Python Module Index

g | l | m | p | t
 
g
galaxy
    galaxy.actions
    galaxy.actions.admin
    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.config
    galaxy.dataset_collections
    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.dataset_collections.types.list
    galaxy.dataset_collections.types.paired
    galaxy.datatypes
    galaxy.datatypes.assembly
    galaxy.datatypes.binary
    galaxy.datatypes.checkers
    galaxy.datatypes.chrominfo
    galaxy.datatypes.constructive_solid_geometry
    galaxy.datatypes.converters
    galaxy.datatypes.converters.bcf_bgzip_to_bcf_converter
    galaxy.datatypes.converters.bcf_to_bcf_bgzip_converter
    galaxy.datatypes.converters.bed_to_gff_converter
    galaxy.datatypes.converters.bedgraph_to_array_tree_converter
    galaxy.datatypes.converters.bgzip
    galaxy.datatypes.converters.fasta_to_len
    galaxy.datatypes.converters.fasta_to_tabular_converter
    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_bed_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.maf_to_fasta_converter
    galaxy.datatypes.converters.maf_to_interval_converter
    galaxy.datatypes.converters.pbed_ldreduced_converter
    galaxy.datatypes.converters.pbed_to_lped_converter
    galaxy.datatypes.converters.picard_interval_list_to_bed6_converter
    galaxy.datatypes.converters.pileup_to_interval_index_converter
    galaxy.datatypes.converters.sam_to_bam
    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
    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
    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.metadata
    galaxy.datatypes.msa
    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.util
    galaxy.datatypes.util.generic_util
    galaxy.datatypes.util.gff_util
    galaxy.datatypes.xml
    galaxy.dependencies
    galaxy.eggs
    galaxy.exceptions
    galaxy.exceptions.error_codes
    galaxy.external_services
    galaxy.external_services.actions
    galaxy.external_services.parameters
    galaxy.external_services.result_handlers
    galaxy.external_services.result_handlers.basic
    galaxy.external_services.service
    galaxy.forms
    galaxy.forms.forms
    galaxy.jobs
    galaxy.jobs.actions
    galaxy.jobs.actions.post
    galaxy.jobs.command_factory
    galaxy.jobs.datasets
    galaxy.jobs.deferred
    galaxy.jobs.deferred.data_transfer
    galaxy.jobs.deferred.manual_data_transfer
    galaxy.jobs.deferred.pacific_biosciences_smrt_portal
    galaxy.jobs.error_level
    galaxy.jobs.handler
    galaxy.jobs.manager
    galaxy.jobs.mapper
    galaxy.jobs.metrics
    galaxy.jobs.metrics.collectl
    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.metrics.instrumenters.collectl
    galaxy.jobs.metrics.instrumenters.core
    galaxy.jobs.metrics.instrumenters.cpuinfo
    galaxy.jobs.metrics.instrumenters.env
    galaxy.jobs.metrics.instrumenters.meminfo
    galaxy.jobs.metrics.instrumenters.uname
    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.local
    galaxy.jobs.runners.pbs
    galaxy.jobs.runners.pulsar
    galaxy.jobs.runners.slurm
    galaxy.jobs.runners.state_handler_factory
    galaxy.jobs.runners.state_handlers
    galaxy.jobs.runners.state_handlers.resubmit
    galaxy.jobs.runners.tasks
    galaxy.jobs.runners.util
    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.cli.shell.local
    galaxy.jobs.runners.util.cli.shell.rsh
    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.splitters
    galaxy.jobs.splitters.basic
    galaxy.jobs.splitters.multi
    galaxy.jobs.stock_rules
    galaxy.jobs.transfer_manager
    galaxy.main
    galaxy.managers
    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.histories
    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.migrate
    galaxy.model.migrate.check
    galaxy.model.orm
    galaxy.model.orm.engine_factory
    galaxy.model.orm.logging_connection_proxy
    galaxy.model.orm.now
    galaxy.model.orm.scripts
    galaxy.model.search
    galaxy.model.tool_shed_install
    galaxy.model.tool_shed_install.mapping
    galaxy.model.tool_shed_install.migrate
    galaxy.model.tool_shed_install.migrate.check
    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
    galaxy.openid.providers
    galaxy.queue_worker
    galaxy.queues
    galaxy.quota
    galaxy.sample_tracking
    galaxy.sample_tracking.data_transfer
    galaxy.sample_tracking.external_service_types
    galaxy.sample_tracking.request_types
    galaxy.sample_tracking.sample
    galaxy.security
    galaxy.security.passwords
    galaxy.security.validate_user_input
    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.upload
    galaxy.tools.actions.upload_common
    galaxy.tools.data
    galaxy.tools.data_manager
    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.containers
    galaxy.tools.deps.dependencies
    galaxy.tools.deps.docker_util
    galaxy.tools.deps.dockerfiles
    galaxy.tools.deps.requirements
    galaxy.tools.deps.resolvers
    galaxy.tools.deps.resolvers.brewed_tool_shed_packages
    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.errors
    galaxy.tools.evaluation
    galaxy.tools.exception_handling
    galaxy.tools.execute
    galaxy.tools.filters
    galaxy.tools.imp_exp
    galaxy.tools.imp_exp.export_history
    galaxy.tools.imp_exp.unpack_tar_gz_archive
    galaxy.tools.lint
    galaxy.tools.linters
