root/galaxy-central/universe_wsgi.ini.sample

リビジョン 2, 16.0 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
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://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer
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# Config hackers are encouraged to check there before asking for help.
15
16# ---- HTTP Server ----------------------------------------------------------
17
18# Configuration of the internal HTTP server.
19
20[server:main]
21
22# The internal HTTP server to use.  Currently only Paste is provided.  This
23# option is required.
24use = egg:Paste#http
25
26# The port on which to listen.
27#port = 8080
28
29# The address on which to listen.  By default, only listen to localhost (Galaxy
30# will not be accessible over the network).  Use '0.0.0.0' to listen on all
31# available network interfaces.
32#host = 127.0.0.1
33
34# Use a threadpool for the web server instead of creating a thread for each
35# request.
36use_threadpool = True
37
38# Number of threads in the web server thread pool.
39#threadpool_workers = 10
40
41# ---- Filters --------------------------------------------------------------
42
43# Filters sit between Galaxy and the HTTP server.
44
45# These filters are disabled by default.  They can be enabled with
46# 'filter-with' in the [app:main] section below.
47
48# Define the gzip filter.
49[filter:gzip]
50use = egg:Paste#gzip
51
52# Define the proxy-prefix filter.
53[filter:proxy-prefix]
54use = egg:PasteDeploy#prefix
55prefix = /galaxy
56
57# ---- Galaxy ---------------------------------------------------------------
58
59# Configuration of the Galaxy application.
60
61[app:main]
62
63# -- Application and filtering
64
65# The factory for the WSGI application.  This should not be changed.
66paste.app_factory = galaxy.web.buildapp:app_factory
67
68# If not running behind a proxy server, you may want to enable gzip compression
69# to decrease the size of data transferred over the network.  If using a proxy
70# server, please enable gzip compression there instead.
71#filter-with = gzip
72
73# If running behind a proxy server and Galaxy is served from a subdirectory,
74# enable the proxy-prefix filter and set the prefix in the
75# [filter:proxy-prefix] section above.
76#filter-with = proxy-prefix
77
78# If proxy-prefix is enabled and you're running more than one Galaxy instance
79# behind one hostname, you will want to set this to the same path as the prefix
80# in the filter above.  This value becomes the "path" attribute set in the
81# cookie so the cookies from each instance will not clobber each other.
82#cookie_path = None
83
84# -- Database
85
86# By default, Galaxy uses a SQLite database at 'database/universe.sqlite'.  You
87# may use a SQLAlchemy connection string to specify an external database
88# instead.  This string takes many options which are explained in detail in the
89# config file documentation.
90#database_connection = sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE
91
92# If the server logs errors about not having enough database pool connections,
93# you will want to increase these values, or consider running more Galaxy
94# processes.
95#database_engine_option_pool_size = 5
96#database_engine_option_max_overflow = 10
97
98# If using MySQL and the server logs the error "MySQL server has gone away",
99# you will want to set this to some positive value (7200 should work).
100#database_engine_option_pool_recycle = -1
101
102# If large database query results are causing memory or response time issues in
103# the Galaxy process, leave the result on the server instead.  This option is
104# only available for PostgreSQL and is highly recommended.
105#database_engine_option_server_side_cursors = False
106
107# Create only one connection to the database per thread, to reduce the
108# connection overhead.  Recommended when not using SQLite:
109#database_engine_option_strategy = threadlocal
110
111# -- Files and directories
112
113# Dataset files are stored in this directory.
114#file_path = database/files
115
116# Temporary files are stored in this directory.
117#new_file_path = database/tmp
118
119# Tool config file, defines what tools are available in Galaxy.
120#tool_config_file = tool_conf.xml
121
122# Path to the directory containing the tools defined in the config.
123#tool_path = tools
124
125# Directory where data used by tools is located, see the samples in that
126# directory and the wiki for help:
127# http://bitbucket.org/galaxy/galaxy-central/wiki/DataIntegration
128#tool_data_path = tool-data
129
130# Datatypes config file, defines what data (file) types are available in
131# Galaxy.
