. This should NEVER be enabled on a
  277. # public site. Enabled in the sample config for development.
  278. use_interactive = False
  279. # Write thread status periodically to 'heartbeat.log', (careful, uses disk
  280. # space rapidly!). Useful to determine why your processes may be consuming a
  281. # lot of CPU.
  282. #use_heartbeat = False
  283. # Enable the memory debugging interface (careful, negatively impacts server
  284. # performance).
  285. #use_memdump = False
  286. # -- Data Libraries
  287. # These library upload options are described in much more detail in the wiki:
  288. # http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files
  289. # Add an option to the library upload form which allows administrators to
  290. # upload a directory of files.
  291. #library_import_dir = ../ap_lib/import
  292. # Add an option to the library upload form which allows authorized
  293. # non-administrators to upload a directory of files. The configured directory
  294. # must contain sub-directories named the same as the non-admin user's Galaxy
  295. # login ( email ). The non-admin user is restricted to uploading files or
  296. # sub-directories of files contained in their directory.
  297. #user_library_import_dir = ../ap_lib/import/users
  298. # Add an option to the admin library upload tool allowing admins to paste
  299. # filesystem paths to files and directories in a box, and these paths will be
  300. # added to a library. Set to True to enable. Please note the security
  301. # implication that this will give Galaxy Admins access to anything your Galaxy
  302. # user has access to.
  303. #allow_library_path_paste = False
  304. # Users may choose to download multiple files from a library in an archive. By
  305. # default, Galaxy allows users to select from a few different archive formats
  306. # if testing shows that Galaxy is able to create files using these formats.
  307. # Specific formats can be disabled with this option, separate more than one
  308. # format with commas. Available formats are currently 'zip', 'gz', and 'bz2'.
  309. #disable_library_comptypes =
  310. # Some sequencer integration features in beta allow you to automatically
  311. # transfer datasets. This is done using a lightweight transfer manager which
  312. # runs outside of Galaxy (but is spawned by it automatically). Galaxy will
  313. # communicate with this manager over the port specified here.
  314. #transfer_manager_port = 8163
  315. # Search data libraries with whoosh
  316. #enable_whoosh_library_search = True
  317. # Whoosh indexes are stored in this directory.
  318. #whoosh_index_dir = database/whoosh_indexes
  319. # Search data libraries with lucene
  320. #enable_lucene_library_search = False
  321. # maxiumum file size to index for searching, in MB
  322. #fulltext_max_size = 500
  323. #fulltext_noindex_filetypes=bam,sam,wig,bigwig,fasta,fastq,fastqsolexa,fastqillumina,fastqsanger
  324. # base URL of server providing search functionality using lucene
  325. #fulltext_url = http://localhost:8081
  326. # -- Users and Security
  327. # Galaxy encodes various internal values when these values will be output in
  328. # some format (for example, in a URL or cookie). You should set a key to be
  329. # used by the algorithm that encodes and decodes these values. It can be any
  330. # string. If left unchanged, anyone could construct a cookie that would grant
  331. # them access to others' sessions.
  332. id_secret = SETTHISAFTERDEPLOYMENT
  333. # User authentication can be delegated to an upstream proxy server (usually
  334. # Apache). The upstream proxy should set a REMOTE_USER header in the request.
  335. # Enabling remote user disables regular logins. For more information, see:
  336. # http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy
  337. use_remote_user = False
  338. # If use_remote_user is enabled and your external authentication
  339. # method just returns bare usernames, set a default mail domain to be appended
  340. # to usernames, to become your Galaxy usernames (email addresses).
  341. #remote_user_maildomain = None
  342. # If use_remote_user is enabled, you can set this to a URL that will log your
  343. # users out.
  344. #remote_user_logout_href = None
  345. # Administrative users - set this to a comma-separated list of valid Galaxy
  346. # users (email addresses). These users will have access to the Admin section
  347. # of the server, and will have access to create users, groups, roles,
  348. # libraries, and more. For more information, see:
  349. # http://wiki.g2.bx.psu.edu/Admin/Interface
  350. #admin_users = user1@gmail.com,user2@gmail.com
  351. # Force everyone to log in (disable anonymous access).
  352. require_login = True
  353. # Allow unregistered users to create new accounts (otherwise, they will have to
  354. # be created by an admin).
  355. allow_user_creation = True
  356. # Allow administrators to delete accounts.