    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
    galaxy.tools.loader_directory
    galaxy.tools.parameters
    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
    galaxy.tools.parser.factory
    galaxy.tools.parser.interface
    galaxy.tools.parser.util
    galaxy.tools.parser.xml
    galaxy.tools.parser.yaml
    galaxy.tools.search
    galaxy.tools.test
    galaxy.tools.toolbox
    galaxy.tools.toolbox.base
    galaxy.tools.toolbox.filters
    galaxy.tools.toolbox.integrated_panel
    galaxy.tools.toolbox.lineages
    galaxy.tools.toolbox.lineages.factory
    galaxy.tools.toolbox.lineages.interface
    galaxy.tools.toolbox.lineages.stock
    galaxy.tools.toolbox.lineages.tool_shed
    galaxy.tools.toolbox.panel
    galaxy.tools.toolbox.tags
    galaxy.tools.toolbox.watcher
    galaxy.tools.util
    galaxy.tools.util.galaxyops
    galaxy.tools.util.maf_utilities
    galaxy.tools.wrappers
    galaxy.util
    galaxy.util.aliaspickler
    galaxy.util.backports
    galaxy.util.biostar
    galaxy.util.bunch
    galaxy.util.checkers
    galaxy.util.dbkeys
    galaxy.util.dictifiable
    galaxy.util.expressions
    galaxy.util.filelock
    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.log
    galaxy.util.log.fluent_log
    galaxy.util.multi_byte
    galaxy.util.none_like
    galaxy.util.object_wrapper
    galaxy.util.odict
    galaxy.util.pastescript
    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.version
    galaxy.visualization
    galaxy.visualization.data_providers
    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.genome
    galaxy.visualization.genomes
    galaxy.visualization.plugins
    galaxy.visualization.plugins.config_parser
    galaxy.visualization.plugins.plugin
    galaxy.visualization.plugins.registry
    galaxy.visualization.plugins.resource_parser
    galaxy.visualization.plugins.utils
    galaxy.visualization.tracks
    galaxy.web
    galaxy.web.base
    galaxy.web.base.controller
    galaxy.web.base.controllers
    galaxy.web.base.controllers.admin
    galaxy.web.base.interactive_environments
    galaxy.web.base.pluginframework
    galaxy.web.buildapp
    galaxy.web.form_builder
    galaxy.web.formatting
    galaxy.web.framework
    galaxy.web.framework.base
    galaxy.web.framework.decorators
    galaxy.web.framework.formbuilder
    galaxy.web.framework.helpers
    galaxy.web.framework.helpers.grids
    galaxy.web.framework.middleware
    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.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.webapps
    galaxy.webapps.galaxy
    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.lda_datasets
    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.request_types
    galaxy.webapps.galaxy.api.requests
    galaxy.webapps.galaxy.api.roles
    galaxy.webapps.galaxy.api.samples
    galaxy.webapps.galaxy.api.search
    galaxy.webapps.galaxy.api.tool_data
    galaxy.webapps.galaxy.api.tool_shed_repositories
    galaxy.webapps.galaxy.api.tools
    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.controllers
    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.external_service
    galaxy.webapps.galaxy.controllers.external_services
    galaxy.webapps.galaxy.controllers.forms
    galaxy.webapps.galaxy.controllers.history
    galaxy.webapps.galaxy.controllers.library
    galaxy.webapps.galaxy.controllers.library_admin
    galaxy.webapps.galaxy.controllers.library_common
    galaxy.webapps.galaxy.controllers.mobile
    galaxy.webapps.galaxy.controllers.page
    galaxy.webapps.galaxy.controllers.request_type
    galaxy.webapps.galaxy.controllers.requests
    galaxy.webapps.galaxy.controllers.requests_admin
    galaxy.webapps.galaxy.controllers.requests_common
    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
    galaxy.webapps.reports.app
    galaxy.webapps.reports.buildapp
    galaxy.webapps.reports.config
    galaxy.webapps.reports.controllers
    galaxy.webapps.reports.controllers.home
    galaxy.webapps.reports.controllers.jobs
    galaxy.webapps.reports.controllers.query
    galaxy.webapps.reports.controllers.root
    galaxy.webapps.reports.controllers.sample_tracking
    galaxy.webapps.reports.controllers.system
    galaxy.webapps.reports.controllers.users
    galaxy.webapps.reports.controllers.workflows
    galaxy.webapps.tool_shed
    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
    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
    galaxy.webapps.tool_shed.framework.middleware
    galaxy.webapps.tool_shed.framework.middleware.remoteuser
    galaxy.webapps.tool_shed.model
    galaxy.webapps.tool_shed.model.mapping
    galaxy.webapps.tool_shed.model.migrate
    galaxy.webapps.tool_shed.model.migrate.check
    galaxy.webapps.tool_shed.search
    galaxy.webapps.tool_shed.search.repo_search
    galaxy.webapps.tool_shed.search.tool_search
    galaxy.webapps.tool_shed.security
    galaxy.webapps.tool_shed.util
    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.work
    galaxy.work.context
    galaxy.workflow
    galaxy.workflow.extract
    galaxy.workflow.modules
    galaxy.workflow.render
    galaxy.workflow.run
    galaxy.workflow.run_request
    galaxy.workflow.schedulers
    galaxy.workflow.schedulers.core
    galaxy.workflow.scheduling_manager
    galaxy.workflow.steps
galaxy_ext
    galaxy_ext.metadata
    galaxy_ext.metadata.set_metadata
 
