galaxy package¶
Galaxy root package – this is a namespace package.
Subpackages¶
- galaxy.actions package
- galaxy.auth package
- galaxy.authnz package
- galaxy.containers package
- galaxy.dataset_collections package
- galaxy.datatypes package
- Subpackages
- galaxy.datatypes.converters package
- Submodules
- galaxy.datatypes.converters.bed_to_gff_converter module
- galaxy.datatypes.converters.bedgraph_to_array_tree_converter module
- galaxy.datatypes.converters.bgzip module
- galaxy.datatypes.converters.cram_to_bam module
- galaxy.datatypes.converters.fasta_to_len module
- galaxy.datatypes.converters.fasta_to_tabular_converter module
- galaxy.datatypes.converters.fastq_to_fqtoc module
- galaxy.datatypes.converters.fastqsolexa_to_fasta_converter module
- galaxy.datatypes.converters.fastqsolexa_to_qual_converter module
- galaxy.datatypes.converters.gff_to_bed_converter module
- galaxy.datatypes.converters.gff_to_interval_index_converter module
- galaxy.datatypes.converters.interval_to_bed_converter module
- galaxy.datatypes.converters.interval_to_bedstrict_converter module
- galaxy.datatypes.converters.interval_to_coverage module
- galaxy.datatypes.converters.interval_to_fli module
- galaxy.datatypes.converters.interval_to_interval_index_converter module
- galaxy.datatypes.converters.interval_to_tabix_converter module
- galaxy.datatypes.converters.lped_to_fped_converter module
- galaxy.datatypes.converters.lped_to_pbed_converter module
- galaxy.datatypes.converters.maf_to_fasta_converter module
- galaxy.datatypes.converters.maf_to_interval_converter module
- galaxy.datatypes.converters.pbed_ldreduced_converter module
- galaxy.datatypes.converters.pbed_to_lped_converter module
- galaxy.datatypes.converters.picard_interval_list_to_bed6_converter module
- galaxy.datatypes.converters.pileup_to_interval_index_converter module
- galaxy.datatypes.converters.ref_to_seq_taxonomy_converter module
- galaxy.datatypes.converters.sam_to_bam module
- galaxy.datatypes.converters.tabular_to_dbnsfp module
- galaxy.datatypes.converters.vcf_to_interval_index_converter module
- galaxy.datatypes.converters.vcf_to_vcf_bgzip module
- galaxy.datatypes.converters.wiggle_to_array_tree_converter module
- galaxy.datatypes.converters.wiggle_to_simple_converter module
- galaxy.datatypes.dataproviders package
- Submodules
- galaxy.datatypes.dataproviders.base module
- galaxy.datatypes.dataproviders.chunk module
- galaxy.datatypes.dataproviders.column module
- galaxy.datatypes.dataproviders.dataset module
- galaxy.datatypes.dataproviders.decorators module
- galaxy.datatypes.dataproviders.exceptions module
- galaxy.datatypes.dataproviders.external module
- galaxy.datatypes.dataproviders.hierarchy module
- galaxy.datatypes.dataproviders.line module
- galaxy.datatypes.display_applications package
- galaxy.datatypes.util package
- galaxy.datatypes.converters package
- Submodules
- galaxy.datatypes.annotation module
- galaxy.datatypes.assembly module
- galaxy.datatypes.binary module
- galaxy.datatypes.blast module
- galaxy.datatypes.checkers module
- galaxy.datatypes.chrominfo module
- galaxy.datatypes.constructive_solid_geometry module
- galaxy.datatypes.coverage module
- galaxy.datatypes.data module
- galaxy.datatypes.genetics module
- galaxy.datatypes.graph module
- galaxy.datatypes.images module
- galaxy.datatypes.interval module
- galaxy.datatypes.metadata module
- galaxy.datatypes.molecules module
- galaxy.datatypes.mothur module
- galaxy.datatypes.msa module
- galaxy.datatypes.neo4j module
- galaxy.datatypes.ngsindex module
- galaxy.datatypes.phylip module
- galaxy.datatypes.plant_tribes module
- galaxy.datatypes.proteomics module
