Warning
This document is for an in-development version of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.
All modules for which code is available
- _hashlib
- builtins
- cwltool.context
- cwltool.job
- cwltool.load_tool
- cwltool.stdfsaccess
- cwltool.utils
- galaxy.actions.library
- galaxy.app
- galaxy.app_unittest_utils.galaxy_mock
- galaxy.app_unittest_utils.tools_support
- galaxy.auth
- galaxy.auth.providers
- galaxy.auth.providers.alwaysreject
- galaxy.auth.providers.ldap_ad
- galaxy.auth.providers.localdb
- galaxy.auth.providers.pam_auth
- galaxy.auth.util
- galaxy.authnz
- galaxy.celery
- galaxy.config
- galaxy.config_watchers
- galaxy.datatypes._schema
- galaxy.datatypes.annotation
- galaxy.datatypes.anvio
- galaxy.datatypes.assembly
- galaxy.datatypes.binary
- galaxy.datatypes.blast
- galaxy.datatypes.chrominfo
- galaxy.datatypes.constructive_solid_geometry
- galaxy.datatypes.converters.fasta_to_len
- galaxy.datatypes.converters.fastq_to_fqtoc
- galaxy.datatypes.converters.gff_to_interval_index_converter
- galaxy.datatypes.converters.interval_to_bedstrict_converter
- galaxy.datatypes.converters.interval_to_fli
- galaxy.datatypes.converters.interval_to_interval_index_converter
- galaxy.datatypes.converters.lped_to_fped_converter
- galaxy.datatypes.converters.lped_to_pbed_converter
- galaxy.datatypes.converters.pbed_ldreduced_converter
- galaxy.datatypes.converters.pbed_to_lped_converter
- galaxy.datatypes.converters.pileup_to_interval_index_converter
- galaxy.datatypes.converters.tabular_csv
- galaxy.datatypes.converters.wiggle_to_simple_converter
- galaxy.datatypes.coverage
- galaxy.datatypes.data
- galaxy.datatypes.dataproviders.base
- galaxy.datatypes.dataproviders.chunk
- galaxy.datatypes.dataproviders.column
- galaxy.datatypes.dataproviders.dataset
- galaxy.datatypes.dataproviders.decorators
- galaxy.datatypes.dataproviders.exceptions
- galaxy.datatypes.dataproviders.external
- galaxy.datatypes.dataproviders.hierarchy
- galaxy.datatypes.dataproviders.line
- galaxy.datatypes.display_applications.application
- galaxy.datatypes.display_applications.parameters
- galaxy.datatypes.display_applications.util
- galaxy.datatypes.flow
- galaxy.datatypes.genetics
- galaxy.datatypes.gis
- galaxy.datatypes.goldenpath
- galaxy.datatypes.graph
- galaxy.datatypes.hdf5
- galaxy.datatypes.images
- galaxy.datatypes.interval
- galaxy.datatypes.isa
- galaxy.datatypes.media
- galaxy.datatypes.metacyto
- galaxy.datatypes.microarrays
- galaxy.datatypes.molecules
- galaxy.datatypes.mothur
- galaxy.datatypes.msa
- galaxy.datatypes.neo4j
- galaxy.datatypes.ngsindex
- galaxy.datatypes.phylip
- galaxy.datatypes.plant_tribes
- galaxy.datatypes.proteomics
- galaxy.datatypes.qiime2
- galaxy.datatypes.qualityscore
- galaxy.datatypes.registry
- galaxy.datatypes.sequence
- galaxy.datatypes.sniff
- galaxy.datatypes.spaln
- galaxy.datatypes.speech
- galaxy.datatypes.tabular
- galaxy.datatypes.text
- galaxy.datatypes.tracks
- galaxy.datatypes.triples
- galaxy.datatypes.upload_util
- galaxy.datatypes.util.generic_util
- galaxy.datatypes.util.gff_util
- galaxy.datatypes.util.maf_utilities
- galaxy.datatypes.xml
- galaxy.dependencies
- galaxy.di
- galaxy.exceptions
- galaxy.files
- galaxy.files.sources
- galaxy.files.sources.anvil
- galaxy.files.sources.basespace
- galaxy.files.sources.dropbox
- galaxy.files.sources.ftp
- galaxy.files.sources.galaxy
- galaxy.files.sources.googlecloudstorage
- galaxy.files.sources.googledrive
- galaxy.files.sources.onedata
- galaxy.files.sources.posix
- galaxy.files.sources.s3fs
- galaxy.files.sources.ssh
- galaxy.files.sources.webdav
- galaxy.files.unittest_utils
- galaxy.files.uris
- galaxy.forms.forms
- galaxy.job_execution.actions.post
- galaxy.job_execution.compute_environment
- galaxy.job_execution.datasets
- galaxy.job_execution.output_collect
- galaxy.job_execution.ports.view
- galaxy.job_execution.setup
- galaxy.job_metrics
- galaxy.job_metrics.formatting
- galaxy.job_metrics.instrumenters
