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Relevant Search: With Applications for Solr and Elasticsearch

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https://bitbucket.org/cistrome/cistrome-harvard/
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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
  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# http://wiki.g2.bx.psu.edu/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.
 29port = 10096
 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.
 34host = 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.
 41threadpool_workers = 10
 42
 43# ---- Filters --------------------------------------------------------------
 44
 45# Filters sit between Galaxy and the HTTP server.
 46
 47# These filters are disabled by default.  They can be enabled with
 48# 'filter-with' in the [app:main] section below.
 49
 50# Define the gzip filter.
 51[filter:gzip]
 52use = egg:Paste#gzip
 53
 54# Define the proxy-prefix filter.
 55[filter:proxy-prefix]
 56use = egg:PasteDeploy#prefix
 57prefix = /ap
 58
 59# ---- Galaxy ---------------------------------------------------------------
 60
 61# Configuration of the Galaxy application.
 62
 63[app:main]
 64
 65# -- Application and filtering
 66
 67# The factory for the WSGI application.  This should not be changed.
 68paste.app_factory = galaxy.web.buildapp:app_factory
 69
 70# If not running behind a proxy server, you may want to enable gzip compression
 71# to decrease the size of data transferred over the network.  If using a proxy
 72# server, please enable gzip compression there instead.
 73#filter-with = gzip
 74
 75# If running behind a proxy server and Galaxy is served from a subdirectory,
 76# enable the proxy-prefix filter and set the prefix in the
 77# [filter:proxy-prefix] section above.
 78filter-with = proxy-prefix
 79
 80# If proxy-prefix is enabled and you're running more than one Galaxy instance
 81# behind one hostname, you will want to set this to the same path as the prefix
 82# in the filter above.  This value becomes the "path" attribute set in the
 83# cookie so the cookies from each instance will not clobber each other.
 84cookie_path = /ap
 85
 86# -- Database
 87
 88# By default, Galaxy uses a SQLite database at 'database/universe.sqlite'.  You
 89# may use a SQLAlchemy connection string to specify an external database
 90# instead.  This string takes many options which are explained in detail in the
 91# config file documentation.
 92#database_connection = postgres://cistrome:cistrome@localhost/cistromeap
 93database_connection = mysql://cistrome:cistrome@localhost/cistromeap
 94
 95# If the server logs errors about not having enough database pool connections,
 96# you will want to increase these values, or consider running more Galaxy
 97# processes.
 98database_engine_option_pool_size = 10
 99database_engine_option_max_overflow = 20
100
101# If using MySQL and the server logs the error "MySQL server has gone away",
102# you will want to set this to some positive value (7200 should work).
103#database_engine_option_pool_recycle = -1
104
105# If large database query results are causing memory or response time issues in
106# the Galaxy process, leave the result on the server instead.  This option is
107# only available for PostgreSQL and is highly recommended.
108#database_engine_option_server_side_cursors = False
109
110# Create only one connection to the database per thread, to reduce the
111# connection overhead.  Recommended when not using SQLite:
112#database_engine_option_strategy = threadlocal
113
114# Log all database transactions, can be useful for debugging and performance
115# profiling.  Logging is done via Python's 'logging' module under the qualname
116# 'galaxy.model.orm.logging_connection_proxy'
117#database_query_profiling_proxy = False
118
119# -- Files and directories
120
121# Path where genome builds are stored. This defaults to tool-data/genome
122#genome_data_path = tool-data/genome
123
124# URL for rsync server to download pre-built indexes.
125#rsync_url = rsync://scofield.bx.psu.edu/indexes
126
127# Dataset files are stored in this directory.
128file_path = database/files
129
130# Temporary files are stored in this directory.
131new_file_path = database/tmp
132
133# Tool config files, defines what tools are available in Galaxy.
134# Tools can be locally developed or installed from Galaxy tool sheds.
135tool_config_file = tool_conf.xml,shed_tool_conf.xml
136
137# Default path to the directory containing the tools defined in tool_conf.xml.
138# Other tool config files must include the tool_path as an attribute in the <toolbox> tag.