- galaxy.datatypes.qualityscore module
- galaxy.datatypes.registry module
- galaxy.datatypes.sequence module
- galaxy.datatypes.sniff module
- galaxy.datatypes.tabular module
- galaxy.datatypes.text module
- galaxy.datatypes.tracks module
- galaxy.datatypes.triples module
- galaxy.datatypes.upload_util module
- galaxy.datatypes.xml module
- Subpackages
- galaxy.dependencies package
- galaxy.eggs package
- galaxy.exceptions package
- galaxy.forms package
- galaxy.jobs package
- Subpackages
- galaxy.jobs.actions package
- galaxy.jobs.metrics package
- Subpackages
- galaxy.jobs.metrics.collectl package
- galaxy.jobs.metrics.instrumenters package
- Submodules
- galaxy.jobs.metrics.instrumenters.cgroup module
- galaxy.jobs.metrics.instrumenters.collectl module
- galaxy.jobs.metrics.instrumenters.core module
- galaxy.jobs.metrics.instrumenters.cpuinfo module
- galaxy.jobs.metrics.instrumenters.env module
- galaxy.jobs.metrics.instrumenters.hostname module
- galaxy.jobs.metrics.instrumenters.meminfo module
- galaxy.jobs.metrics.instrumenters.uname module
- Submodules
- galaxy.jobs.metrics.formatting module
- Subpackages
- galaxy.jobs.runners package
- Subpackages
- galaxy.jobs.runners.state_handlers package
- galaxy.jobs.runners.util package
- Subpackages
- Submodules
- galaxy.jobs.runners.util.env module
- galaxy.jobs.runners.util.external module
- galaxy.jobs.runners.util.kill module
- galaxy.jobs.runners.util.sudo module
- Submodules
- galaxy.jobs.runners.chronos module
- galaxy.jobs.runners.cli module
- galaxy.jobs.runners.condor module
- galaxy.jobs.runners.drmaa module
- galaxy.jobs.runners.godocker module
- galaxy.jobs.runners.kubernetes module
- galaxy.jobs.runners.local module
- galaxy.jobs.runners.pbs module
- galaxy.jobs.runners.pulsar module
- galaxy.jobs.runners.slurm module
- galaxy.jobs.runners.state_handler_factory module
- galaxy.jobs.runners.tasks module
- Subpackages
- galaxy.jobs.splitters package
- Submodules
- galaxy.jobs.command_factory module
- galaxy.jobs.datasets module
- galaxy.jobs.dynamic_tool_destination module
- galaxy.jobs.handler module
- galaxy.jobs.manager module
- galaxy.jobs.mapper module
- galaxy.jobs.output_checker module
- galaxy.jobs.rule_helper module
- galaxy.jobs.stock_rules module
- galaxy.jobs.transfer_manager module
- Subpackages
- galaxy.managers package
- Submodules
- galaxy.managers.annotatable module
- galaxy.managers.api_keys module
- galaxy.managers.base module
- galaxy.managers.citations module
- galaxy.managers.cloud module
- galaxy.managers.collections module
- galaxy.managers.collections_util module
- galaxy.managers.configuration module
- galaxy.managers.containers module
- galaxy.managers.context module
- galaxy.managers.datasets module
- galaxy.managers.deletable module
- galaxy.managers.folders module
- galaxy.managers.hdas module
- galaxy.managers.hdcas module
- galaxy.managers.histories module
- galaxy.managers.history_contents module
- galaxy.managers.jobs module
- galaxy.managers.lddas module
- galaxy.managers.libraries module
- galaxy.managers.library_datasets module
- galaxy.managers.pages module
- galaxy.managers.ratable module
- galaxy.managers.rbac_secured module
- galaxy.managers.roles module
- galaxy.managers.secured module
- galaxy.managers.sharable module
- galaxy.managers.taggable module
- galaxy.managers.tags module
- galaxy.managers.users module
- galaxy.managers.visualizations module
- galaxy.managers.workflows module
- galaxy.model package
- Subpackages
- Submodules
- galaxy.model.base module
- galaxy.model.custom_types module
- galaxy.model.item_attrs module
- galaxy.model.mapping module
- galaxy.model.metadata module
- galaxy.model.search module
