/universe_wsgi.ini.cistrome
https://bitbucket.org/cistrome/cistrome-harvard/ · Unknown · 766 lines · 602 code · 164 blank · 0 comment · 0 complexity · 3ca696116d6113e1a350c61e0bb7e895 MD5 · raw file
- #
- # Galaxy is configured by default to be useable in a single-user development
- # environment. To tune the application for a multi-user production
- # environment, see the documentation at:
- #
- # http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Production%20Server
- #
- # Throughout this sample configuration file, except where stated otherwise,
- # uncommented values override the default if left unset, whereas commented
- # values are set to the default value.
- # Examples of many of these options are explained in more detail in the wiki:
- #
- # http://wiki.g2.bx.psu.edu/Admin/Config
- #
- # Config hackers are encouraged to check there before asking for help.
- # ---- HTTP Server ----------------------------------------------------------
- # Configuration of the internal HTTP server.
- [server:main]
- # The internal HTTP server to use. Currently only Paste is provided. This
- # option is required.
- use = egg:Paste#http
- # The port on which to listen.
- port = 10096
- # The address on which to listen. By default, only listen to localhost (Galaxy
- # will not be accessible over the network). Use '0.0.0.0' to listen on all
- # available network interfaces.
- host = 127.0.0.1
- # Use a threadpool for the web server instead of creating a thread for each
- # request.
- use_threadpool = True
- # Number of threads in the web server thread pool.
- threadpool_workers = 10
- # ---- Filters --------------------------------------------------------------
- # Filters sit between Galaxy and the HTTP server.
- # These filters are disabled by default. They can be enabled with
- # 'filter-with' in the [app:main] section below.
- # Define the gzip filter.
- [filter:gzip]
- use = egg:Paste#gzip
- # Define the proxy-prefix filter.
- [filter:proxy-prefix]
- use = egg:PasteDeploy#prefix
- prefix = /ap
- # ---- Galaxy ---------------------------------------------------------------
- # Configuration of the Galaxy application.
- [app:main]
- # -- Application and filtering
- # The factory for the WSGI application. This should not be changed.
- paste.app_factory = galaxy.web.buildapp:app_factory
- # If not running behind a proxy server, you may want to enable gzip compression
- # to decrease the size of data transferred over the network. If using a proxy
- # server, please enable gzip compression there instead.
- #filter-with = gzip
- # If running behind a proxy server and Galaxy is served from a subdirectory,
- # enable the proxy-prefix filter and set the prefix in the
- # [filter:proxy-prefix] section above.
- filter-with = proxy-prefix
- # If proxy-prefix is enabled and you're running more than one Galaxy instance
- # behind one hostname, you will want to set this to the same path as the prefix
- # in the filter above. This value becomes the "path" attribute set in the
- # cookie so the cookies from each instance will not clobber each other.
- cookie_path = /ap
- # -- Database
- # By default, Galaxy uses a SQLite database at 'database/universe.sqlite'. You
- # may use a SQLAlchemy connection string to specify an external database
- # instead. This string takes many options which are explained in detail in the
- # config file documentation.
- #database_connection = postgres://cistrome:cistrome@localhost/cistromeap
- database_connection = mysql://cistrome:cistrome@localhost/cistromeap
- # If the server logs errors about not having enough database pool connections,
- # you will want to increase these values, or consider running more Galaxy
- # processes.
- database_engine_option_pool_size = 10
- database_engine_option_max_overflow = 20
- # If using MySQL and the server logs the error "MySQL server has gone away",
- # you will want to set this to some positive value (7200 should work).
- #database_engine_option_pool_recycle = -1
- # If large database query results are causing memory or response time issues in
- # the Galaxy process, leave the result on the server instead. This option is
- # only available for PostgreSQL and is highly recommended.
- #database_engine_option_server_side_cursors = False
- # Create only one connection to the database per thread, to reduce the
- # connection overhead. Recommended when not using SQLite:
- #database_engine_option_strategy = threadlocal
- # Log all database transactions, can be useful for debugging and performance
- # profiling. Logging is done via Python's 'logging' module under the qualname
- # 'galaxy.model.orm.logging_connection_proxy'
- #database_query_profiling_proxy = False
- # -- Files and directories
- # Path where genome builds are stored. This defaults to tool-data/genome
- #genome_data_path = tool-data/genome
- # URL for rsync server to download pre-built indexes.