- galaxy.job_metrics.instrumenters.cgroup
- galaxy.job_metrics.instrumenters.core
- galaxy.job_metrics.instrumenters.cpuinfo
- galaxy.job_metrics.instrumenters.env
- galaxy.job_metrics.instrumenters.hostname
- galaxy.job_metrics.instrumenters.meminfo
- galaxy.job_metrics.instrumenters.uname
- galaxy.job_metrics.safety
- galaxy.jobs
- galaxy.jobs.command_factory
- galaxy.jobs.dynamic_tool_destination
- galaxy.jobs.handler
- galaxy.jobs.manager
- galaxy.jobs.mapper
- galaxy.jobs.rule_helper
- galaxy.jobs.runners
- galaxy.jobs.runners.chronos
- galaxy.jobs.runners.cli
- galaxy.jobs.runners.condor
- galaxy.jobs.runners.drmaa
- galaxy.jobs.runners.godocker
- galaxy.jobs.runners.kubernetes
- galaxy.jobs.runners.local
- galaxy.jobs.runners.pbs
- galaxy.jobs.runners.pulsar
- galaxy.jobs.runners.slurm
- galaxy.jobs.runners.state_handler_factory
- galaxy.jobs.runners.state_handlers.resubmit
- galaxy.jobs.runners.tasks
- galaxy.jobs.runners.univa
- galaxy.jobs.runners.util.cli
- galaxy.jobs.runners.util.cli.factory
- galaxy.jobs.runners.util.cli.job
- galaxy.jobs.runners.util.cli.job.lsf
- galaxy.jobs.runners.util.cli.job.pbs
- galaxy.jobs.runners.util.cli.job.slurm
- galaxy.jobs.runners.util.cli.job.slurm_torque
- galaxy.jobs.runners.util.cli.job.torque
- galaxy.jobs.runners.util.cli.shell
- galaxy.jobs.runners.util.condor
- galaxy.jobs.runners.util.env
- galaxy.jobs.runners.util.external
- galaxy.jobs.runners.util.job_script
- galaxy.jobs.runners.util.kill
- galaxy.jobs.runners.util.process_groups
- galaxy.jobs.runners.util.pykube_util
- galaxy.jobs.runners.util.sudo
- galaxy.jobs.splitters.basic
- galaxy.jobs.splitters.multi
- galaxy.jobs.stock_rules
- galaxy.main
- galaxy.main_config
- galaxy.managers.annotatable
- galaxy.managers.api_keys
- galaxy.managers.base
- galaxy.managers.citations
- galaxy.managers.collections
- galaxy.managers.collections_util
- galaxy.managers.configuration
- galaxy.managers.context
- galaxy.managers.datasets
- galaxy.managers.datatypes
- galaxy.managers.deletable
- galaxy.managers.display_applications
- galaxy.managers.executables
- galaxy.managers.folders
- galaxy.managers.genomes
- galaxy.managers.group_roles
- galaxy.managers.group_users
- galaxy.managers.groups
- galaxy.managers.hdas
- galaxy.managers.hdcas
- galaxy.managers.histories
- galaxy.managers.history_contents
- galaxy.managers.interactivetool
- galaxy.managers.jobs
- galaxy.managers.lddas
- galaxy.managers.libraries
- galaxy.managers.library_datasets
- galaxy.managers.licenses
- galaxy.managers.markdown_parse
- galaxy.managers.markdown_util
- galaxy.managers.metrics
- galaxy.managers.model_stores
- galaxy.managers.pages
- galaxy.managers.quotas
- galaxy.managers.ratable
- galaxy.managers.rbac_secured
- galaxy.managers.remote_files
- galaxy.managers.roles
- galaxy.managers.secured
- galaxy.managers.session
- galaxy.managers.sharable
- galaxy.managers.taggable
- galaxy.managers.tags
- galaxy.managers.tool_data
- galaxy.managers.tools
- galaxy.managers.users
- galaxy.managers.visualizations
- galaxy.managers.workflows
- galaxy.metadata
- galaxy.model
- galaxy.model.base
- galaxy.model.custom_types
- galaxy.model.database_heartbeat
- galaxy.model.database_utils
- galaxy.model.dataset_collections.builder
- galaxy.model.dataset_collections.matching
- galaxy.model.dataset_collections.registry
- galaxy.model.dataset_collections.structure
- galaxy.model.dataset_collections.subcollections
- galaxy.model.dataset_collections.type_description
- galaxy.model.dataset_collections.types
- galaxy.model.deferred
- galaxy.model.index_filter_util
- galaxy.model.item_attrs
- galaxy.model.mapping
- galaxy.model.metadata
- galaxy.model.migrations
- galaxy.model.none_like
- galaxy.model.orm.engine_factory
- galaxy.model.orm.scripts
- galaxy.model.orm.util
- galaxy.model.scoped_session
- galaxy.model.security
- galaxy.model.store
- galaxy.model.tags
- galaxy.model.tool_shed_install
- galaxy.model.triggers.history_update_time_field
- galaxy.model.triggers.update_audit_table
