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
- abc
- builtins
- configparser
- csv
- cwltool.context
- cwltool.job
- cwltool.load_tool
- cwltool.stdfsaccess
- galaxy.actions.admin
- galaxy.actions.library
- galaxy.app
- 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.config
- galaxy.config_watchers
- galaxy.containers
- galaxy.containers.docker
- galaxy.containers.docker_decorators
- galaxy.containers.docker_model
- galaxy.containers.docker_swarm
- 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.bgzip
- galaxy.datatypes.converters.cram_to_bam
- galaxy.datatypes.converters.fasta_to_len
- galaxy.datatypes.converters.fastq_to_fqtoc
- galaxy.datatypes.converters.fastqsolexa_to_fasta_converter
- galaxy.datatypes.converters.fastqsolexa_to_qual_converter
- galaxy.datatypes.converters.gff_to_interval_index_converter
- galaxy.datatypes.converters.interval_to_bed_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.interval_to_tabix_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.tabular_to_dbnsfp
- galaxy.datatypes.converters.vcf_to_interval_index_converter
- galaxy.datatypes.converters.vcf_to_vcf_bgzip
- 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.genetics
- galaxy.datatypes.gis
- galaxy.datatypes.graph
- galaxy.datatypes.images
- galaxy.datatypes.interval
- galaxy.datatypes.isa
- 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.qualityscore
- galaxy.datatypes.registry
- galaxy.datatypes.sequence
- galaxy.datatypes.sniff
- galaxy.datatypes.spaln
- 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.exceptions
- galaxy.forms.forms
- galaxy.job_execution.datasets
- galaxy.job_execution.output_collect
- galaxy.job_execution.ports.view
- galaxy.job_execution.setup
- galaxy.job_metrics
- galaxy.job_metrics.collectl.cli
- galaxy.job_metrics.collectl.processes
- galaxy.job_metrics.collectl.stats
- galaxy.job_metrics.collectl.subsystems
- galaxy.job_metrics.formatting
- galaxy.job_metrics.instrumenters
- galaxy.job_metrics.instrumenters.cgroup
- galaxy.job_metrics.instrumenters.collectl
- 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.jobs
- galaxy.jobs.actions.post
- 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.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.jobs.transfer_manager
- galaxy.main
- galaxy.managers.annotatable
- galaxy.managers.api_keys
- galaxy.managers.base
- galaxy.managers.citations
- galaxy.managers.cloud
- galaxy.managers.cloudauthzs
- galaxy.managers.collections
- galaxy.managers.collections_util
- galaxy.managers.configuration
- galaxy.managers.containers
- galaxy.managers.context
- galaxy.managers.datasets
- galaxy.managers.deletable
- galaxy.managers.executables
- galaxy.managers.folders
- 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.markdown_parse
- galaxy.managers.markdown_util
- galaxy.managers.pages
- galaxy.managers.ratable
- galaxy.managers.rbac_secured
- galaxy.managers.roles
- galaxy.managers.secured
- galaxy.managers.sharable
- galaxy.managers.taggable
- 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.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.item_attrs
- galaxy.model.mapping
- galaxy.model.metadata
- galaxy.model.migrate.check
- galaxy.model.migrate.versions.0001_initial_tables
- galaxy.model.migrate.versions.0002_metadata_file_table
- galaxy.model.migrate.versions.0003_security_and_libraries
- galaxy.model.migrate.versions.0004_indexes_and_defaults
- galaxy.model.migrate.versions.0005_cleanup_datasets_fix
- galaxy.model.migrate.versions.0006_change_qual_datatype
- galaxy.model.migrate.versions.0007_sharing_histories
- galaxy.model.migrate.versions.0008_galaxy_forms
- galaxy.model.migrate.versions.0009_request_table
- galaxy.model.migrate.versions.0010_hda_display_at_authz_table
- galaxy.model.migrate.versions.0011_v0010_mysql_index_fix
- galaxy.model.migrate.versions.0012_user_address
- galaxy.model.migrate.versions.0013_change_lib_item_templates_to_forms
- galaxy.model.migrate.versions.0014_pages