139tool_path = tools
140
141# Path to the directory in which managed tool dependencies are placed.  To use
142# the dependency system, see the documentation at:
143# http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies
144#tool_dependency_dir = None
145
146# Enable automatic polling of relative tool sheds to see if any updates
147# are available for installed repositories.  Ideally only one Galaxy 
148# server process should be able to check for repository updates.  The
149# setting for hours_between_check should be an integer between 1 and 24.
150#enable_tool_shed_check = False
151#hours_between_check = 12
152
153# Directory where data used by tools is located, see the samples in that
154# directory and the wiki for help:
155# http://wiki.g2.bx.psu.edu/Admin/Data%20Integration
156tool_data_path = tool-data
157
158# Directory where chrom len files are kept, currently mainly used by trackster
159len_file_path = tool-data/shared/ucsc/chrom
160
161# Datatypes config file, defines what data (file) types are available in
162# Galaxy.
163datatypes_config_file = datatypes_conf.xml
164
165# Each job is given a unique empty directory as its current working directory.
166# This option defines in what parent directory those directories will be
167# created.
168job_working_directory = database/job_working_directory
169
170# If using a cluster, Galaxy will write job scripts and stdout/stderr to this
171# directory.
172#cluster_files_directory = database/pbs
173
174# External service types config file, defines what types of external_services configurations 
175# are available in Galaxy.
176#external_service_type_config_file = external_service_types_conf.xml
177
178# Path to the directory containing the external_service_types defined in the config.
179#external_service_type_path = external_service_types
180
181# Tools with a number of outputs not known until runtime can write these
182# outputs to a directory for collection by Galaxy when the job is done.
183# Previously, this directory was new_file_path, but using one global directory
184# can cause performance problems, so using job_working_directory ('.' or cwd
185# when a job is run) is encouraged.  By default, both are checked to avoid
186# breaking existing tools.
187#collect_outputs_from = new_file_path,job_working_directory
188
189# -- Mail and notification
190
191# Galaxy sends mail for various things: Subscribing users to the mailing list
192# if they request it, emailing password resets, notification from the Galaxy
193# Sample Tracking system, and reporting dataset errors.  To do this, it needs
194# to send mail through an SMTP server, which you may define here (host:port).
195# Galaxy will automatically try STARTTLS but will continue upon failure.
196smtp_server = localhost
197
198# If your SMTP server requires a username and password, you can provide them
199# here (password in cleartext here, but if your server supports STARTTLS it
200# will be sent over the network encrypted).
201#smtp_username = None
202#smtp_password = None
203
204# On the user registration form, users may choose to join the mailing list.
205# This is the address of the list they'll be subscribed to.
206#mailing_join_addr = galaxy-announce-join@bx.psu.edu
207
208# Datasets in an error state include a link to report the error.  Those reports
209# will be sent to this address.  Error reports are disabled if no address is set.
210error_email_to = cistrome-bugs@jimmy.harvard.edu
211
212# -- Display sites
213
214# Galaxy can display data at various external browsers.  These options specify
215# which browsers should be available.  URLs and builds available at these
216# browsers are defined in the specifield files.
217
218# UCSC browsers: tool-data/shared/ucsc/ucsc_build_sites.txt
219ucsc_display_sites = main,test,archaea,ucla
220
221# GBrowse servers: tool-data/shared/gbrowse/gbrowse_build_sites.txt
222#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
223
224# GeneTrack servers: tool-data/shared/genetrack/genetrack_sites.txt
225#genetrack_display_sites = main,test
226
227# If use_remote_user = True, display application servers will be denied access
228# to Galaxy and so displaying datasets in these sites will fail.
229# display_servers contains a list of hostnames which should be allowed to
230# bypass security to display datasets.  Please be aware that there are security
231# implications if this is allowed.  More details (including required changes to
232# the proxy server config) are available in the Apache proxy documentation on
233# the wiki.
234#
235# The list of servers in this sample config are for the UCSC Main, Test and
236# Archaea browsers, but the default if left commented is to not allow any
237# display sites to bypass security (you must uncomment the line below to allow
238# them).
239#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
240
241# -- Next gen LIMS interface on top of existing Galaxy Sample/Request management code.
242
243use_nglims = False
244nglims_config_file = tool-data/nglims.yaml
245
246# -- UI Localization
247
248# Append "/{brand}" to the "Galaxy" text in the masthead.