- #rsync_url = rsync://scofield.bx.psu.edu/indexes
- # Dataset files are stored in this directory.
- file_path = database/files
- # Temporary files are stored in this directory.
- new_file_path = database/tmp
- # Tool config files, defines what tools are available in Galaxy.
- # Tools can be locally developed or installed from Galaxy tool sheds.
- tool_config_file = tool_conf.xml,shed_tool_conf.xml
- # Default path to the directory containing the tools defined in tool_conf.xml.
- # Other tool config files must include the tool_path as an attribute in the <toolbox> tag.
- tool_path = tools
- # Path to the directory in which managed tool dependencies are placed. To use
- # the dependency system, see the documentation at:
- # http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies
- #tool_dependency_dir = None
- # Enable automatic polling of relative tool sheds to see if any updates
- # are available for installed repositories. Ideally only one Galaxy
- # server process should be able to check for repository updates. The
- # setting for hours_between_check should be an integer between 1 and 24.
- #enable_tool_shed_check = False
- #hours_between_check = 12
- # Directory where data used by tools is located, see the samples in that
- # directory and the wiki for help:
- # http://wiki.g2.bx.psu.edu/Admin/Data%20Integration
- tool_data_path = tool-data
- # Directory where chrom len files are kept, currently mainly used by trackster
- len_file_path = tool-data/shared/ucsc/chrom
- # Datatypes config file, defines what data (file) types are available in
- # Galaxy.
- datatypes_config_file = datatypes_conf.xml
- # Each job is given a unique empty directory as its current working directory.
- # This option defines in what parent directory those directories will be
- # created.
- job_working_directory = database/job_working_directory
- # If using a cluster, Galaxy will write job scripts and stdout/stderr to this
- # directory.
- #cluster_files_directory = database/pbs
- # External service types config file, defines what types of external_services configurations
- # are available in Galaxy.
- #external_service_type_config_file = external_service_types_conf.xml
- # Path to the directory containing the external_service_types defined in the config.
- #external_service_type_path = external_service_types
- # Tools with a number of outputs not known until runtime can write these
- # outputs to a directory for collection by Galaxy when the job is done.
- # Previously, this directory was new_file_path, but using one global directory
- # can cause performance problems, so using job_working_directory ('.' or cwd
- # when a job is run) is encouraged. By default, both are checked to avoid
- # breaking existing tools.
- #collect_outputs_from = new_file_path,job_working_directory
- # -- Mail and notification
- # Galaxy sends mail for various things: Subscribing users to the mailing list
- # if they request it, emailing password resets, notification from the Galaxy
- # Sample Tracking system, and reporting dataset errors. To do this, it needs
- # to send mail through an SMTP server, which you may define here (host:port).
- # Galaxy will automatically try STARTTLS but will continue upon failure.
- smtp_server = localhost
- # If your SMTP server requires a username and password, you can provide them
- # here (password in cleartext here, but if your server supports STARTTLS it
- # will be sent over the network encrypted).
- #smtp_username = None
- #smtp_password = None
- # On the user registration form, users may choose to join the mailing list.
- # This is the address of the list they'll be subscribed to.
- #mailing_join_addr = galaxy-announce-join@bx.psu.edu
- # Datasets in an error state include a link to report the error. Those reports
- # will be sent to this address. Error reports are disabled if no address is set.
- error_email_to = cistrome-bugs@jimmy.harvard.edu
- # -- Display sites
- # Galaxy can display data at various external browsers. These options specify
- # which browsers should be available. URLs and builds available at these
- # browsers are defined in the specifield files.
- # UCSC browsers: tool-data/shared/ucsc/ucsc_build_sites.txt
- ucsc_display_sites = main,test,archaea,ucla
- # GBrowse servers: tool-data/shared/gbrowse/gbrowse_build_sites.txt
- #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
- # GeneTrack servers: tool-data/shared/genetrack/genetrack_sites.txt
- #genetrack_display_sites = main,test
- # If use_remote_user = True, display application servers will be denied access
- # to Galaxy and so displaying datasets in these sites will fail.