- galaxy.model.triggers.utils
- galaxy.model.unittest_utils.data_app
- galaxy.model.unittest_utils.store_fixtures
- galaxy.objectstore
- galaxy.objectstore.azure_blob
- galaxy.objectstore.cloud
- galaxy.objectstore.irods
- galaxy.objectstore.pithos
- galaxy.objectstore.pulsar
- galaxy.objectstore.s3
- galaxy.objectstore.s3_multipart_upload
- galaxy.objectstore.unittest_utils
- galaxy.queue_worker
- galaxy.queues
- galaxy.quota
- galaxy.schema
- galaxy.schema.fetch_data
- galaxy.schema.fields
- galaxy.schema.remote_files
- galaxy.schema.schema
- galaxy.schema.tasks
- galaxy.schema.types
- galaxy.security
- galaxy.security.idencoding
- galaxy.security.object_wrapper
- galaxy.security.passwords
- galaxy.security.ssh_util
- galaxy.security.validate_user_input
- galaxy.security.vault
- galaxy.selenium.cli
- galaxy.selenium.context
- galaxy.selenium.driver_factory
- galaxy.selenium.has_driver
- galaxy.selenium.jupyter_context
- galaxy.selenium.navigates_galaxy
- galaxy.selenium.scripts.dump_tour
- galaxy.selenium.sizzle
- galaxy.selenium.smart_components
- galaxy.selenium.toolbox.filters
- galaxy.structured_app
- galaxy.tool_shed.galaxy_install.install_manager
- galaxy.tool_shed.galaxy_install.installed_repository_manager
- galaxy.tool_shed.galaxy_install.metadata.installed_repository_metadata_manager
- galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager
- galaxy.tool_shed.galaxy_install.tools.data_manager
- galaxy.tool_shed.galaxy_install.tools.tool_panel_manager
- galaxy.tool_shed.galaxy_install.update_repository_manager
- galaxy.tool_shed.metadata.metadata_generator
- galaxy.tool_shed.tools.data_table_manager
- galaxy.tool_shed.tools.tool_validator
- galaxy.tool_shed.util.basic_util
- galaxy.tool_shed.util.container_util
- galaxy.tool_shed.util.hg_util
- galaxy.tool_shed.util.metadata_util
- galaxy.tool_shed.util.repository_util
- galaxy.tool_shed.util.shed_util_common
- galaxy.tool_shed.util.tool_dependency_util
- galaxy.tool_shed.util.tool_util
- galaxy.tool_util.biotools.interface
- galaxy.tool_util.biotools.source
- galaxy.tool_util.client.staging
- galaxy.tool_util.cwl.cwltool_deps
- galaxy.tool_util.cwl.parser
- galaxy.tool_util.cwl.representation
- galaxy.tool_util.cwl.runnable
- galaxy.tool_util.cwl.runtime_actions
- galaxy.tool_util.cwl.schema
- galaxy.tool_util.cwl.util
- galaxy.tool_util.data
- galaxy.tool_util.deps
- galaxy.tool_util.deps.brew_exts
- galaxy.tool_util.deps.brew_util
- galaxy.tool_util.deps.conda_compat
- galaxy.tool_util.deps.conda_util
- galaxy.tool_util.deps.container_classes
- galaxy.tool_util.deps.container_resolvers
- galaxy.tool_util.deps.container_volumes
- galaxy.tool_util.deps.containers
- galaxy.tool_util.deps.dependencies
- galaxy.tool_util.deps.docker_util
- galaxy.tool_util.deps.dockerfiles
- galaxy.tool_util.deps.installable
- galaxy.tool_util.deps.mulled.get_tests
- galaxy.tool_util.deps.mulled.mulled_build
- galaxy.tool_util.deps.mulled.mulled_build_channel
- galaxy.tool_util.deps.mulled.mulled_build_files
- galaxy.tool_util.deps.mulled.mulled_build_tool
- galaxy.tool_util.deps.mulled.mulled_hash
- galaxy.tool_util.deps.mulled.mulled_list
- galaxy.tool_util.deps.mulled.mulled_search
- galaxy.tool_util.deps.mulled.mulled_update_singularity_containers
- galaxy.tool_util.deps.mulled.util
- galaxy.tool_util.deps.requirements
- galaxy.tool_util.deps.resolvers
- galaxy.tool_util.deps.resolvers.brewed_tool_shed_packages
- galaxy.tool_util.deps.resolvers.conda
- galaxy.tool_util.deps.resolvers.galaxy_packages
- galaxy.tool_util.deps.resolvers.homebrew
- galaxy.tool_util.deps.resolvers.lmod
- galaxy.tool_util.deps.resolvers.modules
- galaxy.tool_util.deps.resolvers.resolver_mixins
- galaxy.tool_util.deps.resolvers.tool_shed_packages
- galaxy.tool_util.deps.resolvers.unlinked_tool_shed_packages
- galaxy.tool_util.deps.singularity_util
- galaxy.tool_util.deps.views
- galaxy.tool_util.edam_util
- galaxy.tool_util.fetcher
- galaxy.tool_util.lint
- galaxy.tool_util.linters.citations