249brand = Cistrome
250
251# The URL linked by the "Galaxy/brand" text.
252logo_url = http://cistrome.org/ap/
253
254# The URL linked by the "Galaxy Wiki" link in the "Help" menu.
255wiki_url = http://bitbucket.org/cistrome/cistrome-harvard/wiki
256
257# The URL linked by the "Email comments..." link in the "Help" menu.
258bugs_email = mailto:cistrome-bugs@jimmy.harvard.edu
259
260# The URL linked by the "How to Cite..." link in the "Help" menu.
261citation_url = http://bitbucket.org/cistrome/cistrome-harvard/wiki/Citation
262
263# The URL linked by the "Terms and Conditions" link in the "Help" menu, as well
264# as on the user registration and login forms.
265#terms_url = None
266
267# Serve static content, which must be enabled if you're not serving it via a
268# proxy server.  These options should be self explanatory and so are not
269# documented individually.  You can use these paths (or ones in the proxy
270# server) to point to your own styles.
271static_enabled = True
272static_cache_time = 360
273static_dir = %(here)s/static/
274static_images_dir = %(here)s/static/images
275static_favicon_dir = %(here)s/static/favicon.ico
276static_scripts_dir = %(here)s/static/scripts/
277static_style_dir = %(here)s/static/june_2007_style/blue
278static_robots_txt = %(here)s/static/robots.txt
279
280# Pack javascript at launch (/static/scripts/*.js)
281# This only happens if the modified timestamp of the source .js is newer
282# than the version (if it exists) in /static/scripts/packed/
283# Note that this requires java > 1.4 for executing yuicompressor.jar
284#pack_scripts = False
285
286# Enable Cloud Launch
287
288#enable_cloud_launch = False
289
290# -- Advanced proxy features
291
292# For help on configuring the Advanced proxy features, see:
293# http://usegalaxy.org/production
294
295# Apache can handle file downloads (Galaxy-to-user) via mod_xsendfile.  Set
296# this to True to inform Galaxy that mod_xsendfile is enabled upstream.
297#apache_xsendfile = False
298
299# The same download handling can be done by nginx using X-Accel-Redirect.  This
300# should be set to the path defined in the nginx config as an internal redirect
301# with access to Galaxy's data files (see documentation linked above).
302#nginx_x_accel_redirect_base = False
303
304# nginx can make use of mod_zip to create zip files containing multiple library
305# files.  If using X-Accel-Redirect, this can be the same value as that option.
306#nginx_x_archive_files_base = False
307
308# If using compression in the upstream proxy server, use this option to disable
309# gzipping of library .tar.gz and .zip archives, since the proxy server will do
310# it faster on the fly.
311upstream_gzip = False
312
313# nginx can also handle file uploads (user-to-Galaxy) via nginx_upload_module.
314# Configuration for this is complex and explained in detail in the
315# documentation linked above.  The upload store is a temporary directory in
316# which files uploaded by the upload module will be placed.
317#nginx_upload_store = False
318
319# This value overrides the action set on the file upload form, e.g. the web
320# path where the nginx_upload_module has been configured to intercept upload
321# requests.
322#nginx_upload_path = False
323
324# -- Logging and Debugging
325
326# Verbosity of console log messages.  Acceptable values can be found here:
327# http://docs.python.org/library/logging.html#logging-levels
328log_level = DEBUG
329
330# Print database operations to the server log (warning, quite verbose!).
331#database_engine_option_echo = False
332
333# Print database pool operations to the server log (warning, quite verbose!).
334#database_engine_option_echo_pool = False
335
336# Turn on logging of application events and some user events to the database.
337log_events = True
338
339# Turn on logging of user actions to the database. Actions currently logged are
340# grid views, tool searches, and use of "recently" used tools menu.  The
341# log_events and log_actions functionality will eventually be merged.
342log_actions = True
343
344# Sanitize All HTML Tool Output
345# By default, all tool output served as 'text/html' will be sanitized
346# thoroughly. This can be disabled if you have special tools that require
347# unaltered output.
348#sanitize_all_html = True
349
350# Debug enables access to various config options useful for development and
351# debugging: use_lint, use_profile, use_printdebug and use_interactive.  It
352# also causes the files used by PBS/SGE (submission script, output, and error)
353# to remain on disk after the job is complete.  Debug mode is disabled if
354# commented, but is uncommented by default in the sample config.
