mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-10-29 17:42:12 +08:00
Nate Coraor
8e8c1c9cf2
A database change is necessary: ALTER TABLE galaxy_user ADD COLUMN external boolean; To use: http://g2.trac.bx.psu.edu/wiki/HowToInstall/ApacheProxy I've tried to be as friendly as possible with respect to enabling and disabling $REMOTE_USER support. If you have an existing server and enable use_remote_user, users whose external login matches their Galaxy username will have access to their existing history/session. If the logins don't match, any existing credentials they had are destroyed. Likewise, when disabled, users who weren't created automatically may continue to access their histories/sessions. Automatically created users are logged out, and can't log in unless enabled by an administrator.
175 lines
5.8 KiB
Plaintext
175 lines
5.8 KiB
Plaintext
# ---- HTTP Server ----------------------------------------------------------
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[server:main]
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use = egg:Paste#http
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port = 8080
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host = 127.0.0.1
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use_threadpool = true
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threadpool_workers = 10
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# ---- Galaxy Web Interface -------------------------------------------------
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[app:main]
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# Specifies the factory for the universe WSGI application
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paste.app_factory = galaxy.web.buildapp:app_factory
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log_level = DEBUG
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# Should jobs be tracked through the database, rather than in memory
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## track_jobs_in_database = true
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# Number of concurrent jobs to run (local runner)
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job_queue_workers = 5
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# Job scheduling policy to be used.
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# module/package name and classname should be in "module:classname" format.
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# Comment / uncomment the following policies depending upon which is to be used.
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#job_scheduler_policy = FIFO
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job_scheduler_policy = galaxy.jobs.schedulingpolicy.roundrobin:UserRoundRobin
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# Job queue cleanup interval in minutes. Currently only used by RoundRobin
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job_queue_cleanup_interval = 30
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# Database connection
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database_file = database/universe.sqlite
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# You may use a SQLAlchemy connection string to specify an external database instead
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## database_connection = postgres:///galaxy_test
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## database_engine_option_echo = true
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## database_engine_option_echo_pool = true
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## database_engine_option_pool_size = 10
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## database_engine_option_max_overflow = 20
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# Where dataset files are saved
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file_path = database/files
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# Temporary storage for additional datasets, this should be shared through the cluster
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new_file_path = database/tmp
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# Tools
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tool_config_file = tool_conf.xml
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tool_path = tools
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tool_data_path = tool-data
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# Datatype converters
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datatype_converters_config_file = datatype_converters_conf.xml
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datatype_converters_path = %(here)s/lib/galaxy/datatypes/converters
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# Session support (beaker)
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use_beaker_session = True
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session_type = file
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session_data_dir = %(here)s/database/beaker_sessions
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session_key = galaxysessions
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session_secret = changethisinproduction
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# Galaxy session security
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id_secret = changethisinproductiontoo
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# Use user provided in an upstream server's $REMOTE_USER variable
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## use_remote_user = False
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# If use_remote_user is enabled and your external authentication
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# method just returns bare usernames, set a default mail domain
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## remote_user_maildomain = example.org
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# Configuration for debugging middleware
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debug = true
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use_lint = false
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# NEVER enable this on a public site (even test or QA)
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use_interactive = true
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# Admin Password
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admin_pass = galaxy
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# path to sendmail
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sendmail_path = /usr/sbin/sendmail
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# Address to join mailing list
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mailing_join_addr = galaxy-user-join@bx.psu.edu
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# Write thread status periodically to 'heartbeat.log' (careful, uses disk space rapidly!)
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## use_heartbeat = True
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# Profiling middleware (cProfile based)
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## use_profile = True
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# Mail
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smtp_server = coltrane.bx.psu.edu
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error_email_to = galaxy-bugs@bx.psu.edu
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# Use the new iframe / javascript based layout
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use_new_layout = true
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# Comma separated list of UCSC / gbrowse browsers to use for viewing
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ucsc_display_sites = main,test,archaea
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gbrowse_display_sites = elegans,flybase
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# Serving static files (needed if running standalone)
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static_enabled = True
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static_cache_time = 360
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static_dir = %(here)s/static/
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static_images_dir = %(here)s/static/images
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static_favicon_dir = %(here)s/static/favicon.ico
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static_scripts_dir = %(here)s/static/scripts/
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static_style_dir = %(here)s/static/june_2007_style/blue
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## Leave these commented out for the defaults at the main galaxy site
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## Uncomment and adjust these to change locally configurable items in the masthead
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## for a local mirror where you are doing private software development
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##
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## Brand: appends "/[brand]" to the "Galaxy" text in the masthead
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## wiki_url: replaces the default galaxy main wiki
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## bugs_email: replaces the default galaxy bugs email list
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#brand = Private local mirror
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#wiki_url=/path/to/my/local/wiki
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#bugs_email=mailto:bugmaster@this.site.com
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# ---- Job Runners ----------------------------------------------------------
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# Clustering Galaxy is not a straightforward process and requires a lot of
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# pre-configuration. See the ClusteringGalaxy Wiki before attempting to set any
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# of these options. If running normally (without a cluster), do not change
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# anything in this section.
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# start_job_runners: Comma-separated list of job runners to start. local is
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# always started. If left commented, no jobs will be run on the cluster, even
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# if a cluster URL is explicitly defined in the [galaxy:tool_runners] section
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# below. The only runner currently available is 'pbs'.
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#start_job_runners = pbs
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# default_cluster_job_runner: The URL for the default runner to use when a tool
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# doesn't explicity define a runner below. For help on the cluster URL format,
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# see the ClusteringGalaxy Wiki. Leave commented if not using a cluster job runner.
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#default_cluster_job_runner = pbs:///
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# The PBS options are described in detail in the Galaxy Configuration section of
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# the ClusteringGalaxy Wiki
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#pbs_application_server =
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#pbs_stage_path =
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#pbs_dataset_server =
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# Individual per-tool job runner overrides. If not listed here, a tool will
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# run with the runner defined with default_cluster_job_runner.
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[galaxy:tool_runners]
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biomart = local:///
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blat2wig = pbs:///blast
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blat_wrapper = pbs:///blast
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encode_db1 = local:///
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encode_import_all_latest_datasets1 = local:///
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encode_import_chromatin_and_chromosomes1 = local:///
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encode_import_gencode1 = local:///
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encode_import_genes_and_transcripts1 = local:///
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encode_import_multi-species_sequence_analysis1 = local:///
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encode_import_transcription_regulation1 = local:///
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generate_coverage_report = pbs:///blast
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hbvar = local:///
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hist_high_quality_score = pbs:///blast
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megablast_wrapper = pbs:///blast
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megablast_xml_parser = pbs:///blast
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microbial_import1 = local:///
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quality_score_distribution = pbs:///blast
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ucsc_table_direct1 = local:///
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ucsc_table_direct_archaea1 = local:///
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ucsc_table_direct_test1 = local:///
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upload1 = local:///
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