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
- ConfigParser
- __builtin__
- _hashlib
- abc
- csv
- galaxy.actions.admin
- galaxy.app
- galaxy.auth
- galaxy.config
- galaxy.containers
- galaxy.containers.docker
- galaxy.containers.docker_decorators
- galaxy.containers.docker_model
- galaxy.containers.docker_swarm
- galaxy.containers.docker_swarm_manager
- galaxy.dataset_collections.builder
- galaxy.dataset_collections.matching
- galaxy.dataset_collections.registry
- galaxy.dataset_collections.structure
- galaxy.dataset_collections.subcollections
- galaxy.dataset_collections.type_description
- galaxy.dataset_collections.types
- galaxy.datatypes.assembly
- galaxy.datatypes.binary
- galaxy.datatypes.blast
- galaxy.datatypes.chrominfo
- galaxy.datatypes.constructive_solid_geometry
- galaxy.datatypes.converters.bedgraph_to_array_tree_converter
- galaxy.datatypes.converters.bgzip
- 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_coverage
- 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.sam_to_bam
- 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_array_tree_converter
- 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.graph
- galaxy.datatypes.images
- galaxy.datatypes.interval
- galaxy.datatypes.molecules
- galaxy.datatypes.mothur
- galaxy.datatypes.msa
- galaxy.datatypes.neo4j
- galaxy.datatypes.ngsindex
- galaxy.datatypes.proteomics
- galaxy.datatypes.qualityscore
- galaxy.datatypes.registry
- galaxy.datatypes.sequence
- galaxy.datatypes.sniff
- galaxy.datatypes.tabular
- galaxy.datatypes.text
- galaxy.datatypes.tracks
- galaxy.datatypes.triples
- galaxy.datatypes.util.generic_util
- galaxy.datatypes.util.gff_util
- galaxy.datatypes.xml
- galaxy.dependencies
- galaxy.exceptions
- galaxy.forms.forms
- galaxy.jobs
- galaxy.jobs.actions.post
- galaxy.jobs.command_factory
- galaxy.jobs.datasets
- galaxy.jobs.dynamic_tool_destination
- galaxy.jobs.error_level
- galaxy.jobs.handler
- galaxy.jobs.manager
- galaxy.jobs.mapper
- galaxy.jobs.metrics
- galaxy.jobs.metrics.collectl.cli
- galaxy.jobs.metrics.collectl.processes
- galaxy.jobs.metrics.collectl.stats
- galaxy.jobs.metrics.collectl.subsystems
- galaxy.jobs.metrics.formatting
- galaxy.jobs.metrics.instrumenters
- galaxy.jobs.output_checker
- galaxy.jobs.rule_helper
- galaxy.jobs.runners
- 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.util.cli
- galaxy.jobs.runners.util.cli.factory
- galaxy.jobs.runners.util.cli.job
- 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.drmaa
- 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.retry
- 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.collections
- galaxy.managers.collections_util
- galaxy.managers.configuration
- galaxy.managers.containers
- galaxy.managers.context
- galaxy.managers.datasets
- galaxy.managers.deletable
- galaxy.managers.folders
- galaxy.managers.hdas
- galaxy.managers.hdcas
- galaxy.managers.histories
- galaxy.managers.history_contents
- galaxy.managers.lddas
- galaxy.managers.libraries
- galaxy.managers.pages
- galaxy.managers.ratable
- galaxy.managers.rbac_secured
- galaxy.managers.roles
- galaxy.managers.secured
- galaxy.managers.sharable
- galaxy.managers.taggable
- galaxy.managers.tags
- galaxy.managers.users
- galaxy.managers.visualizations
- galaxy.managers.workflows
- galaxy.model
- galaxy.model.base
- galaxy.model.custom_types
- galaxy.model.item_attrs
- galaxy.model.mapping
- galaxy.model.metadata
- galaxy.model.migrate.check
- galaxy.model.orm.engine_factory
- galaxy.model.orm.logging_connection_proxy
- galaxy.model.orm.scripts
- galaxy.model.search
- galaxy.model.tool_shed_install
- galaxy.model.util
- galaxy.objectstore
- galaxy.objectstore.azure_blob
- galaxy.objectstore.pulsar
- galaxy.objectstore.rods
- galaxy.objectstore.s3
- galaxy.objectstore.s3_multipart_upload
- galaxy.openid.providers
- galaxy.queue_worker
- galaxy.queues
- galaxy.quota
- galaxy.security
- 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.cwl.cwltool_deps
- galaxy.tools.cwl.parser
- galaxy.tools.cwl.representation
- galaxy.tools.cwl.runtime_actions
- galaxy.tools.cwl.schema
- galaxy.tools.data
- galaxy.tools.data_manager.manager
- galaxy.tools.deps
- galaxy.tools.deps.brew_exts
- galaxy.tools.deps.brew_util
- galaxy.tools.deps.commands
- galaxy.tools.deps.conda_compat
- galaxy.tools.deps.conda_util
- galaxy.tools.deps.container_resolvers
- galaxy.tools.deps.containers