355debug = True
356
357# Check for WSGI compliance.
358use_lint = False
359
360# Run the Python profiler on each request.
361use_profile = False
362
363# Intercept print statements and show them on the returned page.
364#use_printdebug = True
365
366# Enable live debugging in your browser.  This should NEVER be enabled on a
367# public site.  Enabled in the sample config for development.
368use_interactive = False
369
370# Write thread status periodically to 'heartbeat.log',  (careful, uses disk
371# space rapidly!).  Useful to determine why your processes may be consuming a
372# lot of CPU.
373#use_heartbeat = False
374
375# Enable the memory debugging interface (careful, negatively impacts server
376# performance).
377#use_memdump = False
378
379# -- Data Libraries
380
381# These library upload options are described in much more detail in the wiki:
382# http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files
383
384# Add an option to the library upload form which allows administrators to
385# upload a directory of files.
386#library_import_dir = ../ap_lib/import
387
388# Add an option to the library upload form which allows authorized
389# non-administrators to upload a directory of files.  The configured directory
390# must contain sub-directories named the same as the non-admin user's Galaxy
391# login ( email ).  The non-admin user is restricted to uploading files or
392# sub-directories of files contained in their directory.
393#user_library_import_dir = ../ap_lib/import/users
394
395# Add an option to the admin library upload tool allowing admins to paste
396# filesystem paths to files and directories in a box, and these paths will be
397# added to a library.  Set to True to enable.  Please note the security
398# implication that this will give Galaxy Admins access to anything your Galaxy
399# user has access to.
400#allow_library_path_paste = False
401
402# Users may choose to download multiple files from a library in an archive.  By
403# default, Galaxy allows users to select from a few different archive formats
404# if testing shows that Galaxy is able to create files using these formats.
405# Specific formats can be disabled with this option, separate more than one
406# format with commas.  Available formats are currently 'zip', 'gz', and 'bz2'.
407#disable_library_comptypes = 
408
409# Some sequencer integration features in beta allow you to automatically
410# transfer datasets.  This is done using a lightweight transfer manager which
411# runs outside of Galaxy (but is spawned by it automatically).  Galaxy will
412# communicate with this manager over the port specified here.
413#transfer_manager_port = 8163
414
415# Search data libraries with whoosh
416#enable_whoosh_library_search = True
417# Whoosh indexes are stored in this directory.
418#whoosh_index_dir = database/whoosh_indexes
419
420# Search data libraries with lucene
421#enable_lucene_library_search = False
422# maxiumum file size to index for searching, in MB
423#fulltext_max_size = 500
424#fulltext_noindex_filetypes=bam,sam,wig,bigwig,fasta,fastq,fastqsolexa,fastqillumina,fastqsanger
425# base URL of server providing search functionality using lucene
426#fulltext_url = http://localhost:8081
427
428# -- Users and Security
429
430# Galaxy encodes various internal values when these values will be output in
431# some format (for example, in a URL or cookie).  You should set a key to be
432# used by the algorithm that encodes and decodes these values.  It can be any
433# string.  If left unchanged, anyone could construct a cookie that would grant
434# them access to others' sessions.
435id_secret = SETTHISAFTERDEPLOYMENT
436
437# User authentication can be delegated to an upstream proxy server (usually
438# Apache).  The upstream proxy should set a REMOTE_USER header in the request.
439# Enabling remote user disables regular logins.  For more information, see:
440# http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy
441use_remote_user = False
442
443# If use_remote_user is enabled and your external authentication
444# method just returns bare usernames, set a default mail domain to be appended
445# to usernames, to become your Galaxy usernames (email addresses).
446#remote_user_maildomain = None
447
448# If use_remote_user is enabled, you can set this to a URL that will log your
449# users out.
450#remote_user_logout_href = None
451
452# Administrative users - set this to a comma-separated list of valid Galaxy
453# users (email addresses).  These users will have access to the Admin section
454# of the server, and will have access to create users, groups, roles,
455# libraries, and more.  For more information, see:
456# http://wiki.g2.bx.psu.edu/Admin/Interface
457#admin_users = user1@gmail.com,user2@gmail.com
458
459# Force everyone to log in (disable anonymous access).