- galaxy.model.migrate.versions.0015_tagging
- galaxy.model.migrate.versions.0016_v0015_mysql_index_fix
- galaxy.model.migrate.versions.0017_library_item_indexes
- galaxy.model.migrate.versions.0018_ordered_tags_and_page_tags
- galaxy.model.migrate.versions.0019_request_library_folder
- galaxy.model.migrate.versions.0020_library_upload_job
- galaxy.model.migrate.versions.0021_user_prefs
- galaxy.model.migrate.versions.0022_visualization_tables
- galaxy.model.migrate.versions.0023_page_published_and_deleted_columns
- galaxy.model.migrate.versions.0024_page_slug_unique_constraint
- galaxy.model.migrate.versions.0025_user_info
- galaxy.model.migrate.versions.0026_cloud_tables
- galaxy.model.migrate.versions.0027_request_events
- galaxy.model.migrate.versions.0028_external_metadata_file_override
- galaxy.model.migrate.versions.0029_user_actions
- galaxy.model.migrate.versions.0030_history_slug_column
- galaxy.model.migrate.versions.0031_community_and_workflow_tags
- galaxy.model.migrate.versions.0032_stored_workflow_slug_column
- galaxy.model.migrate.versions.0033_published_cols_for_histories_and_workflows
- galaxy.model.migrate.versions.0034_page_user_share_association
- galaxy.model.migrate.versions.0035_item_annotations_and_workflow_step_tags
- galaxy.model.migrate.versions.0036_add_deleted_column_to_library_template_assoc_tables
- galaxy.model.migrate.versions.0037_samples_library
- galaxy.model.migrate.versions.0038_add_inheritable_column_to_library_template_assoc_tables
- galaxy.model.migrate.versions.0039_add_synopsis_column_to_library_table
- galaxy.model.migrate.versions.0040_page_annotations
- galaxy.model.migrate.versions.0041_workflow_invocation
- galaxy.model.migrate.versions.0042_workflow_invocation_fix
- galaxy.model.migrate.versions.0043_visualization_sharing_tagging_annotating
- galaxy.model.migrate.versions.0044_add_notify_column_to_request_table
- galaxy.model.migrate.versions.0045_request_type_permissions_table
- galaxy.model.migrate.versions.0046_post_job_actions
- galaxy.model.migrate.versions.0047_job_table_user_id_column
- galaxy.model.migrate.versions.0048_dataset_instance_state_column
- galaxy.model.migrate.versions.0049_api_keys_table
- galaxy.model.migrate.versions.0050_drop_cloud_tables
- galaxy.model.migrate.versions.0051_imported_col_for_jobs_table
- galaxy.model.migrate.versions.0052_sample_dataset_table
- galaxy.model.migrate.versions.0053_item_ratings
- galaxy.model.migrate.versions.0054_visualization_dbkey
- galaxy.model.migrate.versions.0055_add_pja_assoc_for_jobs
- galaxy.model.migrate.versions.0056_workflow_outputs
- galaxy.model.migrate.versions.0057_request_notify
- galaxy.model.migrate.versions.0058_history_import_export
- galaxy.model.migrate.versions.0059_sample_dataset_file_path
- galaxy.model.migrate.versions.0060_history_archive_import
- galaxy.model.migrate.versions.0061_tasks
- galaxy.model.migrate.versions.0062_user_openid_table
- galaxy.model.migrate.versions.0063_sequencer_table
- galaxy.model.migrate.versions.0064_add_run_and_sample_run_association_tables
- galaxy.model.migrate.versions.0065_add_name_to_form_fields_and_values
- galaxy.model.migrate.versions.0066_deferred_job_and_transfer_job_tables
- galaxy.model.migrate.versions.0067_populate_sequencer_table
- galaxy.model.migrate.versions.0068_rename_sequencer_to_external_services
- galaxy.model.migrate.versions.0069_rename_sequencer_form_type
- galaxy.model.migrate.versions.0070_add_info_column_to_deferred_job_table
- galaxy.model.migrate.versions.0071_add_history_and_workflow_to_sample
- galaxy.model.migrate.versions.0072_add_pid_and_socket_columns_to_transfer_job_table
- galaxy.model.migrate.versions.0073_add_ldda_to_implicit_conversion_table
- galaxy.model.migrate.versions.0074_add_purged_column_to_library_dataset_table
- galaxy.model.migrate.versions.0075_add_subindex_column_to_run_table
- galaxy.model.migrate.versions.0076_fix_form_values_data_corruption