  357. allow_user_deletion = True
  358. # Allow administrators to log in as other users (useful for debugging)
  359. #allow_user_impersonation = False
  360. # Allow users to remove their datasets from disk immediately (otherwise,
  361. # datasets will be removed after a time period specified by an administrator in
  362. # the cleanup scripts run via cron)
  363. allow_user_dataset_purge = True
  364. # By default, users' data will be public, but setting this to True will cause
  365. # it to be private. Does not affect existing users and data, only ones created
  366. # after this option is set. Users may still change their default back to
  367. # public.
  368. #new_user_dataset_access_role_default_private = False
  369. # -- Beta features
  370. # Object store mode (valid options are: disk, s3, swift, distributed, hierarchical)
  371. #object_store = disk
  372. #os_access_key = <your cloud object store access key>
  373. #os_secret_key = <your cloud object store secret key>
  374. #os_bucket_name = <name of an existing object store bucket or container>
  375. # If using 'swift' object store, you must specify the following connection properties
  376. #os_host = swift.rc.nectar.org.au
  377. #os_port = 8888
  378. #os_is_secure = False
  379. #os_conn_path = /
  380. # Reduced redundancy can be used only with the 's3' object store
  381. #os_use_reduced_redundancy = False
  382. # Size (in GB) that the cache used by object store should be limited to.
  383. # If the value is not specified, the cache size will be limited only by the
  384. # file system size. The file system location of the cache is considered the
  385. # configuration of the ``file_path`` directive defined above.
  386. #object_store_cache_size = 100
  387. # Configuration file for the distributed object store, if object_store =
  388. # distributed. See the sample at distributed_object_store_conf.xml.sample
  389. #distributed_object_store_config_file = None
  390. # Enable Galaxy to communicate directly with a sequencer
  391. #enable_sequencer_communication = False
  392. # Enable authentication via OpenID. Allows users to log in to their Galaxy
  393. # account by authenticating with an OpenID provider.
  394. #enable_openid = False
  395. #openid_config_file = openid_conf.xml
  396. # Optional list of email addresses of API users who can make calls on behalf of
  397. # other users
  398. #api_allow_run_as = None
  399. # Enable tool tags (associating tools with tags). This has its own option
  400. # since its implementation has a few performance implications on startup for
  401. # large servers.
  402. #enable_tool_tags = False
  403. # Enable a feature when running workflows. When enabled, default datasets
  404. # are selected for "Set at Runtime" inputs from the history such that the
  405. # same input will not be selected twice, unless there are more inputs than
  406. # compatible datasets in the history.
  407. # When False, the most recently added compatible item in the history will
  408. # be used for each "Set at Runtime" input, independent of others in the Workflow
  409. #enable_unique_workflow_defaults = False
  410. # The URL to the myExperiment instance being used (omit scheme but include port)
  411. #myexperiment_url = www.myexperiment.org:80
  412. # Enable Galaxy's "Upload via FTP" interface. You'll need to install and
  413. # configure an FTP server (we've used ProFTPd since it can use Galaxy's
  414. # database for authentication) and set the following two options.
  415. # This should point to a directory containing subdirectories matching users'
  416. # email addresses, where Galaxy will look for files.
  417. ftp_upload_dir = SET-THIS-AS-OUR-ASPERA-SITE-AFTER-DEPLOYMENT
  418. # This should be the hostname of your FTP server, which will be provided to
  419. # users in the help text.
  420. ftp_upload_site = cistrome.dfci.harvard.edu
  421. # Enable enforcement of quotas. Quotas can be set from the Admin interface.
  422. #enable_quotas = False
  423. # Enable a feature when running workflows. When enabled, default datasets
  424. # are selected for "Set at Runtime" inputs from the history such that the
  425. # same input will not be selected twice, unless there are more inputs than
  426. # compatible datasets in the history.
  427. # When False, the most recently added compatible item in the history will
  428. # be used for each "Set at Runtime" input, independent of others in the Workflow
  429. #enable_unique_workflow_defaults = False
  430. # -- Job Execution
  431. # To increase performance of job execution and the web interface, you can
  432. # separate Galaxy into multiple processes. There are more than one way to do
  433. # this, and they are explained in detail in the documentation:
  434. #
  435. # http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Web%20Application%20Scaling
  436. #
  437. # By default, Galaxy manages and executes jobs from within a single process and
  438. # notifies itself of new jobs via in-memory queues. If you change job_manager
  439. # and job_handlers from their default values, notification will instead be done
  440. # using the `state` and `handler` columns of the job table in the database.