- galaxy.tool_util.linters.command
- galaxy.tool_util.linters.cwl
- galaxy.tool_util.linters.general
- galaxy.tool_util.linters.help
- galaxy.tool_util.linters.inputs
- galaxy.tool_util.linters.stdio
- galaxy.tool_util.linters.tests
- galaxy.tool_util.linters.xml_order
- galaxy.tool_util.loader_directory
- galaxy.tool_util.locations
- galaxy.tool_util.locations.dockstore
- galaxy.tool_util.locations.file
- galaxy.tool_util.locations.http
- galaxy.tool_util.ontologies.ontology_data
- galaxy.tool_util.output_checker
- galaxy.tool_util.parser.cwl
- galaxy.tool_util.parser.factory
- galaxy.tool_util.parser.interface
- galaxy.tool_util.parser.output_actions
- galaxy.tool_util.parser.output_collection_def
- galaxy.tool_util.parser.output_objects
- galaxy.tool_util.parser.stdio
- galaxy.tool_util.parser.util
- galaxy.tool_util.parser.xml
- galaxy.tool_util.parser.yaml
- galaxy.tool_util.provided_metadata
- galaxy.tool_util.toolbox.base
- galaxy.tool_util.toolbox.filters
- galaxy.tool_util.toolbox.integrated_panel
- galaxy.tool_util.toolbox.lineages.factory
- galaxy.tool_util.toolbox.lineages.interface
- galaxy.tool_util.toolbox.panel
- galaxy.tool_util.toolbox.parser
- galaxy.tool_util.toolbox.views.definitions
- galaxy.tool_util.toolbox.views.edam
- galaxy.tool_util.toolbox.views.interface
- galaxy.tool_util.toolbox.views.sources
- galaxy.tool_util.toolbox.views.static
- galaxy.tool_util.toolbox.watcher
- galaxy.tool_util.unittest_utils
- galaxy.tool_util.verify
- galaxy.tool_util.verify._types
- galaxy.tool_util.verify.asserts
- galaxy.tool_util.verify.asserts.archive
- galaxy.tool_util.verify.asserts.hdf5
- galaxy.tool_util.verify.asserts.size
- galaxy.tool_util.verify.asserts.tabular
- galaxy.tool_util.verify.asserts.text
- galaxy.tool_util.verify.asserts.xml
- galaxy.tool_util.verify.interactor
- galaxy.tool_util.verify.script
- galaxy.tool_util.verify.test_data
- galaxy.tool_util.verify.wait
- galaxy.tools
- galaxy.tools.actions
- galaxy.tools.actions.data_manager
- galaxy.tools.actions.data_source
- galaxy.tools.actions.history_imp_exp
- galaxy.tools.actions.metadata
- galaxy.tools.actions.model_operations
- galaxy.tools.actions.upload
- galaxy.tools.actions.upload_common
- galaxy.tools.biotools
- galaxy.tools.cache
- galaxy.tools.data
- galaxy.tools.data_fetch
- galaxy.tools.data_manager.manager
- galaxy.tools.error_reports
- galaxy.tools.errors
- galaxy.tools.evaluation
- galaxy.tools.execute
- galaxy.tools.expressions.evaluation
- galaxy.tools.expressions.script
- galaxy.tools.expressions.util
- galaxy.tools.imp_exp
- galaxy.tools.parameters.basic
- galaxy.tools.parameters.dataset_matcher
- galaxy.tools.parameters.dynamic_options
- galaxy.tools.parameters.grouping
- galaxy.tools.parameters.history_query
- galaxy.tools.parameters.input_translation
- galaxy.tools.parameters.meta
- galaxy.tools.parameters.sanitize
- galaxy.tools.parameters.validation
- galaxy.tools.parameters.wrapped
- galaxy.tools.parameters.wrapped_json
- galaxy.tools.recommendations
- galaxy.tools.remote_tool_eval
- galaxy.tools.repositories
- galaxy.tools.search
- galaxy.tools.special_tools
- galaxy.tools.util.galaxyops
- galaxy.tools.util.maf_utilities
- galaxy.tools.wrappers
- galaxy.tours._impl
- galaxy.tours._interface
- galaxy.tours._schema
- galaxy.tours.validate
- galaxy.util
- galaxy.util.aliaspickler
- galaxy.util.bool_expressions
- galaxy.util.bunch
- galaxy.util.bytesize
- galaxy.util.checkers
- galaxy.util.commands
- galaxy.util.compression_utils
- galaxy.util.custom_logging
- galaxy.util.dictifiable
- galaxy.util.expressions
- galaxy.util.facts
- galaxy.util.filelock
- galaxy.util.form_builder
- galaxy.util.hash_util
- galaxy.util.heartbeat
- galaxy.util.image_util
- galaxy.util.inflection
- galaxy.util.json
- galaxy.util.jstree
- galaxy.util.lazy_process
- galaxy.util.monitors
- galaxy.util.odict
- galaxy.util.oset
- galaxy.util.path
- galaxy.util.permutations
- galaxy.util.plugin_config
- galaxy.util.properties