- galaxy.model.migrate.versions.0077_create_tool_tag_association_table
- galaxy.model.migrate.versions.0078_add_columns_for_disk_usage_accounting
- galaxy.model.migrate.versions.0079_input_library_to_job_table
- galaxy.model.migrate.versions.0080_quota_tables
- galaxy.model.migrate.versions.0081_add_tool_version_to_hda_ldda
- galaxy.model.migrate.versions.0082_add_tool_shed_repository_table
- galaxy.model.migrate.versions.0083_add_prepare_files_to_task
- galaxy.model.migrate.versions.0084_add_ldda_id_to_implicit_conversion_table
- galaxy.model.migrate.versions.0085_add_task_info
- galaxy.model.migrate.versions.0086_add_tool_shed_repository_table_columns
- galaxy.model.migrate.versions.0087_tool_id_guid_map_table
- galaxy.model.migrate.versions.0088_add_installed_changeset_revison_column
- galaxy.model.migrate.versions.0089_add_object_store_id_columns
- galaxy.model.migrate.versions.0090_add_tool_shed_repository_table_columns
- galaxy.model.migrate.versions.0091_add_tool_version_tables
- galaxy.model.migrate.versions.0092_add_migrate_tools_table
- galaxy.model.migrate.versions.0093_add_job_params_col
- galaxy.model.migrate.versions.0094_add_job_handler_col
- galaxy.model.migrate.versions.0095_hda_subsets
- galaxy.model.migrate.versions.0096_openid_provider
- galaxy.model.migrate.versions.0097_add_ctx_rev_column
- galaxy.model.migrate.versions.0098_genome_index_tool_data_table
- galaxy.model.migrate.versions.0099_add_tool_dependency_table
- galaxy.model.migrate.versions.0100_alter_tool_dependency_table_version_column
- galaxy.model.migrate.versions.0101_drop_installed_changeset_revision_column
- galaxy.model.migrate.versions.0102_add_tool_dependency_status_columns
- galaxy.model.migrate.versions.0103_add_tool_shed_repository_status_columns
- galaxy.model.migrate.versions.0104_update_genome_downloader_job_parameters
- galaxy.model.migrate.versions.0105_add_cleanup_event_table
- galaxy.model.migrate.versions.0106_add_missing_indexes
- galaxy.model.migrate.versions.0107_add_exit_code_to_job_and_task
- galaxy.model.migrate.versions.0108_add_extended_metadata
- galaxy.model.migrate.versions.0109_add_repository_dependency_tables
- galaxy.model.migrate.versions.0110_add_dataset_uuid
- galaxy.model.migrate.versions.0111_add_job_destinations
- galaxy.model.migrate.versions.0112_add_data_manager_history_association_and_data_manager_job_association_tables
- galaxy.model.migrate.versions.0113_update_migrate_tools_table
- galaxy.model.migrate.versions.0114_update_migrate_tools_table_again
- galaxy.model.migrate.versions.0115_longer_user_password_field
- galaxy.model.migrate.versions.0116_drop_update_available_col_add_tool_shed_status_col
- galaxy.model.migrate.versions.0117_add_user_activation
- galaxy.model.migrate.versions.0118_add_hda_extended_metadata
- galaxy.model.migrate.versions.0119_job_metrics
- galaxy.model.migrate.versions.0120_dataset_collections
- galaxy.model.migrate.versions.0121_workflow_uuids
- galaxy.model.migrate.versions.0122_grow_mysql_blobs
- galaxy.model.migrate.versions.0123_add_workflow_request_tables
- galaxy.model.migrate.versions.0124_job_state_history
- galaxy.model.migrate.versions.0125_workflow_step_tracking
- galaxy.model.migrate.versions.0126_password_reset
- galaxy.model.migrate.versions.0127_output_collection_adjustments
- galaxy.model.migrate.versions.0128_session_timeout
- galaxy.model.migrate.versions.0129_job_external_output_metadata_validity
- galaxy.model.migrate.versions.0130_change_pref_datatype
- galaxy.model.migrate.versions.0131_subworkflow_and_input_parameter_modules
- galaxy.model.migrate.versions.0132_add_lastpasswordchange_to_user
- galaxy.model.migrate.versions.0133_add_dependency_column_to_job
- galaxy.model.migrate.versions.0134_hda_set_deleted_if_purged
- galaxy.model.migrate.versions.0135_add_library_tags
- galaxy.model.migrate.versions.0136_collection_and_workflow_state
- galaxy.model.migrate.versions.0137_add_copied_from_job_id_column
- galaxy.model.migrate.versions.0138_add_hda_version