- # display_servers contains a list of hostnames which should be allowed to
- # bypass security to display datasets. Please be aware that there are security
- # implications if this is allowed. More details (including required changes to
- # the proxy server config) are available in the Apache proxy documentation on
- # the wiki.
- #
- # The list of servers in this sample config are for the UCSC Main, Test and
- # Archaea browsers, but the default if left commented is to not allow any
- # display sites to bypass security (you must uncomment the line below to allow
- # them).
- #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
- # -- Next gen LIMS interface on top of existing Galaxy Sample/Request management code.
- use_nglims = False
- nglims_config_file = tool-data/nglims.yaml
- # -- UI Localization
- # Append "/{brand}" to the "Galaxy" text in the masthead.
- brand = Cistrome
- # The URL linked by the "Galaxy/brand" text.
- logo_url = http://cistrome.org/ap/
- # The URL linked by the "Galaxy Wiki" link in the "Help" menu.
- wiki_url = http://bitbucket.org/cistrome/cistrome-harvard/wiki
- # The URL linked by the "Email comments..." link in the "Help" menu.
- bugs_email = mailto:cistrome-bugs@jimmy.harvard.edu
- # The URL linked by the "How to Cite..." link in the "Help" menu.
- citation_url = http://bitbucket.org/cistrome/cistrome-harvard/wiki/Citation
- # The URL linked by the "Terms and Conditions" link in the "Help" menu, as well
- # as on the user registration and login forms.
- #terms_url = None
- # Serve static content, which must be enabled if you're not serving it via a
- # proxy server. These options should be self explanatory and so are not
- # documented individually. You can use these paths (or ones in the proxy
- # server) to point to your own styles.
- static_enabled = True
- static_cache_time = 360
- static_dir = %(here)s/static/
- static_images_dir = %(here)s/static/images
- static_favicon_dir = %(here)s/static/favicon.ico
- static_scripts_dir = %(here)s/static/scripts/
- static_style_dir = %(here)s/static/june_2007_style/blue
- static_robots_txt = %(here)s/static/robots.txt
- # Pack javascript at launch (/static/scripts/*.js)
- # This only happens if the modified timestamp of the source .js is newer
- # than the version (if it exists) in /static/scripts/packed/
- # Note that this requires java > 1.4 for executing yuicompressor.jar
- #pack_scripts = False
- # Enable Cloud Launch
- #enable_cloud_launch = False
- # -- Advanced proxy features
- # For help on configuring the Advanced proxy features, see:
- # http://usegalaxy.org/production
- # Apache can handle file downloads (Galaxy-to-user) via mod_xsendfile. Set
- # this to True to inform Galaxy that mod_xsendfile is enabled upstream.
- #apache_xsendfile = False
- # The same download handling can be done by nginx using X-Accel-Redirect. This
- # should be set to the path defined in the nginx config as an internal redirect
- # with access to Galaxy's data files (see documentation linked above).
- #nginx_x_accel_redirect_base = False
- # nginx can make use of mod_zip to create zip files containing multiple library
- # files. If using X-Accel-Redirect, this can be the same value as that option.
- #nginx_x_archive_files_base = False
- # If using compression in the upstream proxy server, use this option to disable
- # gzipping of library .tar.gz and .zip archives, since the proxy server will do
- # it faster on the fly.
- upstream_gzip = False
- # nginx can also handle file uploads (user-to-Galaxy) via nginx_upload_module.
- # Configuration for this is complex and explained in detail in the
- # documentation linked above. The upload store is a temporary directory in
- # which files uploaded by the upload module will be placed.
- #nginx_upload_store = False
- # This value overrides the action set on the file upload form, e.g. the web
- # path where the nginx_upload_module has been configured to intercept upload
- # requests.
- #nginx_upload_path = False
- # -- Logging and Debugging
- # Verbosity of console log messages. Acceptable values can be found here:
- # http://docs.python.org/library/logging.html#logging-levels
- log_level = DEBUG
- # Print database operations to the server log (warning, quite verbose!).
- #database_engine_option_echo = False
- # Print database pool operations to the server log (warning, quite verbose!).
- #database_engine_option_echo_pool = False
- # Turn on logging of application events and some user events to the database.
- log_events = True
- # Turn on logging of user actions to the database. Actions currently logged are
- # grid views, tool searches, and use of "recently" used tools menu. The
- # log_events and log_actions functionality will eventually be merged.