- galaxy.util.renamed_temporary_file
- galaxy.util.resources
- galaxy.util.rules_dsl
- galaxy.util.sanitize_html
- galaxy.util.script
- galaxy.util.search
- galaxy.util.simplegraph
- galaxy.util.sleeper
- galaxy.util.sockets
- galaxy.util.specs
- galaxy.util.sqlite
- galaxy.util.submodules
- galaxy.util.task
- galaxy.util.template
- galaxy.util.tool_shed.common_util
- galaxy.util.tool_shed.encoding_util
- galaxy.util.tool_shed.xml_util
- galaxy.util.tool_version
- galaxy.util.topsort
- galaxy.util.ucsc
- galaxy.util.validation
- galaxy.util.watcher
- galaxy.util.xml_macros
- galaxy.util.yaml_util
- galaxy.util.zipstream
- galaxy.visualization.data_providers.basic
- galaxy.visualization.data_providers.cigar
- galaxy.visualization.data_providers.genome
- galaxy.visualization.data_providers.phyloviz
- galaxy.visualization.data_providers.phyloviz.baseparser
- galaxy.visualization.data_providers.phyloviz.newickparser
- galaxy.visualization.data_providers.phyloviz.nexusparser
- galaxy.visualization.data_providers.phyloviz.phyloxmlparser
- galaxy.visualization.data_providers.registry
- galaxy.visualization.genomes
- galaxy.visualization.plugins.config_parser
- galaxy.visualization.plugins.plugin
- galaxy.visualization.plugins.registry
- galaxy.visualization.plugins.resource_parser
- galaxy.visualization.plugins.utils
- galaxy.web.framework
- galaxy.web.framework.base
- galaxy.web.framework.decorators
- galaxy.web.framework.helpers
- galaxy.web.framework.middleware.error
- galaxy.web.framework.middleware.profile
- galaxy.web.framework.middleware.remoteuser
- galaxy.web.framework.middleware.request_id
- galaxy.web.framework.middleware.sqldebug
- galaxy.web.framework.middleware.static
- galaxy.web.framework.middleware.statsd
- galaxy.web.framework.middleware.translogger
- galaxy.web.framework.middleware.xforwardedhost
- galaxy.web.legacy_framework.grids
- galaxy.web.proxy
- galaxy.web_stack
- galaxy.web_stack.gunicorn_config
- galaxy.web_stack.handlers
- galaxy.web_stack.message
- galaxy.web_stack.transport
- galaxy.webapps.base.api
- galaxy.webapps.base.controller
- galaxy.webapps.base.webapp
- galaxy.webapps.galaxy.api
- galaxy.webapps.galaxy.api.annotations
- galaxy.webapps.galaxy.api.authenticate
- galaxy.webapps.galaxy.api.common
- galaxy.webapps.galaxy.api.configuration
- galaxy.webapps.galaxy.api.container_resolution
- galaxy.webapps.galaxy.api.dataset_collections
- galaxy.webapps.galaxy.api.datasets
- galaxy.webapps.galaxy.api.datatypes
- galaxy.webapps.galaxy.api.display_applications
- galaxy.webapps.galaxy.api.dynamic_tools
- galaxy.webapps.galaxy.api.extended_metadata
- galaxy.webapps.galaxy.api.folder_contents
- galaxy.webapps.galaxy.api.folders
- galaxy.webapps.galaxy.api.forms
- galaxy.webapps.galaxy.api.genomes
- galaxy.webapps.galaxy.api.group_roles
- galaxy.webapps.galaxy.api.group_users
- galaxy.webapps.galaxy.api.groups
- galaxy.webapps.galaxy.api.histories
- galaxy.webapps.galaxy.api.item_tags
- galaxy.webapps.galaxy.api.job_files
- galaxy.webapps.galaxy.api.job_lock
- galaxy.webapps.galaxy.api.job_ports
- galaxy.webapps.galaxy.api.libraries
- galaxy.webapps.galaxy.api.library_datasets
- galaxy.webapps.galaxy.api.licenses
- galaxy.webapps.galaxy.api.metrics
- galaxy.webapps.galaxy.api.page_revisions
- galaxy.webapps.galaxy.api.pages
- galaxy.webapps.galaxy.api.plugins
- galaxy.webapps.galaxy.api.provenance
- galaxy.webapps.galaxy.api.quotas
- galaxy.webapps.galaxy.api.remote_files
- galaxy.webapps.galaxy.api.roles
- galaxy.webapps.galaxy.api.sanitize_allow
- galaxy.webapps.galaxy.api.short_term_storage
- galaxy.webapps.galaxy.api.tags
- galaxy.webapps.galaxy.api.tasks
- galaxy.webapps.galaxy.api.tool_data
- galaxy.webapps.galaxy.api.tool_dependencies
- galaxy.webapps.galaxy.api.tool_entry_points
- galaxy.webapps.galaxy.api.tool_shed_repositories
- galaxy.webapps.galaxy.api.tools
- galaxy.webapps.galaxy.api.toolshed
- galaxy.webapps.galaxy.api.tours
- galaxy.webapps.galaxy.api.trs_consumer
- galaxy.webapps.galaxy.api.trs_search
