All modules for which code is available
- __builtin__
- galaxy
- galaxy.actions.admin
- galaxy.config
- galaxy.datatypes.assembly
- galaxy.datatypes.binary
- galaxy.datatypes.checkers
- galaxy.datatypes.chrominfo
- 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.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.display_applications.application
- galaxy.datatypes.display_applications.parameters
- galaxy.datatypes.display_applications.util
- galaxy.datatypes.genetics
- galaxy.datatypes.images
- galaxy.datatypes.interval
- galaxy.datatypes.metadata
- galaxy.datatypes.ngsindex
- galaxy.datatypes.qualityscore
- galaxy.datatypes.registry
- galaxy.datatypes.sequence
- galaxy.datatypes.sniff
- galaxy.datatypes.tabular
- galaxy.datatypes.tracks
- galaxy.datatypes.util.gff_util
- galaxy.datatypes.util.image_util
- galaxy.datatypes.xml
- galaxy.eggs
- galaxy.exceptions
- galaxy.external_services.actions
- galaxy.external_services.parameters
- galaxy.external_services.result_handlers.basic
- galaxy.external_services.service
- galaxy.forms.forms
- galaxy.jobs
- galaxy.jobs.actions.post
- galaxy.jobs.deferred
- galaxy.jobs.deferred.data_transfer
- galaxy.jobs.deferred.manual_data_transfer
- galaxy.jobs.deferred.pacific_biosciences_smrt_portal
- galaxy.jobs.handler
- galaxy.jobs.manager
- galaxy.jobs.mapper
- galaxy.jobs.runners
- galaxy.jobs.runners.cli
- galaxy.jobs.runners.condor
- galaxy.jobs.runners.drmaa
- galaxy.jobs.runners.local
- galaxy.jobs.runners.lwr
- galaxy.jobs.runners.tasks
- galaxy.jobs.splitters.basic
- galaxy.jobs.splitters.multi
- galaxy.jobs.transfer_manager
- galaxy.managers.api_keys
- galaxy.managers.base
- galaxy.managers.citations
- galaxy.managers.collections
- galaxy.managers.collections_util
- galaxy.managers.context
- galaxy.managers.folders
- galaxy.managers.hdas
- galaxy.managers.histories
- galaxy.managers.lddas
- galaxy.managers.libraries
- galaxy.managers.roles
- galaxy.managers.tags
- galaxy.managers.workflows
- galaxy.model
- galaxy.model.custom_types
- galaxy.model.item_attrs
- galaxy.model.mapping
- galaxy.model.migrate.check
- galaxy.model.orm
- galaxy.model.tool_shed_install
- galaxy.objectstore
- galaxy.openid.providers
- galaxy.quota
- galaxy.sample_tracking.data_transfer
- galaxy.sample_tracking.external_service_types
- galaxy.sample_tracking.request_types
- galaxy.sample_tracking.sample
- 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.upload
- galaxy.tools.actions.upload_common
- galaxy.tools.data
- galaxy.tools.deps
- galaxy.tools.exception_handling
- galaxy.tools.imp_exp
- galaxy.tools.parameters
- galaxy.tools.parameters.basic
- galaxy.tools.parameters.dynamic_options
- galaxy.tools.parameters.grouping
- galaxy.tools.parameters.input_translation
- galaxy.tools.parameters.output
- galaxy.tools.parameters.sanitize
- galaxy.tools.parameters.validation
- galaxy.tools.search
- galaxy.tools.test
- galaxy.tools.util.galaxyops
- galaxy.tools.util.maf_utilities
- galaxy.util
- galaxy.util.aliaspickler
- galaxy.util.backports.importlib
- galaxy.util.bunch
- galaxy.util.debugging
- galaxy.util.expressions
- galaxy.util.hash_util
- galaxy.util.heartbeat
- galaxy.util.inflection
- galaxy.util.json
- galaxy.util.lrucache
- galaxy.util.none_like
- galaxy.util.odict
- galaxy.util.sanitize_html
- galaxy.util.streamball
- galaxy.util.template
- galaxy.util.topsort
- galaxy.visualization.data_providers.basic
- 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.genomes
- galaxy.web.base.controller
- galaxy.web.base.controllers.admin
- galaxy.web.form_builder
- galaxy.web.framework.base
- galaxy.web.framework.helpers
- galaxy.web.framework.middleware.profile
- galaxy.web.framework.middleware.remoteuser
- galaxy.web.framework.middleware.static
- galaxy.web.framework.middleware.translogger
- galaxy.web.framework.middleware.xforwardedhost
- galaxy.web.framework.openid_manager
- galaxy.web.params
- galaxy.web.security
- 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.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.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.users
- galaxy.webapps.galaxy.api.visualizations
- galaxy.webapps.galaxy.api.workflows
- galaxy.webapps.galaxy.controllers.admin
- galaxy.webapps.galaxy.controllers.admin_toolshed
- galaxy.webapps.galaxy.controllers.async
- 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.ucsc_proxy
- galaxy.webapps.galaxy.controllers.user
- galaxy.webapps.galaxy.controllers.workflow
- galaxy.webapps.reports.app
- galaxy.webapps.reports.buildapp
- galaxy.webapps.reports.config
- galaxy.webapps.reports.controllers.jobs
- 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.api.repositories
- galaxy.webapps.tool_shed.api.repository_revisions
- 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.hg
- galaxy.webapps.tool_shed.controllers.repository
- galaxy.webapps.tool_shed.controllers.repository_review
- galaxy.webapps.tool_shed.controllers.upload
- galaxy.webapps.tool_shed.framework.middleware.hg
- galaxy.webapps.tool_shed.framework.middleware.remoteuser
- galaxy.webapps.tool_shed.model
- galaxy.webapps.tool_shed.security
- galaxy.webapps.tool_shed.util.hgweb_config
- galaxy.webapps.tool_shed.util.shed_statistics
- galaxy.workflow.modules
- galaxy_utils.sequence.fasta
- galaxy_utils.sequence.fastq
- galaxy_utils.sequence.sequence
- galaxy_utils.sequence.transform
- galaxy_utils.sequence.vcf
- json
- log_tempfile
- mimeparse
- pkg_resources
- pkgutil
- routes.util
- sqlalchemy.orm.attributes
- sqlalchemy.sql.schema
- sqlalchemy.sql.sqltypes
- tool_shed.galaxy_install.grids.admin_toolshed_grids
- tool_shed.galaxy_install.install_manager
- tool_shed.galaxy_install.migrate.check
- tool_shed.galaxy_install.migrate.common
- tool_shed.grids.admin_grids
- tool_shed.grids.repository_grids
- tool_shed.grids.repository_review_grids
- tool_shed.grids.util
- tool_shed.tool_shed_registry
- tool_shed.util.common_util
- tool_shed.util.encoding_util
- tool_shed.util.metadata_util
- tool_shed.util.readme_util
- tool_shed.util.review_util
- tool_shed.util.shed_util_common
- tool_shed.util.tool_dependency_util
- tool_shed.util.tool_util
- tool_shed.util.workflow_util