460require_login = True
461
462# Allow unregistered users to create new accounts (otherwise, they will have to
463# be created by an admin).
464allow_user_creation = True
465
466# Allow administrators to delete accounts.
467allow_user_deletion = True
468
469# Allow administrators to log in as other users (useful for debugging)
470#allow_user_impersonation = False
471
472# Allow users to remove their datasets from disk immediately (otherwise,
473# datasets will be removed after a time period specified by an administrator in
474# the cleanup scripts run via cron)
475allow_user_dataset_purge = True
476
477# By default, users' data will be public, but setting this to True will cause
478# it to be private.  Does not affect existing users and data, only ones created
479# after this option is set.  Users may still change their default back to
480# public.
481#new_user_dataset_access_role_default_private = False
482
483# -- Beta features
484
485# Object store mode (valid options are: disk, s3, swift, distributed, hierarchical)
486#object_store = disk
487#os_access_key = <your cloud object store access key>
488#os_secret_key = <your cloud object store secret key>
489#os_bucket_name = <name of an existing object store bucket or container>
490# If using 'swift' object store, you must specify the following connection properties
491#os_host = swift.rc.nectar.org.au
492#os_port = 8888
493#os_is_secure = False
494#os_conn_path = /
495# Reduced redundancy can be used only with the 's3' object store
496#os_use_reduced_redundancy = False
497# Size (in GB) that the cache used by object store should be limited to.
498# If the value is not specified, the cache size will be limited only by the
499# file system size. The file system location of the cache is considered the
500# configuration of the ``file_path`` directive defined above.
501#object_store_cache_size = 100
502
503# Configuration file for the distributed object store, if object_store =
504# distributed.  See the sample at distributed_object_store_conf.xml.sample
505#distributed_object_store_config_file = None
506
507# Enable Galaxy to communicate directly with a sequencer
508#enable_sequencer_communication = False
509
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
515# Optional list of email addresses of API users who can make calls on behalf of
516# other users
517#api_allow_run_as = None
518
519# Enable tool tags (associating tools with tags).  This has its own option
520# since its implementation has a few performance implications on startup for
521# large servers.
522#enable_tool_tags = False
523
524# Enable a feature when running workflows. When enabled, default datasets
525# are selected for "Set at Runtime" inputs from the history such that the
526# same input will not be selected twice, unless there are more inputs than
527# compatible datasets in the history.
528# When False, the most recently added compatible item in the history will
529# be used for each "Set at Runtime" input, independent of others in the Workflow
530#enable_unique_workflow_defaults = False
531
532# The URL to the myExperiment instance being used (omit scheme but include port)
533#myexperiment_url = www.myexperiment.org:80
534
535# Enable Galaxy's "Upload via FTP" interface.  You'll need to install and
536# configure an FTP server (we've used ProFTPd since it can use Galaxy's
537# database for authentication) and set the following two options.
538
539# This should point to a directory containing subdirectories matching users'
540# email addresses, where Galaxy will look for files.
541ftp_upload_dir = SET-THIS-AS-OUR-ASPERA-SITE-AFTER-DEPLOYMENT
542
543# This should be the hostname of your FTP server, which will be provided to
544# users in the help text.
545ftp_upload_site = cistrome.dfci.harvard.edu
546
547# Enable enforcement of quotas.  Quotas can be set from the Admin interface.
548#enable_quotas = False
549
550# Enable a feature when running workflows. When enabled, default datasets
551# are selected for "Set at Runtime" inputs from the history such that the
552# same input will not be selected twice, unless there are more inputs than
553# compatible datasets in the history.
554# When False, the most recently added compatible item in the history will
555# be used for each "Set at Runtime" input, independent of others in the Workflow
556#enable_unique_workflow_defaults = False
557
558# -- Job Execution
559
560# To increase performance of job execution and the web interface, you can
561# separate Galaxy into multiple processes.  There are more than one way to do
562# this, and they are explained in detail in the documentation:
563#
564#   http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Web%20Application%20Scaling
565#
566# By default, Galaxy manages and executes jobs from within a single process and
567# notifies itself of new jobs via in-memory queues.  If you change job_manager
568# and job_handlers from their default values, notification will instead be done
569# using the `state` and `handler` columns of the job table in the database.