- galaxy.webapps.galaxy.api.uploads
- galaxy.webapps.galaxy.api.users
- galaxy.webapps.galaxy.api.visualizations
- galaxy.webapps.galaxy.api.webhooks
- galaxy.webapps.galaxy.api.workflows
- galaxy.webapps.galaxy.buildapp
- galaxy.webapps.galaxy.controllers.admin
- galaxy.webapps.galaxy.controllers.admin_toolshed
- galaxy.webapps.galaxy.controllers.async
- galaxy.webapps.galaxy.controllers.authnz
- galaxy.webapps.galaxy.controllers.data_manager
- galaxy.webapps.galaxy.controllers.dataset
- galaxy.webapps.galaxy.controllers.error
- galaxy.webapps.galaxy.controllers.forms
- galaxy.webapps.galaxy.controllers.history
- galaxy.webapps.galaxy.controllers.page
- galaxy.webapps.galaxy.controllers.root
- galaxy.webapps.galaxy.controllers.shed_tool_static
- galaxy.webapps.galaxy.controllers.tag
- galaxy.webapps.galaxy.controllers.tool_runner
- galaxy.webapps.galaxy.controllers.user
- galaxy.webapps.galaxy.controllers.visualization
- galaxy.webapps.galaxy.controllers.workflow
- galaxy.webapps.galaxy.fast_app
- galaxy.webapps.galaxy.fast_factory
- galaxy.webapps.galaxy.services.authenticate
- galaxy.webapps.galaxy.services.base
- galaxy.webapps.galaxy.services.dataset_collections
- galaxy.webapps.galaxy.services.datasets
- galaxy.webapps.galaxy.services.histories
- galaxy.webapps.galaxy.services.invocations
- galaxy.webapps.galaxy.services.libraries
- galaxy.webapps.galaxy.services.library_folder_contents
- galaxy.webapps.galaxy.services.library_folders
- galaxy.webapps.galaxy.services.pages
- galaxy.webapps.galaxy.services.quotas
- galaxy.webapps.galaxy.services.sharable
- galaxy.webapps.galaxy.services.tools
- galaxy.webapps.galaxy.services.users
- galaxy.webapps.galaxy.services.visualizations
- galaxy.webapps.galaxy.services.workflows
- galaxy.webapps.openapi.utils
- galaxy.webapps.reports.app
- galaxy.webapps.reports.buildapp
- galaxy.webapps.reports.config
- galaxy.webapps.reports.controllers.history
- galaxy.webapps.reports.controllers.home
- galaxy.webapps.reports.controllers.jobs
- galaxy.webapps.reports.controllers.query
- galaxy.webapps.reports.controllers.root
- galaxy.webapps.reports.controllers.system
- galaxy.webapps.reports.controllers.tools
- galaxy.webapps.reports.controllers.users
- galaxy.webapps.reports.controllers.workflows
- galaxy.webapps.reports.fast_app
- galaxy.webapps.reports.fast_factory
- galaxy.webapps.util
- galaxy.webhooks
- galaxy.work.context
- galaxy.workflow.extract
- galaxy.workflow.modules
- galaxy.workflow.refactor.execute
- galaxy.workflow.refactor.schema
- galaxy.workflow.render
- galaxy.workflow.reports
- galaxy.workflow.resources
- galaxy.workflow.run
- galaxy.workflow.run_request
- galaxy.workflow.schedulers
- galaxy.workflow.scheduling_manager
- galaxy.workflow.steps
- galaxy.workflow.trs_proxy
- galaxy_ext.expressions.handle_job
- galaxy_test.api.sharable
- galaxy_test.api.test_authenticate
- galaxy_test.api.test_configuration
- galaxy_test.api.test_dataset_collections
- galaxy_test.api.test_datasets
- galaxy_test.api.test_datatypes
- galaxy_test.api.test_display_applications
- galaxy_test.api.test_folder_contents
- galaxy_test.api.test_folders
- galaxy_test.api.test_framework
- galaxy_test.api.test_group_roles
- galaxy_test.api.test_group_users
- galaxy_test.api.test_groups
- galaxy_test.api.test_histories
- galaxy_test.api.test_history_contents
- galaxy_test.api.test_history_contents_provenance
- galaxy_test.api.test_jobs
- galaxy_test.api.test_libraries
- galaxy_test.api.test_licenses
- galaxy_test.api.test_page_revisions
- galaxy_test.api.test_pages
- galaxy_test.api.test_roles
- galaxy_test.api.test_tool_data
- galaxy_test.api.test_tools
- galaxy_test.api.test_tools_upload
- galaxy_test.api.test_tours
- galaxy_test.api.test_users
- galaxy_test.api.test_visualizations
- galaxy_test.api.test_webhooks
- galaxy_test.api.test_workflow_extraction
- galaxy_test.api.test_workflows
- galaxy_test.api.test_workflows_cwl
- galaxy_test.api.test_workflows_from_yaml
- galaxy_test.base.api