- galaxy.model.util module
- galaxy.objectstore package
- galaxy.openid package
- galaxy.quota package
- galaxy.security package
- galaxy.tools package
- Subpackages
- galaxy.tools.actions package
- galaxy.tools.cwl package
- galaxy.tools.data package
- galaxy.tools.data_manager package
- galaxy.tools.deps package
- Subpackages
- galaxy.tools.deps.container_resolvers package
- galaxy.tools.deps.mulled package
- galaxy.tools.deps.resolvers package
- Submodules
- galaxy.tools.deps.resolvers.brewed_tool_shed_packages module
- galaxy.tools.deps.resolvers.conda module
- galaxy.tools.deps.resolvers.galaxy_packages module
- galaxy.tools.deps.resolvers.homebrew module
- galaxy.tools.deps.resolvers.lmod module
- galaxy.tools.deps.resolvers.modules module
- galaxy.tools.deps.resolvers.resolver_mixins module
- galaxy.tools.deps.resolvers.tool_shed_packages module
- galaxy.tools.deps.resolvers.unlinked_tool_shed_packages module
- Submodules
- galaxy.tools.deps.brew_exts module
- galaxy.tools.deps.brew_util module
- galaxy.tools.deps.commands module
- galaxy.tools.deps.conda_compat module
- galaxy.tools.deps.conda_util module
- galaxy.tools.deps.containers module
- galaxy.tools.deps.dependencies module
- galaxy.tools.deps.docker_util module
- galaxy.tools.deps.dockerfiles module
- galaxy.tools.deps.installable module
- galaxy.tools.deps.requirements module
- galaxy.tools.deps.singularity_util module
- galaxy.tools.deps.views module
- Subpackages
- galaxy.tools.error_reports package
- Subpackages
- galaxy.tools.error_reports.plugins package
- Submodules
- galaxy.tools.error_reports.plugins.biostars module
- galaxy.tools.error_reports.plugins.email module
- galaxy.tools.error_reports.plugins.github module
- galaxy.tools.error_reports.plugins.influxdb module
- galaxy.tools.error_reports.plugins.json module
- galaxy.tools.error_reports.plugins.sentry module
- galaxy.tools.error_reports.plugins package
- Subpackages
- galaxy.tools.filters package
- galaxy.tools.imp_exp package
- galaxy.tools.linters package
- Submodules
- galaxy.tools.linters.citations module
- galaxy.tools.linters.command module
- galaxy.tools.linters.general module
- galaxy.tools.linters.help module
- galaxy.tools.linters.inputs module
- galaxy.tools.linters.outputs module
- galaxy.tools.linters.stdio module
- galaxy.tools.linters.tests module
- galaxy.tools.linters.xml_order module
- galaxy.tools.locations package
- galaxy.tools.parameters package
- Submodules
- galaxy.tools.parameters.basic module
- galaxy.tools.parameters.dataset_matcher module
- galaxy.tools.parameters.dynamic_options module
- galaxy.tools.parameters.grouping module
- galaxy.tools.parameters.history_query module
- galaxy.tools.parameters.input_translation module
- galaxy.tools.parameters.meta module
- galaxy.tools.parameters.output_collect module
- galaxy.tools.parameters.sanitize module
- galaxy.tools.parameters.validation module
- galaxy.tools.parameters.wrapped module
- galaxy.tools.parameters.wrapped_json module
- galaxy.tools.parser package
- Submodules
- galaxy.tools.parser.cwl module
- galaxy.tools.parser.error_level module
- galaxy.tools.parser.factory module
- galaxy.tools.parser.interface module
- galaxy.tools.parser.output_actions module
- galaxy.tools.parser.output_collection_def module
- galaxy.tools.parser.output_objects module
- galaxy.tools.parser.util module
- galaxy.tools.parser.xml module
- galaxy.tools.parser.yaml module
- galaxy.tools.search package
- galaxy.tools.toolbox package
- galaxy.tools.util package
- galaxy.tools.verify package
- Submodules
- galaxy.tools.cache module
- galaxy.tools.data_fetch module
- galaxy.tools.errors module
- galaxy.tools.evaluation module