570
571# Identify the server_name (the string following server: at the top of this
572# file) which should be designated as the job manager (only one):
573#job_manager = main
574
575# Identify the server_name(s) which should be designated as job handlers
576# (responsible for starting, tracking, finishing, and cleaning up jobs) as a
577# comma-separated list.
578job_handlers = main
579
580# By default, a handler from job_handlers will be selected at random if the
581# tool to run does specify a handler below in [galaxy:tool_handlers].  If you
582# want certain handlers to only handle jobs for tools/params explicitly
583# assigned below, use default_job_handlers to specify which handlers should be
584# used for jobs without explicit handlers.
585default_job_handlers = main
586
587# In multiprocess configurations, notification between processes about new jobs
588# is done via the database.  In single process configurations, this is done in
589# memory, which is a bit quicker.  Galaxy tries to automatically determine
590# which method it should used based on your manager/handler configuration
591# above, but can't reliably determine if you have multiple processes for web
592# servers but only a single process as a manager/handler.  In that scenario,
593# you can override the tracking method by setting the following to True:
594track_jobs_in_database = True
595
596# This enables splitting of jobs into tasks, if specified by the particular tool config.
597# This is a new feature and not recommended for production servers yet.
598#use_tasked_jobs = False
599#local_task_queue_workers = 2
600
601# Enable job recovery (if Galaxy is restarted while cluster jobs are running,
602# it can "recover" them when it starts).  This is not safe to use if you are
603# running more than one Galaxy server using the same database.
604#enable_job_recovery = True
605
606# Setting metadata on job outputs to in a separate process (or if using a
607# cluster, on the cluster).  Thanks to Python's Global Interpreter Lock and the
608# hefty expense that setting metadata incurs, your Galaxy process may become
609# unresponsive when this operation occurs internally.
610#set_metadata_externally = False
611
612# Although it is fairly reliable, setting metadata can occasionally fail.  In
613# these instances, you can choose to retry setting it internally or leave it in
614# a failed state (since retrying internally may cause the Galaxy process to be
615# unresponsive).  If this option is set to False, the user will be given the
616# option to retry externally, or set metadata manually (when possible).
617#retry_metadata_internally = True
618
619# If (for example) you run on a cluster and your datasets (by default,
620# database/files/) are mounted read-only, this option will override tool output
621# paths to write outputs to the working directory instead, and the job manager
622# will move the outputs to their proper place in the dataset directory on the
623# Galaxy server after the job completes.
624#outputs_to_working_directory = False
625
626# If your network filesystem's caching prevents the Galaxy server from seeing
627# the job's stdout and stderr files when it completes, you can retry reading
628# these files.  The job runner will retry the number of times specified below,
629# waiting 1 second between tries.  For NFS, you may want to try the -noac mount
630# option (Linux) or -actimeo=0 (Solaris).
631#retry_job_output_collection = 0
632
633# Clean up various bits of jobs left on the filesystem after completion.  These
634# bits include the job working directory, external metadata temporary files,
635# and DRM stdout and stderr files (if using a DRM).  Possible values are:
636# always, onsuccess, never
637#cleanup_job = always
638
639# Number of concurrent jobs to run (local job runner)
640local_job_queue_workers = 10
641
642# Jobs can be killed after a certain amount of execution time.  Format is in
643# hh:mm:ss.  Currently only implemented for PBS.
644# job_walltime = 24:00:00
645
646# Jobs can be killed if any of their outputs grow over a certain size (in
647# bytes).  0 for no limit.
648#output_size_limit = 0
649
650# Cistrome admin: set this to 10GBytes
651output_size_limit = 10000000000
652# Jobs can be held back from submission to a runner if a user already has more
653# jobs queued or running than the number specified below.  This prevents a
654# single user from stuffing the queue and preventing other users from being
655# able to run jobs.
656#user_job_limit = None
657
658# Clustering Galaxy is not a straightforward process and requires some
659# pre-configuration.  See the the wiki before attempting to set any of these
660# options:
661# http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster
662
663# Comma-separated list of job runners to start.  local is always started.  If
664# left commented, no jobs will be run on the cluster, even if a cluster URL is
665# explicitly defined in the [galaxy:tool_runners] section below.  The runners
666# currently available are 'pbs' and 'drmaa'.