l
log_tempfile
 
m
mimeparse
 
p
psyco_full
 
t
tool_shed
    tool_shed.capsule
    tool_shed.capsule.capsule_manager
    tool_shed.dependencies
    tool_shed.dependencies.attribute_handlers
    tool_shed.dependencies.repository
    tool_shed.dependencies.repository.relation_builder
    tool_shed.dependencies.tool
    tool_shed.dependencies.tool.tag_attribute_handler
    tool_shed.galaxy_install
    tool_shed.galaxy_install.datatypes
    tool_shed.galaxy_install.datatypes.custom_datatype_manager
    tool_shed.galaxy_install.dependency_display
    tool_shed.galaxy_install.grids
    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
    tool_shed.galaxy_install.metadata.installed_repository_metadata_manager
    tool_shed.galaxy_install.migrate
    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
    tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager
    tool_shed.galaxy_install.tool_dependencies
    tool_shed.galaxy_install.tool_dependencies.env_manager
    tool_shed.galaxy_install.tool_dependencies.recipe
    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
    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
    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
    tool_shed.managers.groups
    tool_shed.managers.repositories
    tool_shed.metadata
    tool_shed.metadata.metadata_generator
    tool_shed.metadata.repository_metadata_manager
    tool_shed.repository_registry
    tool_shed.repository_types
    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
    tool_shed.tools.data_table_manager
    tool_shed.tools.tool_validator
    tool_shed.tools.tool_version_manager
    tool_shed.util
    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
    tool_shed.utility_containers.utility_container_manager