- galaxy_test.base.api_asserts
- galaxy_test.base.api_util
- galaxy_test.base.env
- galaxy_test.base.interactor
- galaxy_test.base.populators
- galaxy_test.base.rules_test_data
- galaxy_test.base.testcase
- galaxy_test.conftest
- galaxy_test.driver.driver_util
- galaxy_test.driver.integration_setup
- galaxy_test.driver.integration_util
- galaxy_test.driver.testcase
- galaxy_test.performance.test_workflow_framework_performance
- galaxy_test.selenium.conftest
- galaxy_test.selenium.jupyter_context
- galaxy_test.selenium.test_admin_app
- galaxy_test.selenium.test_anon_history
- galaxy_test.selenium.test_change_password
- galaxy_test.selenium.test_collection_builders
- galaxy_test.selenium.test_collection_edit
- galaxy_test.selenium.test_custom_builds
- galaxy_test.selenium.test_data_source_tools
- galaxy_test.selenium.test_dataset_metadata_download
- galaxy_test.selenium.test_histories_list
- galaxy_test.selenium.test_history_copy_elements
- galaxy_test.selenium.test_history_dataset_state
- galaxy_test.selenium.test_history_multi_view
- galaxy_test.selenium.test_history_options
- galaxy_test.selenium.test_history_panel
- galaxy_test.selenium.test_history_panel_collections
- galaxy_test.selenium.test_history_sharing
- galaxy_test.selenium.test_invocation_grid
- galaxy_test.selenium.test_library_contents
- galaxy_test.selenium.test_library_landing
- galaxy_test.selenium.test_library_to_collections
- galaxy_test.selenium.test_login
- galaxy_test.selenium.test_navigates_galaxy
- galaxy_test.selenium.test_pages
- galaxy_test.selenium.test_personal_information
- galaxy_test.selenium.test_registration
- galaxy_test.selenium.test_sign_out
- galaxy_test.selenium.test_sizzle_loading
- galaxy_test.selenium.test_stock_tours
- galaxy_test.selenium.test_tool_describing_tours
- galaxy_test.selenium.test_tool_form
- galaxy_test.selenium.test_uploads
- galaxy_test.selenium.test_workflow_editor
- galaxy_test.selenium.test_workflow_invocation_details
- galaxy_test.selenium.test_workflow_management
- galaxy_test.selenium.test_workflow_run
- galaxy_test.selenium.test_workflow_sharing
- importlib_resources._common
- importlib_resources.abc
- posixpath
- ruamel.yaml.comments
- schema_salad.utils
- tool_shed.dependencies.attribute_handlers
- tool_shed.dependencies.repository.relation_builder
- tool_shed.dependencies.tool.tag_attribute_handler
- tool_shed.grids.admin_grids
- tool_shed.grids.repository_grid_filter_manager
- tool_shed.grids.repository_grids
- tool_shed.grids.util
- tool_shed.managers.groups
- tool_shed.managers.repositories
- tool_shed.metadata.repository_metadata_manager
- tool_shed.repository_registry
- tool_shed.repository_types.metadata
- tool_shed.repository_types.registry
- tool_shed.repository_types.repository_suite_definition
- tool_shed.repository_types.tool_dependency_definition
- tool_shed.repository_types.unrestricted
- tool_shed.repository_types.util
- tool_shed.test.base.test_db_util
- tool_shed.test.base.twilltestcase
- tool_shed.test.functional.test_0000_basic_repository_features
- tool_shed.test.functional.test_0010_repository_with_tool_dependencies
- tool_shed.test.functional.test_0020_basic_repository_dependencies
- tool_shed.test.functional.test_0030_repository_dependency_revisions
- tool_shed.test.functional.test_0040_repository_circular_dependencies
- tool_shed.test.functional.test_0050_circular_dependencies_4_levels
- tool_shed.test.functional.test_0070_invalid_tool
- tool_shed.test.functional.test_0080_advanced_circular_dependencies
- tool_shed.test.functional.test_0090_tool_search
- tool_shed.test.functional.test_0100_complex_repository_dependencies
- tool_shed.test.functional.test_0110_invalid_simple_repository_dependencies
- tool_shed.test.functional.test_0120_simple_repository_dependency_multiple_owners
- tool_shed.test.functional.test_0140_tool_help_images
- tool_shed.test.functional.test_0150_prior_installation_required
- tool_shed.test.functional.test_0160_circular_prior_installation_required