- galaxy.tools.deps.dependencies
- galaxy.tools.deps.docker_util
- galaxy.tools.deps.dockerfiles
- galaxy.tools.deps.installable
- galaxy.tools.deps.mulled.mulled_build
- galaxy.tools.deps.mulled.mulled_build_channel
- galaxy.tools.deps.mulled.mulled_build_files
- galaxy.tools.deps.mulled.mulled_build_tool
- galaxy.tools.deps.mulled.mulled_search
- galaxy.tools.deps.mulled.util
- galaxy.tools.deps.requirements
- galaxy.tools.deps.resolvers
- galaxy.tools.deps.resolvers.brewed_tool_shed_packages
- galaxy.tools.deps.resolvers.conda
- galaxy.tools.deps.resolvers.galaxy_packages
- galaxy.tools.deps.resolvers.homebrew
- galaxy.tools.deps.resolvers.modules
- galaxy.tools.deps.resolvers.resolver_mixins
- galaxy.tools.deps.resolvers.tool_shed_packages
- galaxy.tools.deps.resolvers.unlinked_tool_shed_packages
- galaxy.tools.deps.views
- galaxy.tools.errors
- galaxy.tools.evaluation
- galaxy.tools.execute
- galaxy.tools.fetcher
- galaxy.tools.imp_exp
- galaxy.tools.lint
- galaxy.tools.lint_util
- galaxy.tools.linters.citations
- galaxy.tools.linters.command
- galaxy.tools.linters.general
- galaxy.tools.linters.help
- galaxy.tools.linters.inputs
- galaxy.tools.linters.outputs
- galaxy.tools.linters.stdio
- galaxy.tools.linters.tests
- galaxy.tools.linters.xml_order
- galaxy.tools.loader_directory
- galaxy.tools.locations
- 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.output_collect
- galaxy.tools.parameters.sanitize
- galaxy.tools.parameters.validation
- galaxy.tools.parameters.wrapped
- galaxy.tools.parameters.wrapped_json
- galaxy.tools.parser.cwl
- galaxy.tools.parser.factory
- galaxy.tools.parser.interface
- galaxy.tools.parser.output_actions
- galaxy.tools.parser.output_collection_def
- galaxy.tools.parser.output_objects
- galaxy.tools.parser.util
- galaxy.tools.parser.xml
- galaxy.tools.parser.yaml
- galaxy.tools.search
- galaxy.tools.special_tools
- galaxy.tools.test
- galaxy.tools.toolbox.base
- galaxy.tools.toolbox.filters
- galaxy.tools.toolbox.integrated_panel
- galaxy.tools.toolbox.lineages.factory
- 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.verify
- galaxy.tools.verify.asserts
- galaxy.tools.verify.asserts.tabular
- galaxy.tools.verify.asserts.text
- galaxy.tools.verify.asserts.xml
- galaxy.tools.verify.test_data
- galaxy.tools.wrappers
- galaxy.tours
- galaxy.util
- galaxy.util.aliaspickler
- galaxy.util.biostar
- galaxy.util.bunch
- galaxy.util.checkers
- galaxy.util.compression_utils
- galaxy.util.dbkeys
- galaxy.util.dictifiable
- galaxy.util.expressions
- galaxy.util.filelock
- galaxy.util.handlers
- 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.none_like
- galaxy.util.object_wrapper
- galaxy.util.odict
- galaxy.util.oset
- galaxy.util.pastescript.loadwsgi
- galaxy.util.pastescript.serve
- galaxy.util.permutations
- galaxy.util.plugin_config
- galaxy.util.properties
- galaxy.util.sanitize_html
- 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.topsort
- galaxy.util.ucsc
- galaxy.util.validation
- galaxy.util.xml_macros
- 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.base.controller
- galaxy.web.form_builder
- 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.graphite
- 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.static
- galaxy.web.framework.middleware.statsd
- galaxy.web.framework.middleware.translogger
- galaxy.web.framework.middleware.xforwardedhost
- galaxy.web.framework.openid_manager
- galaxy.web.framework.webapp
- galaxy.web.params
- galaxy.web.proxy
- galaxy.web.security
- galaxy.web.stack
- galaxy.webapps.galaxy.api.annotations
- galaxy.webapps.galaxy.api.authenticate
- galaxy.webapps.galaxy.api.configuration
- galaxy.webapps.galaxy.api.dataset_collections
- galaxy.webapps.galaxy.api.datasets
- galaxy.webapps.galaxy.api.datatypes
- 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.jobs
- galaxy.webapps.galaxy.api.libraries
- galaxy.webapps.galaxy.api.library_contents
- galaxy.webapps.galaxy.api.metrics
- galaxy.webapps.galaxy.api.page_revisions
- galaxy.webapps.galaxy.api.pages
- 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.tool_data
- galaxy.webapps.galaxy.api.tool_dependencies
- 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.users
- galaxy.webapps.galaxy.api.visualizations
- galaxy.webapps.galaxy.api.webhooks
- galaxy.webapps.galaxy.api.workflows
- galaxy.webapps.galaxy.buildapp
- galaxy.webapps.galaxy.config_watchers
- galaxy.webapps.galaxy.controllers.admin