667#start_job_runners = None
668
669# For sites where all users in Galaxy match users on the system on which Galaxy
670# runs, the DRMAA job runner can be configured to submit jobs to the DRM as the
671# actual user instead of as the user running the Galaxy server process.  For
672# details on these options, see the documentation at:
673#
674# http://galaxyproject.org/wiki/Admin/Config/Performance/Cluster
675#
676#drmaa_external_runjob_script = scripts/drmaa_external_runner.py
677#drmaa_external_killjob_script = scripts/drmaa_external_killer.py
678#external_chown_script = scripts/external_chown_script.py
679
680# File to source to set up the environment when running jobs.  By default, the
681# environment in which the Galaxy server starts is used when running jobs
682# locally, and the environment set up per the DRM's submission method and
683# policy is used when running jobs on a cluster (try testing with `qsub` on the
684# command line).  environment_setup_file can be set to the path of a file on
685# the cluster that should be sourced by the user to set up the environment
686# prior to running tools.  This can be especially useful for running jobs as
687# the actual user, to remove the need to configure each user's environment
688# individually.  This only affects cluster jobs, not local jobs.
689#environment_setup_file = None
690
691# The URL for the default runner to use when a tool doesn't explicitly define a
692# runner below.
693#default_cluster_job_runner = local:///
694
695# The cluster runners have their own thread pools used to prepare and finish
696# jobs (so that these sometimes lengthy operations do not block normal queue
697# operation).  The value here is the number of worker threads available to each
698# started runner.
699#cluster_job_queue_workers = 3
700
701# These options are only used when using file staging with PBS.
702#pbs_application_server = 
703#pbs_stage_path = 
704#pbs_dataset_server = 
705
706# Path to the static library files for assembly, ceaslib, chromLen, conservation, liftOver and MAT-lib
707# Then in other tool configuration xml file, we can use 'from galaxy import config' then '$config.Configuration().cistrome_static_library_path'
708# default would be in tool-data/ folder
709cistrome_static_library_path = tool-data
710# This option allows users to see the full path of datasets via the "View
711# Details" option in the history.  Administrators can always see this.
712#expose_dataset_path = False
713
714# ---- Per-Tool Job Management ----------------------------------------------
715
716# Per-tool job handler and runner overrides. Parameters can be included to define multiple
717# runners per tool. E.g. to run Cufflinks jobs initiated from Trackster
718# differently than standard Cufflinks jobs:
719#
720#   cufflinks = local:///
721#   cufflinks[source@trackster] = local:///
722
723[galaxy:tool_handlers]
724
725# By default, Galaxy will select a handler at random from the list of
726# job_handlers set above.  You can override as in the following examples:
727#
728#upload1 = upload_handler
729#cufflinks[source@trackster] = realtime_handler
730
731[galaxy:tool_runners]
732
733# If not listed here, a tool will run with the runner defined with 
734# default_cluster_job_runner.  These overrides for local:/// are done because
735# these tools can fetch data from remote sites, which may not be suitable to
736# run on a cluster (if it does not have access to the Internet, for example).
737
738biomart = local:///
739encode_db1 = local:///
740hbvar = local:///
741microbial_import1 = local:///
742ucsc_table_direct1 = local:///
743ucsc_table_direct_archaea1 = local:///
744ucsc_table_direct_test1 = local:///
745upload1 = local:///
746
747# ---- Galaxy Message Queue -------------------------------------------------
748
749# Galaxy uses AMQ protocol to receive messages from external sources like 
750# bar code scanners. Galaxy has been tested against RabbitMQ AMQP implementation.
751# For Galaxy to receive messages from a message queue the RabbitMQ server has 
752# to be set up with a user account and other parameters listed below. The 'host'
753# and 'port' fields should point to where the RabbitMQ server is running. 
754
755[galaxy_amqp]
756
757#host = 127.0.0.1
758#port = 5672
759#userid = galaxy
760#password = galaxy
761#virtual_host = galaxy_messaging_engine
762#queue = galaxy_queue
763#exchange = galaxy_exchange
764#routing_key = bar_code_scanner
765#rabbitmqctl_path = /path/to/rabbitmqctl
766