  441. # Identify the server_name (the string following server: at the top of this
  442. # file) which should be designated as the job manager (only one):
  443. #job_manager = main
  444. # Identify the server_name(s) which should be designated as job handlers
  445. # (responsible for starting, tracking, finishing, and cleaning up jobs) as a
  446. # comma-separated list.
  447. job_handlers = main
  448. # By default, a handler from job_handlers will be selected at random if the
  449. # tool to run does specify a handler below in [galaxy:tool_handlers]. If you
  450. # want certain handlers to only handle jobs for tools/params explicitly
  451. # assigned below, use default_job_handlers to specify which handlers should be
  452. # used for jobs without explicit handlers.
  453. default_job_handlers = main
  454. # In multiprocess configurations, notification between processes about new jobs
  455. # is done via the database. In single process configurations, this is done in
  456. # memory, which is a bit quicker. Galaxy tries to automatically determine
  457. # which method it should used based on your manager/handler configuration
  458. # above, but can't reliably determine if you have multiple processes for web
  459. # servers but only a single process as a manager/handler. In that scenario,
  460. # you can override the tracking method by setting the following to True:
  461. track_jobs_in_database = True
  462. # This enables splitting of jobs into tasks, if specified by the particular tool config.
  463. # This is a new feature and not recommended for production servers yet.
  464. #use_tasked_jobs = False
  465. #local_task_queue_workers = 2
  466. # Enable job recovery (if Galaxy is restarted while cluster jobs are running,
  467. # it can "recover" them when it starts). This is not safe to use if you are
  468. # running more than one Galaxy server using the same database.
  469. #enable_job_recovery = True
  470. # Setting metadata on job outputs to in a separate process (or if using a
  471. # cluster, on the cluster). Thanks to Python's Global Interpreter Lock and the
  472. # hefty expense that setting metadata incurs, your Galaxy process may become
  473. # unresponsive when this operation occurs internally.
  474. #set_metadata_externally = False
  475. # Although it is fairly reliable, setting metadata can occasionally fail. In
  476. # these instances, you can choose to retry setting it internally or leave it in
  477. # a failed state (since retrying internally may cause the Galaxy process to be
  478. # unresponsive). If this option is set to False, the user will be given the
  479. # option to retry externally, or set metadata manually (when possible).
  480. #retry_metadata_internally = True
  481. # If (for example) you run on a cluster and your datasets (by default,
  482. # database/files/) are mounted read-only, this option will override tool output
  483. # paths to write outputs to the working directory instead, and the job manager
  484. # will move the outputs to their proper place in the dataset directory on the
  485. # Galaxy server after the job completes.
  486. #outputs_to_working_directory = False
  487. # If your network filesystem's caching prevents the Galaxy server from seeing
  488. # the job's stdout and stderr files when it completes, you can retry reading
  489. # these files. The job runner will retry the number of times specified below,
  490. # waiting 1 second between tries. For NFS, you may want to try the -noac mount
  491. # option (Linux) or -actimeo=0 (Solaris).
  492. #retry_job_output_collection = 0
  493. # Clean up various bits of jobs left on the filesystem after completion. These
  494. # bits include the job working directory, external metadata temporary files,
  495. # and DRM stdout and stderr files (if using a DRM). Possible values are:
  496. # always, onsuccess, never
  497. #cleanup_job = always
  498. # Number of concurrent jobs to run (local job runner)
  499. local_job_queue_workers = 10
  500. # Jobs can be killed after a certain amount of execution time. Format is in
  501. # hh:mm:ss. Currently only implemented for PBS.
  502. # job_walltime = 24:00:00
  503. # Jobs can be killed if any of their outputs grow over a certain size (in
  504. # bytes). 0 for no limit.
  505. #output_size_limit = 0
  506. # Cistrome admin: set this to 10GBytes
  507. output_size_limit = 10000000000
  508. # Jobs can be held back from submission to a runner if a user already has more
  509. # jobs queued or running than the number specified below. This prevents a
  510. # single user from stuffing the queue and preventing other users from being
  511. # able to run jobs.
  512. #user_job_limit = None
  513. # Clustering Galaxy is not a straightforward process and requires some
  514. # pre-configuration. See the the wiki before attempting to set any of these
  515. # options:
  516. # http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster
  517. # Comma-separated list of job runners to start. local is always started. If
  518. # left commented, no jobs will be run on the cluster, even if a cluster URL is
  519. # explicitly defined in the [galaxy:tool_runners] section below. The runners
  520. # currently available are 'pbs' and 'drmaa'.