- log_actions = True
- # Sanitize All HTML Tool Output
- # By default, all tool output served as 'text/html' will be sanitized
- # thoroughly. This can be disabled if you have special tools that require
- # unaltered output.
- #sanitize_all_html = True
- # Debug enables access to various config options useful for development and
- # debugging: use_lint, use_profile, use_printdebug and use_interactive. It
- # also causes the files used by PBS/SGE (submission script, output, and error)
- # to remain on disk after the job is complete. Debug mode is disabled if
- # commented, but is uncommented by default in the sample config.
- debug = True
- # Check for WSGI compliance.
- use_lint = False
- # Run the Python profiler on each request.
- use_profile = False
- # Intercept print statements and show them on the returned page.
- #use_printdebug = True
- # Enable live debugging in your browser. This should NEVER be enabled on a
- # public site. Enabled in the sample config for development.
- use_interactive = False
- # Write thread status periodically to 'heartbeat.log', (careful, uses disk
- # space rapidly!). Useful to determine why your processes may be consuming a
- # lot of CPU.
- #use_heartbeat = False
- # Enable the memory debugging interface (careful, negatively impacts server
- # performance).
- #use_memdump = False
- # -- Data Libraries
- # These library upload options are described in much more detail in the wiki:
- # http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files
- # Add an option to the library upload form which allows administrators to
- # upload a directory of files.
- #library_import_dir = ../ap_lib/import
- # Add an option to the library upload form which allows authorized
- # non-administrators to upload a directory of files. The configured directory
- # must contain sub-directories named the same as the non-admin user's Galaxy
- # login ( email ). The non-admin user is restricted to uploading files or
- # sub-directories of files contained in their directory.
- #user_library_import_dir = ../ap_lib/import/users
- # Add an option to the admin library upload tool allowing admins to paste
- # filesystem paths to files and directories in a box, and these paths will be
- # added to a library. Set to True to enable. Please note the security
- # implication that this will give Galaxy Admins access to anything your Galaxy
- # user has access to.
- #allow_library_path_paste = False
- # Users may choose to download multiple files from a library in an archive. By
- # default, Galaxy allows users to select from a few different archive formats
- # if testing shows that Galaxy is able to create files using these formats.
- # Specific formats can be disabled with this option, separate more than one
- # format with commas. Available formats are currently 'zip', 'gz', and 'bz2'.
- #disable_library_comptypes =
- # Some sequencer integration features in beta allow you to automatically
- # transfer datasets. This is done using a lightweight transfer manager which
- # runs outside of Galaxy (but is spawned by it automatically). Galaxy will
- # communicate with this manager over the port specified here.
- #transfer_manager_port = 8163
- # Search data libraries with whoosh
- #enable_whoosh_library_search = True
- # Whoosh indexes are stored in this directory.
- #whoosh_index_dir = database/whoosh_indexes
- # Search data libraries with lucene
- #enable_lucene_library_search = False
- # maxiumum file size to index for searching, in MB
- #fulltext_max_size = 500
- #fulltext_noindex_filetypes=bam,sam,wig,bigwig,fasta,fastq,fastqsolexa,fastqillumina,fastqsanger
- # base URL of server providing search functionality using lucene
- #fulltext_url = http://localhost:8081
- # -- Users and Security
- # Galaxy encodes various internal values when these values will be output in
- # some format (for example, in a URL or cookie). You should set a key to be
- # used by the algorithm that encodes and decodes these values. It can be any
- # string. If left unchanged, anyone could construct a cookie that would grant
- # them access to others' sessions.
- id_secret = SETTHISAFTERDEPLOYMENT
- # User authentication can be delegated to an upstream proxy server (usually
- # Apache). The upstream proxy should set a REMOTE_USER header in the request.
- # Enabling remote user disables regular logins. For more information, see:
- # http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy
- use_remote_user = False
- # If use_remote_user is enabled and your external authentication
- # method just returns bare usernames, set a default mail domain to be appended
- # to usernames, to become your Galaxy usernames (email addresses).
- #remote_user_maildomain = None
- # If use_remote_user is enabled, you can set this to a URL that will log your
- # users out.