- galaxy.tools.exception_handling module
- galaxy.tools.execute module
- galaxy.tools.fetcher module
- galaxy.tools.lint module
- galaxy.tools.lint_util module
- galaxy.tools.loader module
- galaxy.tools.loader_directory module
- galaxy.tools.repositories module
- galaxy.tools.special_tools module
- galaxy.tools.test module
- galaxy.tools.wrappers module
- Subpackages
- galaxy.tours package
- galaxy.util package
- Subpackages
- Submodules
- galaxy.util.aliaspickler module
- galaxy.util.biostar module
- galaxy.util.bunch module
- galaxy.util.checkers module
- galaxy.util.compression_utils module
- galaxy.util.create_history_template module
- galaxy.util.dbkeys module
- galaxy.util.dictifiable module
- galaxy.util.expressions module
- galaxy.util.facts module
- galaxy.util.filelock module
- galaxy.util.handlers module
- galaxy.util.hash_util module
- galaxy.util.heartbeat module
- galaxy.util.image_util module
- galaxy.util.inflection module
- galaxy.util.json module
- galaxy.util.jstree module
- galaxy.util.lazy_process module
- galaxy.util.monitors module
- galaxy.util.none_like module
- galaxy.util.object_wrapper module
- galaxy.util.odict module
- galaxy.util.oset module
- galaxy.util.permutations module
- galaxy.util.plugin_config module
- galaxy.util.properties module
- galaxy.util.renamed_temporary_file module
- galaxy.util.rules_dsl module
- galaxy.util.sanitize_html module
- galaxy.util.script module
- galaxy.util.simplegraph module
- galaxy.util.sleeper module
- galaxy.util.sockets module
- galaxy.util.specs module
- galaxy.util.sqlite module
- galaxy.util.streamball module
- galaxy.util.submodules module
- galaxy.util.template module
- galaxy.util.tool_version module
- galaxy.util.topsort module
- galaxy.util.ucsc module
- galaxy.util.validation module
- galaxy.util.watcher module
- galaxy.util.xml_macros module
- galaxy.visualization package
- Subpackages
- galaxy.visualization.data_providers package
- galaxy.visualization.genome package
- galaxy.visualization.plugins package
- Submodules
- galaxy.visualization.plugins.config_parser module
- galaxy.visualization.plugins.interactive_environments module
- galaxy.visualization.plugins.plugin module
- galaxy.visualization.plugins.registry module
- galaxy.visualization.plugins.resource_parser module
- galaxy.visualization.plugins.utils module
- galaxy.visualization.tracks package
- Submodules
- galaxy.visualization.genomes module
- Subpackages
- galaxy.web package
- Subpackages
- galaxy.web.base package
- galaxy.web.framework package
- Subpackages
- galaxy.web.framework.helpers package
- galaxy.web.framework.middleware package
- Submodules
- galaxy.web.framework.middleware.batch module
- galaxy.web.framework.middleware.error module
- galaxy.web.framework.middleware.profile module
- galaxy.web.framework.middleware.remoteuser module
- galaxy.web.framework.middleware.request_id module
- galaxy.web.framework.middleware.sentry module
- galaxy.web.framework.middleware.sqldebug module
- galaxy.web.framework.middleware.static module
- galaxy.web.framework.middleware.statsd module
- galaxy.web.framework.middleware.translogger module
- galaxy.web.framework.middleware.xforwardedhost module
- Submodules
- galaxy.web.framework.base module
- galaxy.web.framework.decorators module
- galaxy.web.framework.openid_manager module
- galaxy.web.framework.webapp module
- Subpackages
- galaxy.web.proxy package
- galaxy.web.security package
- galaxy.web.stack package
- Submodules
- galaxy.web.buildapp module
- galaxy.web.form_builder module
- galaxy.web.formatting module
- galaxy.web.params module
- Subpackages
- galaxy.webapps package
- Subpackages
- galaxy.webapps.galaxy package
- Subpackages