- galaxy.model.migrate.versions.0139_add_history_dataset_association_history_table
- galaxy.model.migrate.versions.0140_add_dataset_version_to_job_to_input_dataset_association_table
- galaxy.model.migrate.versions.0141_add_oidc_tables
- galaxy.model.migrate.versions.0142_change_numeric_metric_precision
- galaxy.model.migrate.versions.0143_add_cloudauthz_tables
- galaxy.model.migrate.versions.0144_add_cleanup_event_user_table
- galaxy.model.migrate.versions.0145_add_workflow_step_input
- galaxy.model.migrate.versions.0146_workflow_paths
- galaxy.model.migrate.versions.0147_job_messages
- galaxy.model.migrate.versions.0148_add_checksum_table
- galaxy.model.migrate.versions.0149_dynamic_tools
- galaxy.model.migrate.versions.0150_add_create_time_field_for_cloudauthz
- galaxy.model.migrate.versions.0151_add_worker_process
- galaxy.model.migrate.versions.0152_add_metadata_file_uuid
- galaxy.model.migrate.versions.0153_add_custos_authnz_token_table
- galaxy.model.migrate.versions.0154_created_from_basename
- galaxy.model.migrate.versions.0155_job_galaxy_version
- galaxy.model.migrate.versions.0156_add_interactivetools
- galaxy.model.migrate.versions.0157_rework_dataset_validation
- galaxy.model.migrate.versions.0158_workflow_reports
- galaxy.model.migrate.versions.0159_add_job_external_id_index
- galaxy.model.migrate.versions.0160_hda_set_deleted_if_purged_again
- galaxy.model.migrate.versions.0161_add_workflow_invocation_output_table
- galaxy.model.migrate.versions.0162_job_only_pjas
- galaxy.model.migrate.versions.0163_worker_process_pid
- galaxy.model.migrate.versions.0164_page_format
- galaxy.model.migrate.versions.0165_add_content_update_time
- galaxy.model.migrate.versions.util
- galaxy.model.none_like
- galaxy.model.orm.engine_factory
- galaxy.model.orm.logging_connection_proxy
- galaxy.model.orm.scripts
- galaxy.model.search
- galaxy.model.security
- galaxy.model.store
- galaxy.model.tags
- galaxy.model.tool_shed_install
- galaxy.model.triggers
- 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.openid.openid_manager
- galaxy.openid.providers
- galaxy.queue_worker
- galaxy.queues
- galaxy.quota
- galaxy.security
- galaxy.selenium.cli
- galaxy.selenium.components
- galaxy.selenium.driver_factory
- galaxy.selenium.has_driver
- galaxy.selenium.navigates_galaxy
- galaxy.selenium.scripts.dump_tour
- galaxy.selenium.sizzle
- galaxy.selenium.smart_components
- galaxy.tool_shed.galaxy_install.datatypes.custom_datatype_manager
- 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.migrate.check
- galaxy.tool_shed.galaxy_install.migrate.common
- galaxy.tool_shed.galaxy_install.migrate.versions.0001_tools
- galaxy.tool_shed.galaxy_install.migrate.versions.0002_tools
- galaxy.tool_shed.galaxy_install.migrate.versions.0003_tools
- galaxy.tool_shed.galaxy_install.migrate.versions.0004_tools
- galaxy.tool_shed.galaxy_install.migrate.versions.0005_tools
- galaxy.tool_shed.galaxy_install.migrate.versions.0006_tools
- galaxy.tool_shed.galaxy_install.migrate.versions.0007_tools
- galaxy.tool_shed.galaxy_install.migrate.versions.0008_tools
- galaxy.tool_shed.galaxy_install.migrate.versions.0009_tools
- galaxy.tool_shed.galaxy_install.migrate.versions.0010_tools
- galaxy.tool_shed.galaxy_install.migrate.versions.0011_tools
- galaxy.tool_shed.galaxy_install.migrate.versions.0012_tools
- galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager
- galaxy.tool_shed.galaxy_install.tool_dependencies.env_manager
- galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.asynchronous_reader
- galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.env_file_builder
- galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.install_environment
- galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager
- galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler
- galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler
- galaxy.tool_shed.galaxy_install.tool_migration_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.tool_shed_registry