  521. #start_job_runners = None
  522. # For sites where all users in Galaxy match users on the system on which Galaxy
  523. # runs, the DRMAA job runner can be configured to submit jobs to the DRM as the
  524. # actual user instead of as the user running the Galaxy server process. For
  525. # details on these options, see the documentation at:
  526. #
  527. # http://galaxyproject.org/wiki/Admin/Config/Performance/Cluster
  528. #
  529. #drmaa_external_runjob_script = scripts/drmaa_external_runner.py
  530. #drmaa_external_killjob_script = scripts/drmaa_external_killer.py
  531. #external_chown_script = scripts/external_chown_script.py
  532. # File to source to set up the environment when running jobs. By default, the
  533. # environment in which the Galaxy server starts is used when running jobs
  534. # locally, and the environment set up per the DRM's submission method and
  535. # policy is used when running jobs on a cluster (try testing with `qsub` on the
  536. # command line). environment_setup_file can be set to the path of a file on
  537. # the cluster that should be sourced by the user to set up the environment
  538. # prior to running tools. This can be especially useful for running jobs as
  539. # the actual user, to remove the need to configure each user's environment
  540. # individually. This only affects cluster jobs, not local jobs.
  541. #environment_setup_file = None
  542. # The URL for the default runner to use when a tool doesn't explicitly define a
  543. # runner below.
  544. #default_cluster_job_runner = local:///
  545. # The cluster runners have their own thread pools used to prepare and finish
  546. # jobs (so that these sometimes lengthy operations do not block normal queue
  547. # operation). The value here is the number of worker threads available to each
  548. # started runner.
  549. #cluster_job_queue_workers = 3
  550. # These options are only used when using file staging with PBS.
  551. #pbs_application_server =
  552. #pbs_stage_path =
  553. #pbs_dataset_server =
  554. # Path to the static library files for assembly, ceaslib, chromLen, conservation, liftOver and MAT-lib
  555. # Then in other tool configuration xml file, we can use 'from galaxy import config' then '$config.Configuration().cistrome_static_library_path'
  556. # default would be in tool-data/ folder
  557. cistrome_static_library_path = tool-data
  558. # This option allows users to see the full path of datasets via the "View
  559. # Details" option in the history. Administrators can always see this.
  560. #expose_dataset_path = False
  561. # ---- Per-Tool Job Management ----------------------------------------------
  562. # Per-tool job handler and runner overrides. Parameters can be included to define multiple
  563. # runners per tool. E.g. to run Cufflinks jobs initiated from Trackster
  564. # differently than standard Cufflinks jobs:
  565. #
  566. # cufflinks = local:///
  567. # cufflinks[source@trackster] = local:///
  568. [galaxy:tool_handlers]
  569. # By default, Galaxy will select a handler at random from the list of
  570. # job_handlers set above. You can override as in the following examples:
  571. #
  572. #upload1 = upload_handler
  573. #cufflinks[source@trackster] = realtime_handler
  574. [galaxy:tool_runners]
  575. # If not listed here, a tool will run with the runner defined with
  576. # default_cluster_job_runner. These overrides for local:/// are done because
  577. # these tools can fetch data from remote sites, which may not be suitable to
  578. # run on a cluster (if it does not have access to the Internet, for example).
  579. biomart = local:///
  580. encode_db1 = local:///
  581. hbvar = local:///
  582. microbial_import1 = local:///
  583. ucsc_table_direct1 = local:///
  584. ucsc_table_direct_archaea1 = local:///
  585. ucsc_table_direct_test1 = local:///
  586. upload1 = local:///
  587. # ---- Galaxy Message Queue -------------------------------------------------
  588. # Galaxy uses AMQ protocol to receive messages from external sources like
  589. # bar code scanners. Galaxy has been tested against RabbitMQ AMQP implementation.
  590. # For Galaxy to receive messages from a message queue the RabbitMQ server has
  591. # to be set up with a user account and other parameters listed below. The 'host'
  592. # and 'port' fields should point to where the RabbitMQ server is running.
  593. [galaxy_amqp]
  594. #host = 127.0.0.1
  595. #port = 5672
  596. #userid = galaxy
  597. #password = galaxy
  598. #virtual_host = galaxy_messaging_engine
  599. #queue = galaxy_queue
  600. #exchange = galaxy_exchange
  601. #routing_key = bar_code_scanner
  602. #rabbitmqctl_path = /path/to/rabbitmqctl