- galaxy.webapps.galaxy.api package
- Submodules
- galaxy.webapps.galaxy.api.annotations module
- galaxy.webapps.galaxy.api.authenticate module
- galaxy.webapps.galaxy.api.cloud module
- galaxy.webapps.galaxy.api.configuration module
- galaxy.webapps.galaxy.api.dataset_collections module
- galaxy.webapps.galaxy.api.datasets module
- galaxy.webapps.galaxy.api.datatypes module
- galaxy.webapps.galaxy.api.extended_metadata module
- galaxy.webapps.galaxy.api.folder_contents module
- galaxy.webapps.galaxy.api.folders module
- galaxy.webapps.galaxy.api.forms module
- galaxy.webapps.galaxy.api.genomes module
- galaxy.webapps.galaxy.api.group_roles module
- galaxy.webapps.galaxy.api.group_users module
- galaxy.webapps.galaxy.api.groups module
- galaxy.webapps.galaxy.api.histories module
- galaxy.webapps.galaxy.api.history_contents module
- galaxy.webapps.galaxy.api.item_tags module
- galaxy.webapps.galaxy.api.job_files module
- galaxy.webapps.galaxy.api.jobs module
- galaxy.webapps.galaxy.api.libraries module
- galaxy.webapps.galaxy.api.library_contents module
- galaxy.webapps.galaxy.api.library_datasets module
- galaxy.webapps.galaxy.api.metrics module
- galaxy.webapps.galaxy.api.page_revisions module
- galaxy.webapps.galaxy.api.pages module
- galaxy.webapps.galaxy.api.plugins module
- galaxy.webapps.galaxy.api.provenance module
- galaxy.webapps.galaxy.api.quotas module
- galaxy.webapps.galaxy.api.remote_files module
- galaxy.webapps.galaxy.api.roles module
- galaxy.webapps.galaxy.api.search module
- galaxy.webapps.galaxy.api.tool_data module
- galaxy.webapps.galaxy.api.tool_dependencies module
- galaxy.webapps.galaxy.api.tool_shed_repositories module
- galaxy.webapps.galaxy.api.tools module
- galaxy.webapps.galaxy.api.toolshed module
- galaxy.webapps.galaxy.api.tours module
- galaxy.webapps.galaxy.api.uploads module
- galaxy.webapps.galaxy.api.users module
- galaxy.webapps.galaxy.api.visualizations module
- galaxy.webapps.galaxy.api.webhooks module
- galaxy.webapps.galaxy.api.workflows module
- galaxy.webapps.galaxy.controllers package
- Submodules
- galaxy.webapps.galaxy.controllers.admin module
- galaxy.webapps.galaxy.controllers.admin_toolshed module
- galaxy.webapps.galaxy.controllers.async module
- galaxy.webapps.galaxy.controllers.authnz module
- galaxy.webapps.galaxy.controllers.biostar module
- galaxy.webapps.galaxy.controllers.data_manager module
- galaxy.webapps.galaxy.controllers.dataset module
- galaxy.webapps.galaxy.controllers.error module
- galaxy.webapps.galaxy.controllers.forms module
- galaxy.webapps.galaxy.controllers.history module
- galaxy.webapps.galaxy.controllers.interactive_environments module
- galaxy.webapps.galaxy.controllers.library module
- galaxy.webapps.galaxy.controllers.page module
- galaxy.webapps.galaxy.controllers.root module
- galaxy.webapps.galaxy.controllers.tag module
- galaxy.webapps.galaxy.controllers.tool_runner module
- galaxy.webapps.galaxy.controllers.user module
- galaxy.webapps.galaxy.controllers.userskeys module
- galaxy.webapps.galaxy.controllers.visualization module
- galaxy.webapps.galaxy.controllers.workflow module
- galaxy.webapps.galaxy.api package
- Submodules
- galaxy.webapps.galaxy.buildapp module
- galaxy.webapps.galaxy.config_watchers module
- Subpackages
- galaxy.webapps.reports package
- Subpackages
- galaxy.webapps.reports.controllers package
- Submodules
- galaxy.webapps.reports.controllers.history module
- galaxy.webapps.reports.controllers.home module
- galaxy.webapps.reports.controllers.jobs module
- galaxy.webapps.reports.controllers.query module
- galaxy.webapps.reports.controllers.root module
- galaxy.webapps.reports.controllers.system module