- #remote_user_logout_href = None
- # Administrative users - set this to a comma-separated list of valid Galaxy
- # users (email addresses). These users will have access to the Admin section
- # of the server, and will have access to create users, groups, roles,
- # libraries, and more. For more information, see:
- # http://wiki.g2.bx.psu.edu/Admin/Interface
- #admin_users = user1@gmail.com,user2@gmail.com
- # Force everyone to log in (disable anonymous access).
- require_login = True
- # Allow unregistered users to create new accounts (otherwise, they will have to
- # be created by an admin).
- allow_user_creation = True
- # Allow administrators to delete accounts.
- allow_user_deletion = True
- # Allow administrators to log in as other users (useful for debugging)
- #allow_user_impersonation = False
- # Allow users to remove their datasets from disk immediately (otherwise,
- # datasets will be removed after a time period specified by an administrator in
- # the cleanup scripts run via cron)
- allow_user_dataset_purge = True
- # By default, users' data will be public, but setting this to True will cause
- # it to be private. Does not affect existing users and data, only ones created
- # after this option is set. Users may still change their default back to
- # public.
- #new_user_dataset_access_role_default_private = False
- # -- Beta features
- # Object store mode (valid options are: disk, s3, swift, distributed, hierarchical)
- #object_store = disk
- #os_access_key = <your cloud object store access key>
- #os_secret_key = <your cloud object store secret key>
- #os_bucket_name = <name of an existing object store bucket or container>
- # If using 'swift' object store, you must specify the following connection properties
- #os_host = swift.rc.nectar.org.au
- #os_port = 8888
- #os_is_secure = False
- #os_conn_path = /
- # Reduced redundancy can be used only with the 's3' object store
- #os_use_reduced_redundancy = False
- # Size (in GB) that the cache used by object store should be limited to.
- # If the value is not specified, the cache size will be limited only by the
- # file system size. The file system location of the cache is considered the
- # configuration of the ``file_path`` directive defined above.
- #object_store_cache_size = 100
- # Configuration file for the distributed object store, if object_store =
- # distributed. See the sample at distributed_object_store_conf.xml.sample
- #distributed_object_store_config_file = None
- # Enable Galaxy to communicate directly with a sequencer
- #enable_sequencer_communication = False
- # Enable authentication via OpenID. Allows users to log in to their Galaxy
- # account by authenticating with an OpenID provider.
- #enable_openid = False
- #openid_config_file = openid_conf.xml
- # Optional list of email addresses of API users who can make calls on behalf of
- # other users
- #api_allow_run_as = None
- # Enable tool tags (associating tools with tags). This has its own option
- # since its implementation has a few performance implications on startup for
- # large servers.
- #enable_tool_tags = False
- # Enable a feature when running workflows. When enabled, default datasets
- # are selected for "Set at Runtime" inputs from the history such that the
- # same input will not be selected twice, unless there are more inputs than
- # compatible datasets in the history.
- # When False, the most recently added compatible item in the history will
- # be used for each "Set at Runtime" input, independent of others in the Workflow
- #enable_unique_workflow_defaults = False
- # The URL to the myExperiment instance being used (omit scheme but include port)
- #myexperiment_url = www.myexperiment.org:80
- # Enable Galaxy's "Upload via FTP" interface. You'll need to install and
- # configure an FTP server (we've used ProFTPd since it can use Galaxy's
- # database for authentication) and set the following two options.
- # This should point to a directory containing subdirectories matching users'
- # email addresses, where Galaxy will look for files.
- ftp_upload_dir = SET-THIS-AS-OUR-ASPERA-SITE-AFTER-DEPLOYMENT
- # This should be the hostname of your FTP server, which will be provided to
- # users in the help text.
- ftp_upload_site = cistrome.dfci.harvard.edu
- # Enable enforcement of quotas. Quotas can be set from the Admin interface.
- #enable_quotas = False
- # Enable a feature when running workflows. When enabled, default datasets
- # are selected for "Set at Runtime" inputs from the history such that the
- # same input will not be selected twice, unless there are more inputs than
- # compatible datasets in the history.