- galaxy.webapps.galaxy.controllers.admin_toolshed
- galaxy.webapps.galaxy.controllers.async
- galaxy.webapps.galaxy.controllers.biostar
- 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.interactive_environments
- galaxy.webapps.galaxy.controllers.library
- galaxy.webapps.galaxy.controllers.page
- galaxy.webapps.galaxy.controllers.root
- galaxy.webapps.galaxy.controllers.tag
- galaxy.webapps.galaxy.controllers.tool_runner
- galaxy.webapps.galaxy.controllers.user
- galaxy.webapps.galaxy.controllers.userskeys
- galaxy.webapps.galaxy.controllers.visualization
- galaxy.webapps.galaxy.controllers.workflow
- 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.framework.grids
- galaxy.webapps.tool_shed.api.authenticate
- galaxy.webapps.tool_shed.api.categories
- galaxy.webapps.tool_shed.api.configuration
- galaxy.webapps.tool_shed.api.groups
- galaxy.webapps.tool_shed.api.repositories
- galaxy.webapps.tool_shed.api.repository_revisions
- galaxy.webapps.tool_shed.api.tools
- galaxy.webapps.tool_shed.api.users
- galaxy.webapps.tool_shed.app
- galaxy.webapps.tool_shed.buildapp
- galaxy.webapps.tool_shed.config
- galaxy.webapps.tool_shed.controllers.admin
- galaxy.webapps.tool_shed.controllers.groups
- galaxy.webapps.tool_shed.controllers.hg
- galaxy.webapps.tool_shed.controllers.repository
- galaxy.webapps.tool_shed.controllers.repository_review
- galaxy.webapps.tool_shed.controllers.upload
- galaxy.webapps.tool_shed.controllers.user
- galaxy.webapps.tool_shed.framework.middleware.remoteuser
- galaxy.webapps.tool_shed.model
- galaxy.webapps.tool_shed.search.repo_search
- galaxy.webapps.tool_shed.search.tool_search
- galaxy.webapps.tool_shed.security
- galaxy.webapps.tool_shed.util.hgweb_config
- galaxy.webapps.tool_shed.util.ratings_util
- galaxy.webapps.tool_shed.util.shed_statistics
- galaxy.webapps.util
- galaxy.webhooks
- galaxy.work.context
- galaxy.workflow.extract
- galaxy.workflow.modules
- galaxy.workflow.render
- galaxy.workflow.run
- galaxy.workflow.run_request
- galaxy.workflow.schedulers
- galaxy.workflow.scheduling_manager
- galaxy.workflow.steps
- galaxy_ext.metadata.set_metadata
- log_tempfile
- mimeparse
- routes.util
- sqlalchemy.orm.attributes
- sqlalchemy.sql.elements
- sqlalchemy.sql.schema
- sqlalchemy.sql.sqltypes
- tool_shed.capsule.capsule_manager
- tool_shed.dependencies.attribute_handlers
- tool_shed.dependencies.repository.relation_builder
- tool_shed.dependencies.tool.tag_attribute_handler
- tool_shed.galaxy_install.datatypes.custom_datatype_manager
- tool_shed.galaxy_install.dependency_display
- tool_shed.galaxy_install.grids.admin_toolshed_grids
- tool_shed.galaxy_install.install_manager
- tool_shed.galaxy_install.installed_repository_manager
- tool_shed.galaxy_install.metadata.installed_repository_metadata_manager
- tool_shed.galaxy_install.migrate.check
- tool_shed.galaxy_install.migrate.common
- tool_shed.galaxy_install.repair_repository_manager
- tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager
- tool_shed.galaxy_install.tool_dependencies.env_manager
- tool_shed.galaxy_install.tool_dependencies.recipe.asynchronous_reader
- tool_shed.galaxy_install.tool_dependencies.recipe.env_file_builder
- tool_shed.galaxy_install.tool_dependencies.recipe.install_environment
- tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager
- tool_shed.galaxy_install.tool_dependencies.recipe.step_handler
- tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler
- tool_shed.galaxy_install.tool_migration_manager
- tool_shed.galaxy_install.tools.data_manager
- tool_shed.galaxy_install.tools.tool_panel_manager
- tool_shed.galaxy_install.update_repository_manager
- tool_shed.galaxy_install.utility_containers
- tool_shed.grids.admin_grids
- 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.metadata_generator
- 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.tool_shed_registry
- tool_shed.tools.data_table_manager
- tool_shed.tools.tool_validator
- tool_shed.tools.tool_version_manager
- tool_shed.util.basic_util
- tool_shed.util.commit_util
- tool_shed.util.common_util
- tool_shed.util.container_util
- tool_shed.util.encoding_util
- tool_shed.util.hg_util
- 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_util_common
- tool_shed.util.tool_dependency_util
- tool_shed.util.tool_util
- tool_shed.util.web_util
- tool_shed.util.workflow_util
- tool_shed.util.xml_util
- tool_shed.utility_containers