- galaxy.webapps.reports.controllers.tools module
- galaxy.webapps.reports.controllers.users module
- galaxy.webapps.reports.controllers.workflows module
- galaxy.webapps.reports.framework package
- galaxy.webapps.reports.controllers package
- Submodules
- galaxy.webapps.reports.app module
- galaxy.webapps.reports.buildapp module
- galaxy.webapps.reports.config module
- Subpackages
- galaxy.webapps.tool_shed package
- Subpackages
- galaxy.webapps.tool_shed.api package
- Submodules
- galaxy.webapps.tool_shed.api.authenticate module
- galaxy.webapps.tool_shed.api.categories module
- galaxy.webapps.tool_shed.api.configuration module
- galaxy.webapps.tool_shed.api.groups module
- galaxy.webapps.tool_shed.api.repositories module
- galaxy.webapps.tool_shed.api.repository_revisions module
- galaxy.webapps.tool_shed.api.tools module
- galaxy.webapps.tool_shed.api.users module
- galaxy.webapps.tool_shed.controllers package
- Submodules
- galaxy.webapps.tool_shed.controllers.admin module
- galaxy.webapps.tool_shed.controllers.groups module
- galaxy.webapps.tool_shed.controllers.hg module
- galaxy.webapps.tool_shed.controllers.repository module
- galaxy.webapps.tool_shed.controllers.repository_review module
- galaxy.webapps.tool_shed.controllers.upload module
- galaxy.webapps.tool_shed.controllers.user module
- galaxy.webapps.tool_shed.framework package
- galaxy.webapps.tool_shed.model package
- galaxy.webapps.tool_shed.search package
- galaxy.webapps.tool_shed.security package
- galaxy.webapps.tool_shed.util package
- galaxy.webapps.tool_shed.api package
- Submodules
- galaxy.webapps.tool_shed.app module
- galaxy.webapps.tool_shed.buildapp module
- galaxy.webapps.tool_shed.config module
- Subpackages
- galaxy.webapps.galaxy package
- Submodules
- galaxy.webapps.config_manage module
- galaxy.webapps.util module
- Subpackages
- galaxy.webhooks package
- galaxy.work package
- galaxy.workflow package
Submodules¶
galaxy.app module¶
galaxy.config module¶
Universe configuration builder.
-
galaxy.config.
LOGGING_CONFIG_DEFAULT
= {'filters': {'stack': {'()': 'galaxy.web.stack.application_stack_log_filter'}}, 'formatters': {'stack': {'()': 'galaxy.web.stack.application_stack_log_formatter'}}, 'handlers': {'console': {'filters': ['stack'], 'formatter': 'stack', 'class': 'logging.StreamHandler', 'stream': 'ext://sys.stderr', 'level': 'DEBUG'}}, 'loggers': {'paste.httpserver.ThreadPool': {'qualname': 'paste.httpserver.ThreadPool', 'level': 'WARN'}, 'routes.middleware': {'qualname': 'routes.middleware', 'level': 'WARN'}, 'galaxy': {'qualname': 'galaxy', 'level': 'DEBUG', 'propagate': 0, 'handlers': ['console']}}, 'root': {'level': 'INFO', 'handlers': ['console']}, 'version': 1}¶ Default value for logging configuration, passed to
logging.config.dictConfig()
-
galaxy.config.
resolve_path
(path, root)[source]¶ If ‘path’ is relative make absolute by prepending ‘root’
-
galaxy.config.
find_path
(kwargs, var, root)[source]¶ Find a configuration path that may exist at different defaults.
-
class
galaxy.config.
Configuration
(**kwargs)[source]¶ Bases:
object
-
deprecated_options
= ('database_file',)¶
-
sentry_dsn_public
¶ Sentry URL with private key removed for use in client side scripts, sentry server will need to be configured to accept events
-
-
galaxy.config.
get_database_engine_options
(kwargs, model_prefix='')[source]¶ Allow options for the SQLAlchemy database engine to be passed by using the prefix “database_engine_option”.
-
galaxy.config.
init_models_from_config
(config, map_install_models=False, object_store=None, trace_logger=None)[source]¶
galaxy.main module¶
Entry point for starting Galaxy without starting as part of a web server.