- # When False, the most recently added compatible item in the history will
- # be used for each "Set at Runtime" input, independent of others in the Workflow
- #enable_unique_workflow_defaults = False
- # -- Job Execution
- # To increase performance of job execution and the web interface, you can
- # separate Galaxy into multiple processes. There are more than one way to do
- # this, and they are explained in detail in the documentation:
- #
- # http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Web%20Application%20Scaling
- #
- # By default, Galaxy manages and executes jobs from within a single process and
- # notifies itself of new jobs via in-memory queues. If you change job_manager
- # and job_handlers from their default values, notification will instead be done
- # using the `state` and `handler` columns of the job table in the database.
- # Identify the server_name (the string following server: at the top of this
- # file) which should be designated as the job manager (only one):
- #job_manager = main
- # Identify the server_name(s) which should be designated as job handlers
- # (responsible for starting, tracking, finishing, and cleaning up jobs) as a
- # comma-separated list.
- job_handlers = main
- # By default, a handler from job_handlers will be selected at random if the
- # tool to run does specify a handler below in [galaxy:tool_handlers]. If you
- # want certain handlers to only handle jobs for tools/params explicitly
- # assigned below, use default_job_handlers to specify which handlers should be
- # used for jobs without explicit handlers.
- default_job_handlers = main
- # In multiprocess configurations, notification between processes about new jobs
- # is done via the database. In single process configurations, this is done in
- # memory, which is a bit quicker. Galaxy tries to automatically determine
- # which method it should used based on your manager/handler configuration
- # above, but can't reliably determine if you have multiple processes for web
- # servers but only a single process as a manager/handler. In that scenario,
- # you can override the tracking method by setting the following to True:
- track_jobs_in_database = True
- # This enables splitting of jobs into tasks, if specified by the particular tool config.
- # This is a new feature and not recommended for production servers yet.
- #use_tasked_jobs = False
- #local_task_queue_workers = 2
- # Enable job recovery (if Galaxy is restarted while cluster jobs are running,
- # it can "recover" them when it starts). This is not safe to use if you are
- # running more than one Galaxy server using the same database.
- #enable_job_recovery = True
- # Setting metadata on job outputs to in a separate process (or if using a
- # cluster, on the cluster). Thanks to Python's Global Interpreter Lock and the
- # hefty expense that setting metadata incurs, your Galaxy process may become
- # unresponsive when this operation occurs internally.
- #set_metadata_externally = False
- # Although it is fairly reliable, setting metadata can occasionally fail. In
- # these instances, you can choose to retry setting it internally or leave it in
- # a failed state (since retrying internally may cause the Galaxy process to be
- # unresponsive). If this option is set to False, the user will be given the
- # option to retry externally, or set metadata manually (when possible).
- #retry_metadata_internally = True
- # If (for example) you run on a cluster and your datasets (by default,
- # database/files/) are mounted read-only, this option will override tool output
- # paths to write outputs to the working directory instead, and the job manager
- # will move the outputs to their proper place in the dataset directory on the
- # Galaxy server after the job completes.
- #outputs_to_working_directory = False
- # If your network filesystem's caching prevents the Galaxy server from seeing
- # the job's stdout and stderr files when it completes, you can retry reading
- # these files. The job runner will retry the number of times specified below,
- # waiting 1 second between tries. For NFS, you may want to try the -noac mount
- # option (Linux) or -actimeo=0 (Solaris).
- #retry_job_output_collection = 0
- # Clean up various bits of jobs left on the filesystem after completion. These
- # bits include the job working directory, external metadata temporary files,
- # and DRM stdout and stderr files (if using a DRM). Possible values are:
- # always, onsuccess, never
- #cleanup_job = always
- # Number of concurrent jobs to run (local job runner)
- local_job_queue_workers = 10
- # Jobs can be killed after a certain amount of execution time. Format is in
- # hh:mm:ss. Currently only implemented for PBS.
- # job_walltime = 24:00:00
- # Jobs can be killed if any of their outputs grow over a certain size (in
- # bytes). 0 for no limit.
- #output_size_limit = 0
- # Cistrome admin: set this to 10GBytes
- output_size_limit = 10000000000
- # Jobs can be held back from submission to a runner if a user already has more
- # jobs queued or running than the number specified below. This prevents a
- # single user from stuffing the queue and preventing other users from being
- # able to run jobs.
