Warning
This document is for an old release 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
- galaxy.actions.library
- galaxy.app
- galaxy.app_unittest_utils.celery_helper
- 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.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.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.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.s3
- galaxy.files.sources.s3fs
- galaxy.files.sources.ssh
- galaxy.files.sources.webdav
- galaxy.files.unittest_utils
- 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.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.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.cloud
- galaxy.managers.cloudauthzs
- 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.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.item_attrs
- galaxy.model.mapping
- galaxy.model.metadata
- galaxy.model.migrate.check
- galaxy.model.migrate.triggers.history_update_time_field
- galaxy.model.migrate.triggers.update_audit_table
- 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.0166_job_state_summary_view
- galaxy.model.migrate.versions.0167_add_job_to_input_dataset_collection_element_association
- galaxy.model.migrate.versions.0168_stored_workflow_hidden_col
- galaxy.model.migrate.versions.0169_add_missing_indexes
- galaxy.model.migrate.versions.0170_add_more_missing_indexes
- galaxy.model.migrate.versions.0171_schemaorg_metadata
- galaxy.model.migrate.versions.0172_it_entrypoint_requires_domain
- galaxy.model.migrate.versions.0173_add_job_id_to_dataset
- galaxy.model.migrate.versions.0174_readd_update_time_triggers
- galaxy.model.migrate.versions.0175_history_audit
- galaxy.model.migrate.versions.0176_add_indexes_on_update_time
- galaxy.model.migrate.versions.0177_update_job_state_summary
- galaxy.model.migrate.versions.0178_drop_deferredjob_table
- galaxy.model.migrate.versions.0179_drop_transferjob_table
- galaxy.model.migrate.versions.0180_add_vault_table
- galaxy.model.migrate.versions.util
- galaxy.model.none_like
- galaxy.model.orm.engine_factory
- galaxy.model.orm.scripts
- galaxy.model.scoped_session
- galaxy.model.search
- galaxy.model.security
- galaxy.model.store
- galaxy.model.tags
- galaxy.model.tool_shed_install
- galaxy.model.tool_shed_install.mapping
- galaxy.model.tool_shed_install.migrate.check
- galaxy.model.tool_shed_install.migrate.versions.0001_add_tool_shed_repository_table
- galaxy.model.tool_shed_install.migrate.versions.0002_add_tool_shed_repository_table_columns
- galaxy.model.tool_shed_install.migrate.versions.0003_tool_id_guid_map_table
- galaxy.model.tool_shed_install.migrate.versions.0004_add_installed_changeset_revison_column
- galaxy.model.tool_shed_install.migrate.versions.0005_add_tool_shed_repository_table_columns
- galaxy.model.tool_shed_install.migrate.versions.0006_add_tool_version_tables
- galaxy.model.tool_shed_install.migrate.versions.0007_add_migrate_tools_table
- galaxy.model.tool_shed_install.migrate.versions.0008_add_ctx_rev_column
- galaxy.model.tool_shed_install.migrate.versions.0009_add_tool_dependency_table
- galaxy.model.tool_shed_install.migrate.versions.0010_alter_tool_dependency_table_version_column
- galaxy.model.tool_shed_install.migrate.versions.0011_drop_installed_changeset_revision_column
- galaxy.model.tool_shed_install.migrate.versions.0012_add_tool_dependency_status_columns
- galaxy.model.tool_shed_install.migrate.versions.0013_add_tool_shed_repository_status_columns
- galaxy.model.tool_shed_install.migrate.versions.0014_add_repository_dependency_tables
- galaxy.model.tool_shed_install.migrate.versions.0015_update_migrate_tools_table
- galaxy.model.tool_shed_install.migrate.versions.0016_update_migrate_tools_table_again
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- tool_shed.test.functional.test_0070_invalid_tool
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- tool_shed.test.functional.test_0150_prior_installation_required
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- tool_shed.test.functional.test_0400_repository_component_reviews
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- 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
- tool_shed.test.functional.test_1210_uninstall_reinstall_repository_with_tool_dependencies
- tool_shed.test.functional.test_1220_uninstall_reinstall_repository_with_repository_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_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.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.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
- tool_shed.webapp.model.migrate.versions.0022_add_repository_admin_roles
- tool_shed.webapp.model.migrate.versions.0023_add_repository_url_and_hompeage_url
- 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