- tool_shed.test.functional.test_0170_complex_prior_installation_required
- tool_shed.test.functional.test_0300_reset_all_metadata
- tool_shed.test.functional.test_0310_hg_api_features
- tool_shed.test.functional.test_0420_citable_urls_for_repositories
- tool_shed.test.functional.test_0430_browse_utilities
- tool_shed.test.functional.test_0440_deleting_dependency_definitions
- tool_shed.test.functional.test_0460_upload_to_repository
- tool_shed.test.functional.test_0470_tool_dependency_repository_type
- tool_shed.test.functional.test_0480_tool_dependency_xml_verification
- tool_shed.test.functional.test_0530_repository_admin_feature
- tool_shed.test.functional.test_0550_metadata_updated_dependencies
- tool_shed.test.functional.test_1000_install_basic_repository
- tool_shed.test.functional.test_1010_install_repository_with_tool_dependencies
- tool_shed.test.functional.test_1020_install_repository_with_repository_dependencies
- tool_shed.test.functional.test_1030_install_repository_with_dependency_revisions
- tool_shed.test.functional.test_1040_install_repository_basic_circular_dependencies
- tool_shed.test.functional.test_1050_circular_dependencies_4_levels
- tool_shed.test.functional.test_1070_invalid_tool
- tool_shed.test.functional.test_1080_advanced_circular_dependency_installation
- tool_shed.test.functional.test_1090_repository_dependency_handling
- tool_shed.test.functional.test_1100_install_updated_repository_dependencies
- tool_shed.test.functional.test_1120_install_repository_with_complex_dependencies
- tool_shed.test.functional.test_1130_install_repository_with_invalid_repository_dependency
- tool_shed.test.functional.test_1140_simple_repository_dependency_multiple_owners
- tool_shed.test.functional.test_1160_tool_help_images
- tool_shed.test.functional.test_1170_prior_installation_required
- tool_shed.test.functional.test_1180_circular_prior_installation_required
- tool_shed.test.functional.test_1190_complex_prior_installation_required
- tool_shed.test.functional.test_1200_uninstall_and_reinstall_basic_repository
- tool_shed.test.functional.test_1210_uninstall_reinstall_repository_with_tool_dependencies
- tool_shed.test.functional.test_1230_uninstall_reinstall_repository_with_dependency_revisions
- tool_shed.test.functional.test_1300_reset_all_metadata
- tool_shed.test.functional.test_1410_update_manager
- tool_shed.test.functional.test_1430_repair_installed_repository
- tool_shed.test.functional.test_1460_data_managers
- tool_shed.test.functional.test_1470_updating_installed_repositories
- tool_shed.tools.tool_validator
- tool_shed.tools.tool_version_manager
- tool_shed.util.admin_util
- tool_shed.util.commit_util
- tool_shed.util.common_util
- tool_shed.util.hg_util
- tool_shed.util.hgweb_config
- tool_shed.util.metadata_util
- tool_shed.util.readme_util
- tool_shed.util.repository_content_util
- tool_shed.util.repository_util
- tool_shed.util.search_util
- tool_shed.util.shed_index
- tool_shed.util.shed_util_common
- tool_shed.util.tool_util
- tool_shed.util.web_util
- tool_shed.utility_containers
- tool_shed.webapp.api
- tool_shed.webapp.api.authenticate
- tool_shed.webapp.api.categories
- tool_shed.webapp.api.configuration
- tool_shed.webapp.api.groups
- tool_shed.webapp.api.repositories
- tool_shed.webapp.api.repository_revisions
- tool_shed.webapp.api.tools
- tool_shed.webapp.api.users
- tool_shed.webapp.app
- tool_shed.webapp.buildapp
- tool_shed.webapp.config
- tool_shed.webapp.controllers.admin
- tool_shed.webapp.controllers.groups
- tool_shed.webapp.controllers.hg
- tool_shed.webapp.controllers.repository
- tool_shed.webapp.controllers.user
- tool_shed.webapp.fast_app
- tool_shed.webapp.fast_factory
- tool_shed.webapp.framework.decorators
- tool_shed.webapp.framework.middleware.remoteuser
- tool_shed.webapp.model
- tool_shed.webapp.search.repo_search
- tool_shed.webapp.search.tool_search
- tool_shed.webapp.security
- tool_shed.webapp.util.ratings_util
- tool_shed.webapp.util.shed_statistics
- webob.exc