132#datatypes_config_file = datatypes_conf.xml
133
134# -- Mail and notification
135
136# Galaxy sends mail for various things: Subscribing users to the mailing list
137# if they request it, emailing password resets, notification from the Galaxy
138# Sample Tracking system, and reporting dataset errors.  To do this, it needs
139# to send mail through an SMTP server, which you may define here.
140#smtp_server = None
141
142# On the user registration form, users may choose to join the mailing list.
143# This is the address of the list they'll be subscribed to.
144#mailing_join_addr = galaxy-user-join@bx.psu.edu
145
146# Datasets in an error state include a link to report the error.  Those reports
147# will be sent to this address.  Error reports are disabled if no address is set.
148#error_email_to = None
149
150# -- Display sites
151
152# Galaxy can display data at various external browsers.  These options specify
153# which browsers should be available.  URLs and builds available at these
154# browsers are defined in the specifield files.
155
156# UCSC browsers: tool-data/shared/ucsc/ucsc_build_sites.txt
157#ucsc_display_sites = main,test,archaea,ucla
158
159# GBrowse servers: tool-data/shared/gbrowse/gbrowse_build_sites.txt
160#gbrowse_display_sites = wormbase,tair,modencode_worm,modencode_fly
161
162# GeneTrack servers: tool-data/shared/genetrack/genetrack_sites.txt
163#genetrack_display_sites = main,test
164
165# -- UI Localization
166
167# Append "/{brand}" to the "Galaxy" text in the masthead.
168#brand = None
169
170# The URL linked by the "Galaxy/brand" text.
171#logo_url = /
172
173# The URL linked by the "Galaxy Wiki" link in the "Help" menu.
174#wiki_url = http://bitbucket.org/galaxy/galaxy-central/wiki
175
176# The URL linked by the "Email comments..." link in the "Help" menu.
177#bugs_email = None
178
179# The URL linked by the "How to Cite..." link in the "Help" menu.
180#citation_url = http://bitbucket.org/galaxy/galaxy-central/wiki/Citations
181
182# Serve static content, which must be enabled if you're not serving it via a
183# proxy server.  These options should be self explanatory and so are not
184# documented individually.  You can use these paths (or ones in the proxy
185# server) to point to your own styles.
186static_enabled = True
187static_cache_time = 360
188static_dir = %(here)s/static/
189static_images_dir = %(here)s/static/images
190static_favicon_dir = %(here)s/static/favicon.ico
191static_scripts_dir = %(here)s/static/scripts/
192static_style_dir = %(here)s/static/june_2007_style/blue
193
194# -- Logging and Debugging
195
196# Verbosity of console log messages.  Acceptable values can be found here:
197# http://docs.python.org/library/logging.html#logging-levels
198#log_level = DEBUG
199
200# Print database operations to the server log (warning, quite verbose!).
201#database_engine_option_echo = False
202
203# Print database pool operations to the server log (warning, quite verbose!).
204#database_engine_option_echo_pool = False
205
206# Turn on logging of application events and some user events to the database.
207#log_events = True
208
209# Turn on logging of user actions to the database. Actions currently logged are
210# grid views, tool searches, and use of "recently" used tools menu.  The
211# log_events and log_actions functionality will eventually be merged.
212#log_actions = True
213
214# Debug enables access to various config options useful for development and
215# debugging: use_lint, use_profile, use_printdebug and use_interactive.  It
216# also causes the files used by PBS/SGE (submission script, output, and error)
217# to remain on disk after the job is complete.  Debug mode is disabled if
218# commented, but is uncommented by default in the sample config.
219debug = True
220
221# Check for WSGI compliance.
222#use_lint = False
223
224# Run the Python profiler on each request.
225#use_profile = False
226
227# Intercept print statements and show them on the returned page.