- 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.cwl.cwltool_deps
- galaxy.tool_util.cwl.parser
- galaxy.tool_util.cwl.representation
- galaxy.tool_util.cwl.runtime_actions
- galaxy.tool_util.cwl.schema
- galaxy.tool_util.cwl.util
- 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.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_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.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.outputs
- 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.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.verify
- galaxy.tool_util.verify.asserts
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- galaxy.tool_util.verify.asserts.xml
- galaxy.tool_util.verify.interactor
- galaxy.tool_util.verify.script
- galaxy.tool_util.verify.test_data
- 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.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.repositories
- galaxy.tools.search
- galaxy.tools.special_tools
- galaxy.tools.test
- galaxy.tools.toolbox.base
- galaxy.tools.toolbox.filters
- galaxy.tools.toolbox.integrated_panel
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- galaxy.tools.toolbox.lineages.interface
- galaxy.tools.toolbox.panel
- galaxy.tools.toolbox.parser
- galaxy.tools.toolbox.tags
- galaxy.tools.toolbox.watcher
- galaxy.tools.util.galaxyops
- galaxy.tools.util.maf_utilities
- galaxy.tools.wrappers
- galaxy.tours
- galaxy.util
- galaxy.util.aliaspickler
- galaxy.util.bunch
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- galaxy.util.commands
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- galaxy.util.dbkeys
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- galaxy.util.expressions
- galaxy.util.facts
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- galaxy.util.form_builder
- galaxy.util.getargspec
- galaxy.util.hash_util
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- galaxy.util.image_util
- galaxy.util.inflection
- galaxy.util.json
- galaxy.util.jstree
- galaxy.util.lazy_process
- galaxy.util.monitors
- galaxy.util.object_wrapper
- galaxy.util.odict
- galaxy.util.oset
- galaxy.util.pastescript.loadwsgi
- galaxy.util.pastescript.serve
- galaxy.util.path
- galaxy.util.permutations
- galaxy.util.plugin_config
- galaxy.util.properties
- galaxy.util.renamed_temporary_file
- galaxy.util.rules_dsl
- galaxy.util.sanitize_html
- galaxy.util.script
- galaxy.util.simplegraph
- galaxy.util.sleeper
- galaxy.util.sockets
- galaxy.util.specs
- galaxy.util.sqlite
- galaxy.util.streamball
- galaxy.util.submodules
- 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.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.interactive_environments
- galaxy.visualization.plugins.plugin
- galaxy.visualization.plugins.registry
- galaxy.visualization.plugins.resource_parser
- galaxy.visualization.plugins.utils
- galaxy.web.formatting
- galaxy.web.framework.base
- galaxy.web.framework.decorators
- galaxy.web.framework.helpers
- galaxy.web.framework.middleware.batch
- 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.sentry
- 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.params
- galaxy.web.proxy
- galaxy.web.statsd_client
- galaxy.web_stack
- galaxy.webapps.base.controller
- galaxy.webapps.galaxy.api.annotations
- galaxy.webapps.galaxy.api.authenticate
- galaxy.webapps.galaxy.api.cloud
- galaxy.webapps.galaxy.api.cloudauthz
- 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.history_contents
- galaxy.webapps.galaxy.api.item_tags
- galaxy.webapps.galaxy.api.job_files
- galaxy.webapps.galaxy.api.job_ports
- galaxy.webapps.galaxy.api.jobs
- galaxy.webapps.galaxy.api.libraries
- galaxy.webapps.galaxy.api.library_contents
- galaxy.webapps.galaxy.api.library_datasets
- 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.search
- galaxy.webapps.galaxy.api.tags
- 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