- #user_job_limit = None
- # Clustering Galaxy is not a straightforward process and requires some
- # pre-configuration. See the the wiki before attempting to set any of these
- # options:
- # http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster
- # Comma-separated list of job runners to start. local is always started. If
- # left commented, no jobs will be run on the cluster, even if a cluster URL is
- # explicitly defined in the [galaxy:tool_runners] section below. The runners
- # currently available are 'pbs' and 'drmaa'.
- #start_job_runners = None
- # For sites where all users in Galaxy match users on the system on which Galaxy
- # runs, the DRMAA job runner can be configured to submit jobs to the DRM as the
- # actual user instead of as the user running the Galaxy server process. For
- # details on these options, see the documentation at:
- #
- # http://galaxyproject.org/wiki/Admin/Config/Performance/Cluster
- #
- #drmaa_external_runjob_script = scripts/drmaa_external_runner.py
- #drmaa_external_killjob_script = scripts/drmaa_external_killer.py
- #external_chown_script = scripts/external_chown_script.py
- # File to source to set up the environment when running jobs. By default, the
- # environment in which the Galaxy server starts is used when running jobs
- # locally, and the environment set up per the DRM's submission method and
- # policy is used when running jobs on a cluster (try testing with `qsub` on the
- # command line). environment_setup_file can be set to the path of a file on
- # the cluster that should be sourced by the user to set up the environment
- # prior to running tools. This can be especially useful for running jobs as
- # the actual user, to remove the need to configure each user's environment
- # individually. This only affects cluster jobs, not local jobs.
- #environment_setup_file = None
- # The URL for the default runner to use when a tool doesn't explicitly define a
- # runner below.
- #default_cluster_job_runner = local:///
- # The cluster runners have their own thread pools used to prepare and finish
- # jobs (so that these sometimes lengthy operations do not block normal queue
- # operation). The value here is the number of worker threads available to each
- # started runner.
- #cluster_job_queue_workers = 3
- # These options are only used when using file staging with PBS.
- #pbs_application_server =
- #pbs_stage_path =
- #pbs_dataset_server =
- # Path to the static library files for assembly, ceaslib, chromLen, conservation, liftOver and MAT-lib
- # Then in other tool configuration xml file, we can use 'from galaxy import config' then '$config.Configuration().cistrome_static_library_path'
- # default would be in tool-data/ folder
- cistrome_static_library_path = tool-data
- # This option allows users to see the full path of datasets via the "View
- # Details" option in the history. Administrators can always see this.
- #expose_dataset_path = False
- # ---- Per-Tool Job Management ----------------------------------------------
- # Per-tool job handler and runner overrides. Parameters can be included to define multiple
- # runners per tool. E.g. to run Cufflinks jobs initiated from Trackster
- # differently than standard Cufflinks jobs:
- #
- # cufflinks = local:///
- # cufflinks[source@trackster] = local:///
- [galaxy:tool_handlers]
- # By default, Galaxy will select a handler at random from the list of
- # job_handlers set above. You can override as in the following examples:
- #
- #upload1 = upload_handler
- #cufflinks[source@trackster] = realtime_handler
- [galaxy:tool_runners]
- # If not listed here, a tool will run with the runner defined with
- # default_cluster_job_runner. These overrides for local:/// are done because
- # these tools can fetch data from remote sites, which may not be suitable to
- # run on a cluster (if it does not have access to the Internet, for example).
- biomart = local:///
- encode_db1 = local:///
- hbvar = local:///
- microbial_import1 = local:///
- ucsc_table_direct1 = local:///
- ucsc_table_direct_archaea1 = local:///
- ucsc_table_direct_test1 = local:///
- upload1 = local:///
- # ---- Galaxy Message Queue -------------------------------------------------
- # Galaxy uses AMQ protocol to receive messages from external sources like
- # bar code scanners. Galaxy has been tested against RabbitMQ AMQP implementation.
- # For Galaxy to receive messages from a message queue the RabbitMQ server has
- # to be set up with a user account and other parameters listed below. The 'host'
- # and 'port' fields should point to where the RabbitMQ server is running.
- [galaxy_amqp]
- #host = 127.0.0.1
- #port = 5672
- #userid = galaxy
- #password = galaxy
- #virtual_host = galaxy_messaging_engine
- #queue = galaxy_queue
- #exchange = galaxy_exchange
- #routing_key = bar_code_scanner
- #rabbitmqctl_path = /path/to/rabbitmqctl