228#use_printdebug = True
229
230# Enable live debugging in your browser.  This should NEVER be enabled on a
231# public site.  Enabled in the sample config for development.
232use_interactive = True
233
234# Write thread status periodically to 'heartbeat.log',  (careful, uses disk
235# space rapidly!).  Useful to determine why your processes may be consuming a
236# lot of CPU.
237#use_heartbeat = False
238
239# Enable the memory debugging interface (careful, negatively impacts server
240# performance).
241#use_memdump = False
242
243# -- Data Libraries
244
245# These library upload options are described in much more detail in the wiki:
246# http://bitbucket.org/galaxy/galaxy-central/wiki/DataLibraries/UploadingFiles
247
248# Add an option to the library upload form which allows administrators to
249# upload a directory of files.
250#library_import_dir = None
251
252# Add an option to the library upload form which allows authorized
253# non-administrators to upload a directory of files.  The configured directory
254# must contain sub-directories named the same as the non-admin user's Galaxy
255# login ( email ).  The non-admin user is restricted to uploading files or
256# sub-directories of files contained in their directory.
257#user_library_import_dir = None
258
259# Add an option to the admin library upload tool allowing admins to paste
260# filesystem paths to files and directories in a box, and these paths will be
261# added to a library.  Set to True to enable.  Please note the security
262# implication that this will give Galaxy Admins access to anything your Galaxy
263# user has access to.
264#allow_library_path_paste = False
265
266# -- Users and Security
267
268# Galaxy encodes various internal values when these values will be output in
269# some format (for example, in a URL or cookie).  You should set a key to be
270# used by the algorithm that encodes and decodes these values.  It can be any
271# string.  If left unchanged, anyone could construct a cookie that would grant
272# them access to others' sessions.
273#id_secret = USING THE DEFAULT IS NOT SECURE!
274
275# User authentication can be delegated to an upstream proxy server (usually
276# Apache).  The upstream proxy should set a REMOTE_USER header in the request.
277# Enabling remote user disables regular logins.  For more information, see:
278# http://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy
279#use_remote_user = False
280
281# If use_remote_user is enabled and your external authentication
282# method just returns bare usernames, set a default mail domain to be appended
283# to usernames, to become your Galaxy usernames (email addresses).
284#remote_user_maildomain = None
285
286# If use_remote_user is enabled, you can set this to a URL that will log your
287# users out.
288#remote_user_logout_href = None
289
290# Administrative users - set this to a comma-separated list of valid Galaxy
291# users (email addresses).  These users will have access to the Admin section
292# of the server, and will have access to create users, groups, roles,
293# libraries, and more.  For more information, see:
294# http://bitbucket.org/galaxy/galaxy-central/wiki/Admin/AdminInterface
295#admin_users = None
296
297# Force everyone to log in (disable anonymous access).
298#require_login = False
299
300# Allow unregistered users to create new accounts (otherwise, they will have to
301# be created by an admin).
302#allow_user_creation = True
303
304# Allow administrators to delete accounts.
305#allow_user_deletion = False
306
307# By default, users' data will be public, but setting this to True will cause
308# it to be private.  Does not affect existing users and data, only ones created
309# after this option is set.  Users may still change their default back to
310# public.
311#new_user_dataset_access_role_default_private = False
312
313# -- Beta features
314
315# Enable Galaxy's built-in visualization module, Trackster.
316#enable_tracks = False
317
318# Enable Galaxy Pages. Pages are custom webpages that include embedded Galaxy items,
319# such as datasets, histories, workflows, and visualizations; pages are useful for
320# documenting and sharing multiple analyses or workflows. Pages are created using a
321# WYSIWYG editor that is very similar to a word processor.
322#enable_pages = False
323
324# Enable the (experimental! beta!) Web API.  Documentation forthcoming.