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- galaxy.webapps.galaxy.api.visualizations
- galaxy.webapps.galaxy.api.webhooks
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- 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
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- galaxy.webapps.galaxy.controllers.interactive_environments
- galaxy.webapps.galaxy.controllers.interactivetool
- galaxy.webapps.galaxy.controllers.library
- galaxy.webapps.galaxy.controllers.openid
- galaxy.webapps.galaxy.controllers.page
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- galaxy.webapps.galaxy.controllers.tag
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- galaxy.webapps.galaxy.controllers.user
- galaxy.webapps.galaxy.controllers.userskeys
- galaxy.webapps.galaxy.controllers.visualization
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- galaxy.webapps.reports.app
- galaxy.webapps.reports.buildapp
- galaxy.webapps.reports.config
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- 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
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- galaxy.webapps.reports.framework.grids
- galaxy.webapps.util
- galaxy.webhooks
- galaxy.work.context
- galaxy.workflow.extract
- galaxy.workflow.modules
- galaxy.workflow.render
- galaxy.workflow.reports
- galaxy.workflow.resources
- galaxy.workflow.run
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- galaxy.workflow.scheduling_manager
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- galaxy_ext.expressions.handle_job
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- galaxy_test.api.test_authenticate
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- galaxy_test.api.test_dataset_collections
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- galaxy_test.api.test_framework
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- 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_page_revisions
- galaxy_test.api.test_pages
- galaxy_test.api.test_roles
- galaxy_test.api.test_search
- 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_from_yaml
- galaxy_test.base.api_asserts
- galaxy_test.base.api_util
- galaxy_test.base.instrument
- galaxy_test.base.interactor
- galaxy_test.base.nose_util
- galaxy_test.base.populators
- galaxy_test.base.rules_test_data
- galaxy_test.base.ssh_util
- galaxy_test.driver.driver_util
- galaxy_test.driver.integration_util
- galaxy_test.driver.testcase
- galaxy_test.selenium.framework
- 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_custom_builds
- galaxy_test.selenium.test_histories_list
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- galaxy_test.selenium.test_history_sharing
- galaxy_test.selenium.test_jupyter
- galaxy_test.selenium.test_library_contents
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- galaxy_test.selenium.test_published_histories_grid
- galaxy_test.selenium.test_registration
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- galaxy_test.selenium.test_stock_tours
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- sqlalchemy.ext.associationproxy
- sqlalchemy.orm.attributes
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- sqlalchemy.sql.sqltypes
- tool_shed.dependencies.attribute_handlers
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- tool_shed.galaxy_install.dependency_display
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- tool_shed.grids.repository_grid_filter_manager
- tool_shed.grids.repository_grids
- tool_shed.grids.repository_review_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
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- tool_shed.repository_types.unrestricted
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- tool_shed.test.base.test_db_util
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- 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
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- tool_shed.test.functional.test_0070_invalid_tool