Example Usage: Start a job/workflow handler without a web server and with a given name using.
galaxy-main –server-name handler0
Start as a daemon with (requires daemonized - install with ‘pip install daemonize’):
galaxy-main -d –daemon-log-file=handler0-daemon.log –pid-file handler0.pid –server-name handler0
In daemon mode logging of Galaxy (as opposed to this script) is configured via a loggers section in Galaxy’s ini file - this can be overridden with sensible defaults logging to a single file with the following:
galaxy-main -d –server-name handler0 –daemon-log-file=handler0-daemon.log –pid-file handler0.pid –log-file handler0.log
This can also be used to start Galaxy as a uWSGI mule, e.g. for job handling:
uwsgi … –py-call-osafterfork –mule=lib/galaxy/main.py –mule=lib/galaxy/main.py –farm=job-handlers:1,2
The –py-call-osafterfork allows for proper shutdown on SIGTERM/SIGINT.
galaxy.queue_worker module¶
Galaxy control queue and worker. This is used to handle ‘app’ control like reloading the toolbox, etc., across multiple processes.
-
galaxy.queue_worker.
send_local_control_task
(app, task, kwargs={})[source]¶ This sends a message to the process-local control worker, which is useful for one-time asynchronous tasks like recalculating user disk usage.
-
galaxy.queue_worker.
send_control_task
(app, task, noop_self=False, kwargs={})[source]¶ This sends a control task out to all processes, useful for things like reloading a data table, which needs to happen individually in all processes.
-
galaxy.queue_worker.
create_panel_section
(app, **kwargs)[source]¶ Updates in memory toolbox dictionary.
-
class
galaxy.queue_worker.
GalaxyQueueWorker
(app, queue=None, task_mapping={'admin_job_lock': <function admin_job_lock at 0x7f869ab8cc80>, 'create_panel_section': <function create_panel_section at 0x7f869ab8c758>, 'rebuild_toolbox_search_index': <function rebuild_toolbox_search_index at 0x7f869ab8cb90>, 'recalculate_user_disk_usage': <function recalculate_user_disk_usage at 0x7f869ab8caa0>, 'reload_data_managers': <function reload_data_managers at 0x7f869ab8c938>, 'reload_display_application': <function reload_display_application at 0x7f869ab8c9b0>, 'reload_job_rules': <function reload_job_rules at 0x7f869ab8cc08>, 'reload_sanitize_whitelist': <function reload_sanitize_whitelist at 0x7f869ab8ca28>, 'reload_tool': <function reload_tool at 0x7f869ab8c7d0>, 'reload_tool_data_tables': <function reload_tool_data_tables at 0x7f869ab8cb18>, 'reload_toolbox': <function reload_toolbox at 0x7f869ab8c848>}, connection=None)[source]¶ Bases:
kombu.mixins.ConsumerMixin
,threading.Thread
This is a flexible worker for galaxy’s queues. Each process, web or handler, will have one of these used for dispatching so called ‘control’ tasks.
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__init__
(app, queue=None, task_mapping={'admin_job_lock': <function admin_job_lock at 0x7f869ab8cc80>, 'create_panel_section': <function create_panel_section at 0x7f869ab8c758>, 'rebuild_toolbox_search_index': <function rebuild_toolbox_search_index at 0x7f869ab8cb90>, 'recalculate_user_disk_usage': <function recalculate_user_disk_usage at 0x7f869ab8caa0>, 'reload_data_managers': <function reload_data_managers at 0x7f869ab8c938>, 'reload_display_application': <function reload_display_application at 0x7f869ab8c9b0>, 'reload_job_rules': <function reload_job_rules at 0x7f869ab8cc08>, 'reload_sanitize_whitelist': <function reload_sanitize_whitelist at 0x7f869ab8ca28>, 'reload_tool': <function reload_tool at 0x7f869ab8c7d0>, 'reload_tool_data_tables': <function reload_tool_data_tables at 0x7f869ab8cb18>, 'reload_toolbox': <function reload_toolbox at 0x7f869ab8c848>}, connection=None)[source]¶
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galaxy.queues module¶
All message queues used by Galaxy
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galaxy.queues.
all_control_queues_for_declare
(config, application_stack)[source]¶ For in-memory routing (used by sqlalchemy-based transports), we need to be able to build the entire routing table in producers.
Refactor later to actually persist this somewhere instead of building it repeatedly.