325#enable_api = False
326
327# -- Job Execution
328
329# If running multiple Galaxy processes, one can be designated as the job
330# runner.  For more information, see:
331# http://bitbucket.org/galaxy/galaxy-central/wiki/Config/WebApplicationScaling
332#enable_job_running = True
333
334# Should jobs be tracked through the database, rather than in memory.
335# Necessary if you're running the load balanced setup.
336#track_jobs_in_database = False
337
338# Enable job recovery (if Galaxy is restarted while cluster jobs are running,
339# it can "recover" them when it starts).  This is not safe to use if you are
340# running more than one Galaxy server using the same database.
341#enable_job_recovery = True
342
343# Setting metadata on job outputs to in a separate process (or if using a
344# cluster, on the cluster).  Thanks to Python's Global Interpreter Lock and the
345# hefty expense that setting metadata incurs, your Galaxy process may become
346# unresponsive when this operation occurs internally.
347#set_metadata_externally = False
348
349# Although it is fairly reliable, setting metadata can occasionally fail.  In
350# these instances, you can choose to retry setting it internally or leave it in
351# a failed state (since retrying internally may cause the Galaxy process to be
352# unresponsive).  If this option is set to False, the user will be given the
353# option to retry externally, or set metadata manually (when possible).
354#retry_metadata_internally = True
355
356# Number of concurrent jobs to run (local job runner)
357#local_job_queue_workers = 5
358
359# Jobs can be killed after a certain amount of execution time.  Format is in
360# hh:mm:ss.  Currently only implemented for PBS.
361#job_walltime = None
362
363# Clustering Galaxy is not a straightforward process and requires some
364# pre-configuration.  See the the wiki before attempting to set any of these
365# options:
366# http://bitbucket.org/galaxy/galaxy-central/wiki/Config/Cluster
367
368# Comma-separated list of job runners to start.  local is always started.  If
369# left commented, no jobs will be run on the cluster, even if a cluster URL is
370# explicitly defined in the [galaxy:tool_runners] section below.  The runners
371# currently available are 'pbs' and 'drmaa'.
372#start_job_runners = None
373
374# The URL for the default runner to use when a tool doesn't explicity define a
375# runner below.
376#default_cluster_job_runner = local:///
377
378# The cluster runners have their own thread pools used to prepare and finish
379# jobs (so that these sometimes lengthy operations do not block normal queue
380# operation).  The value here is the number of worker threads available to each
381# started runner.
382#cluster_job_queue_workers = 3
383
384# These options are only used when using file staging with PBS.
385#pbs_application_server =
386#pbs_stage_path =
387#pbs_dataset_server =
388
389# ---- Tool Job Runners -----------------------------------------------------
390
391# Individual per-tool job runner overrides.  If not listed here, a tool will
392# run with the runner defined with default_cluster_job_runner.
393
394[galaxy:tool_runners]
395
396biomart = local:///
397encode_db1 = local:///
398hbvar = local:///
399microbial_import1 = local:///
400ucsc_table_direct1 = local:///
401ucsc_table_direct_archaea1 = local:///
402ucsc_table_direct_test1 = local:///
403upload1 = local:///
404
405# ---- Galaxy Message Queue -------------------------------------------------
406
407# Galaxy uses AMQ protocol to receive messages from external sources like
408# bar code scanners. Galaxy has been tested against RabbitMQ AMQP implementation.
409# For Galaxy to receive messages from a message queue the RabbitMQ server has
410# to be set up with a user account and other parameters listed below. The 'host'
411# and 'port' fields should point to where the RabbitMQ server is running.
412
413[galaxy_amqp]
414
415#host = 127.0.0.1
416#port = 5672
417#userid = galaxy
418#password = galaxy
419#virtual_host = galaxy_messaging_engine
420#queue = galaxy_queue
421#exchange = galaxy_exchange
422#routing_key = bar_code_scanner
423
Note: リポジトリブラウザについてのヘルプは TracBrowser を参照してください。