- tool_shed.test.functional.test_0080_advanced_circular_dependencies
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- tool_shed.test.functional.test_0150_prior_installation_required
- tool_shed.test.functional.test_0160_circular_prior_installation_required
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- tool_shed.test.functional.test_0300_reset_all_metadata
- tool_shed.test.functional.test_0310_hg_api_features
- tool_shed.test.functional.test_0400_repository_component_reviews
- tool_shed.test.functional.test_0410_repository_component_review_access_control
- 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_0540_get_all_metadata_from_api
- 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_1150_datatype_converters
- 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
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- tool_shed.test.functional.test_1300_reset_all_metadata
- tool_shed.test.functional.test_1410_update_manager
- tool_shed.test.functional.test_1420_tool_dependency_environment_inheritance
- tool_shed.test.functional.test_1430_repair_installed_repository
- tool_shed.test.functional.test_1440_missing_env_sh_files
- tool_shed.test.functional.test_1450_installing_datatypes_sniffers
- tool_shed.test.functional.test_1460_data_managers
- tool_shed.test.functional.test_1470_updating_installed_repositories
- tool_shed.test.functional_tests
- tool_shed.tools.tool_validator
- tool_shed.tools.tool_version_manager
- tool_shed.util.admin_util
- tool_shed.util.commit_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.review_util
- tool_shed.util.search_util
- tool_shed.util.shed_index
- tool_shed.util.shed_util_common
- tool_shed.util.web_util
- tool_shed.utility_containers
- 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.repository_review
- tool_shed.webapp.controllers.upload
- tool_shed.webapp.controllers.user
- tool_shed.webapp.framework.middleware.remoteuser
- tool_shed.webapp.model
- tool_shed.webapp.model.mapping
- tool_shed.webapp.model.migrate.check
- tool_shed.webapp.model.migrate.versions.0001_initial_tables
- tool_shed.webapp.model.migrate.versions.0002_add_tool_suite_column
- tool_shed.webapp.model.migrate.versions.0003_review_and_review_association_tables
- tool_shed.webapp.model.migrate.versions.0004_repository_tables
- tool_shed.webapp.model.migrate.versions.0005_drop_tool_related_tables
- tool_shed.webapp.model.migrate.versions.0006_add_email_alerts_column
- tool_shed.webapp.model.migrate.versions.0007_add_long_description_times_downloaded_columns
- tool_shed.webapp.model.migrate.versions.0008_add_repository_metadata_table
- tool_shed.webapp.model.migrate.versions.0009_add_malicious_column
- tool_shed.webapp.model.migrate.versions.0010_add_new_repo_alert_column
- tool_shed.webapp.model.migrate.versions.0011_add_tool_versions_column
- tool_shed.webapp.model.migrate.versions.0012_add_downloadable_column
- tool_shed.webapp.model.migrate.versions.0013_add_review_tables
- tool_shed.webapp.model.migrate.versions.0014_add_deprecated_column
- tool_shed.webapp.model.migrate.versions.0015_add_api_keys_table
- tool_shed.webapp.model.migrate.versions.0016_add_do_not_test_tools_functionally_correct_errors_columns
- tool_shed.webapp.model.migrate.versions.0017_add_galaxy_utility_columns_to_repository_metadata_table
- tool_shed.webapp.model.migrate.versions.0018_add_repository_metadata_flag_columns
- tool_shed.webapp.model.migrate.versions.0019_add_skip_tool_test_table_and_test_install_error_column
- tool_shed.webapp.model.migrate.versions.0020_add_repository_type_column
- tool_shed.webapp.model.migrate.versions.0021_change_repository_type_value
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- tool_shed.webapp.model.migrate.versions.0024_password_reset
- tool_shed.webapp.model.migrate.versions.0025_session_timeout
- tool_shed.webapp.model.migrate.versions.0026_add_numeric_revision_column
- 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
- unittest.case