diff --git a/doc/source/index.rst b/doc/source/index.rst index 18cc1161af3..79dab7fc19b 100644 --- a/doc/source/index.rst +++ b/doc/source/index.rst @@ -3,22 +3,19 @@ Galaxy Documentation Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biomedical research. - - Accessible: Users without programming experience can easily specify - parameters and run tools and workflows. - - Reproducible: Galaxy captures information so that any user can repeat and - understand a complete computational analysis. - - Transparent: Users share and publish analyses via the web and create - Pages, interactive, web-based documents that describe a complete - analysis. + +- Accessible: Users without programming experience can easily specify parameters and run tools and workflows. +- Reproducible: Galaxy captures information so that any user can repeat and understand a complete computational analysis. +- Transparent: Users share and publish analyses via the web and create Pages, interactive, web-based documents that describe a complete analysis. Contents ======== .. toctree:: - :maxdepth: 4 + :maxdepth: 5 - API Documentation + API Documentation - Application Documentation + Application Documentation Indices and tables ================== diff --git a/doc/source/lib/galaxy.datatypes.converters.rst b/doc/source/lib/galaxy.datatypes.converters.rst index 41e39136305..99565bdfd81 100644 --- a/doc/source/lib/galaxy.datatypes.converters.rst +++ b/doc/source/lib/galaxy.datatypes.converters.rst @@ -113,6 +113,14 @@ converters Package :undoc-members: :show-inheritance: +:mod:`interval_to_fli` Module +----------------------------- + +.. automodule:: galaxy.datatypes.converters.interval_to_fli + :members: + :undoc-members: + :show-inheritance: + :mod:`interval_to_interval_index_converter` Module -------------------------------------------------- diff --git a/doc/source/lib/galaxy.jobs.deferred.rst b/doc/source/lib/galaxy.jobs.deferred.rst index 7a244db4de0..19b967685c0 100644 --- a/doc/source/lib/galaxy.jobs.deferred.rst +++ b/doc/source/lib/galaxy.jobs.deferred.rst @@ -17,6 +17,14 @@ deferred Package :undoc-members: :show-inheritance: +:mod:`genome_index` Module +-------------------------- + +.. automodule:: galaxy.jobs.deferred.genome_index + :members: + :undoc-members: + :show-inheritance: + :mod:`genome_transfer` Module ----------------------------- diff --git a/doc/source/lib/galaxy.jobs.rst b/doc/source/lib/galaxy.jobs.rst index 6d912585aa9..587dff8f124 100644 --- a/doc/source/lib/galaxy.jobs.rst +++ b/doc/source/lib/galaxy.jobs.rst @@ -25,6 +25,14 @@ jobs Package :undoc-members: :show-inheritance: +:mod:`mapper` Module +-------------------- + +.. automodule:: galaxy.jobs.mapper + :members: + :undoc-members: + :show-inheritance: + :mod:`transfer_manager` Module ------------------------------ @@ -40,6 +48,7 @@ Subpackages galaxy.jobs.actions galaxy.jobs.deferred + galaxy.jobs.rules galaxy.jobs.runners galaxy.jobs.splitters diff --git a/doc/source/lib/galaxy.jobs.runners.cli_job.rst b/doc/source/lib/galaxy.jobs.runners.cli_job.rst new file mode 100644 index 00000000000..b373a06ae3c --- /dev/null +++ b/doc/source/lib/galaxy.jobs.runners.cli_job.rst @@ -0,0 +1,19 @@ +cli_job Package +=============== + +:mod:`cli_job` Package +---------------------- + +.. automodule:: galaxy.jobs.runners.cli_job + :members: + :undoc-members: + :show-inheritance: + +:mod:`torque` Module +-------------------- + +.. automodule:: galaxy.jobs.runners.cli_job.torque + :members: + :undoc-members: + :show-inheritance: + diff --git a/doc/source/lib/galaxy.jobs.runners.cli_shell.rst b/doc/source/lib/galaxy.jobs.runners.cli_shell.rst new file mode 100644 index 00000000000..9b96bbcfc52 --- /dev/null +++ b/doc/source/lib/galaxy.jobs.runners.cli_shell.rst @@ -0,0 +1,19 @@ +cli_shell Package +================= + +:mod:`cli_shell` Package +------------------------ + +.. automodule:: galaxy.jobs.runners.cli_shell + :members: + :undoc-members: + :show-inheritance: + +:mod:`rsh` Module +----------------- + +.. automodule:: galaxy.jobs.runners.cli_shell.rsh + :members: + :undoc-members: + :show-inheritance: + diff --git a/doc/source/lib/galaxy.jobs.runners.rst b/doc/source/lib/galaxy.jobs.runners.rst index 0fa705ffff1..31e2f7882be 100644 --- a/doc/source/lib/galaxy.jobs.runners.rst +++ b/doc/source/lib/galaxy.jobs.runners.rst @@ -9,6 +9,22 @@ runners Package :undoc-members: :show-inheritance: +:mod:`cli` Module +----------------- + +.. automodule:: galaxy.jobs.runners.cli + :members: + :undoc-members: + :show-inheritance: + +:mod:`condor` Module +-------------------- + +.. automodule:: galaxy.jobs.runners.condor + :members: + :undoc-members: + :show-inheritance: + :mod:`drmaa` Module ------------------- @@ -57,3 +73,11 @@ runners Package :undoc-members: :show-inheritance: +Subpackages +----------- + +.. toctree:: + + galaxy.jobs.runners.cli_job + galaxy.jobs.runners.cli_shell + diff --git a/doc/source/lib/galaxy.util.backports.importlib.rst b/doc/source/lib/galaxy.util.backports.importlib.rst new file mode 100644 index 00000000000..765830ac0bc --- /dev/null +++ b/doc/source/lib/galaxy.util.backports.importlib.rst @@ -0,0 +1,11 @@ +importlib Package +================= + +:mod:`importlib` Package +------------------------ + +.. automodule:: galaxy.util.backports.importlib + :members: + :undoc-members: + :show-inheritance: + diff --git a/doc/source/lib/galaxy.util.backports.rst b/doc/source/lib/galaxy.util.backports.rst new file mode 100644 index 00000000000..ead946d6eca --- /dev/null +++ b/doc/source/lib/galaxy.util.backports.rst @@ -0,0 +1,18 @@ +backports Package +================= + +:mod:`backports` Package +------------------------ + +.. automodule:: galaxy.util.backports + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + + galaxy.util.backports.importlib + diff --git a/doc/source/lib/galaxy.util.rst b/doc/source/lib/galaxy.util.rst index 20abe1f4d6b..47e473824eb 100644 --- a/doc/source/lib/galaxy.util.rst +++ b/doc/source/lib/galaxy.util.rst @@ -137,3 +137,10 @@ util Package :undoc-members: :show-inheritance: +Subpackages +----------- + +.. toctree:: + + galaxy.util.backports + diff --git a/doc/source/lib/galaxy.visualization.data_providers.phyloviz.rst b/doc/source/lib/galaxy.visualization.data_providers.phyloviz.rst new file mode 100644 index 00000000000..7d51bfb4f84 --- /dev/null +++ b/doc/source/lib/galaxy.visualization.data_providers.phyloviz.rst @@ -0,0 +1,43 @@ +phyloviz Package +================ + +:mod:`phyloviz` Package +----------------------- + +.. automodule:: galaxy.visualization.data_providers.phyloviz + :members: + :undoc-members: + :show-inheritance: + +:mod:`baseparser` Module +------------------------ + +.. automodule:: galaxy.visualization.data_providers.phyloviz.baseparser + :members: + :undoc-members: + :show-inheritance: + +:mod:`newickparser` Module +-------------------------- + +.. automodule:: galaxy.visualization.data_providers.phyloviz.newickparser + :members: + :undoc-members: + :show-inheritance: + +:mod:`nexusparser` Module +------------------------- + +.. automodule:: galaxy.visualization.data_providers.phyloviz.nexusparser + :members: + :undoc-members: + :show-inheritance: + +:mod:`phyloxmlparser` Module +---------------------------- + +.. automodule:: galaxy.visualization.data_providers.phyloviz.phyloxmlparser + :members: + :undoc-members: + :show-inheritance: + diff --git a/doc/source/lib/galaxy.visualization.data_providers.rst b/doc/source/lib/galaxy.visualization.data_providers.rst new file mode 100644 index 00000000000..a7561325011 --- /dev/null +++ b/doc/source/lib/galaxy.visualization.data_providers.rst @@ -0,0 +1,42 @@ +data_providers Package +====================== + +:mod:`data_providers` Package +----------------------------- + +.. automodule:: galaxy.visualization.data_providers + :members: + :undoc-members: + :show-inheritance: + +:mod:`basic` Module +------------------- + +.. automodule:: galaxy.visualization.data_providers.basic + :members: + :undoc-members: + :show-inheritance: + +:mod:`genome` Module +-------------------- + +.. automodule:: galaxy.visualization.data_providers.genome + :members: + :undoc-members: + :show-inheritance: + +:mod:`registry` Module +---------------------- + +.. automodule:: galaxy.visualization.data_providers.registry + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + + galaxy.visualization.data_providers.phyloviz + diff --git a/doc/source/lib/galaxy.visualization.genome.rst b/doc/source/lib/galaxy.visualization.genome.rst new file mode 100644 index 00000000000..1605b712107 --- /dev/null +++ b/doc/source/lib/galaxy.visualization.genome.rst @@ -0,0 +1,19 @@ +genome Package +============== + +:mod:`genome` Package +--------------------- + +.. automodule:: galaxy.visualization.genome + :members: + :undoc-members: + :show-inheritance: + +:mod:`visual_analytics` Module +------------------------------ + +.. automodule:: galaxy.visualization.genome.visual_analytics + :members: + :undoc-members: + :show-inheritance: + diff --git a/doc/source/lib/galaxy.visualization.rst b/doc/source/lib/galaxy.visualization.rst index 2de42629f1b..3d85a78ba4e 100644 --- a/doc/source/lib/galaxy.visualization.rst +++ b/doc/source/lib/galaxy.visualization.rst @@ -22,5 +22,7 @@ Subpackages .. toctree:: + galaxy.visualization.data_providers + galaxy.visualization.genome galaxy.visualization.tracks diff --git a/doc/source/lib/galaxy.visualization.tracks.rst b/doc/source/lib/galaxy.visualization.tracks.rst index 232cdb2903f..8242d51dff2 100644 --- a/doc/source/lib/galaxy.visualization.tracks.rst +++ b/doc/source/lib/galaxy.visualization.tracks.rst @@ -9,14 +9,6 @@ tracks Package :undoc-members: :show-inheritance: -:mod:`data_providers` Module ----------------------------- - -.. automodule:: galaxy.visualization.tracks.data_providers - :members: - :undoc-members: - :show-inheritance: - :mod:`summary` Module --------------------- @@ -25,11 +17,3 @@ tracks Package :undoc-members: :show-inheritance: -:mod:`visual_analytics` Module ------------------------------- - -.. automodule:: galaxy.visualization.tracks.visual_analytics - :members: - :undoc-members: - :show-inheritance: - diff --git a/doc/source/lib/galaxy.web.base.controllers.rst b/doc/source/lib/galaxy.web.base.controllers.rst new file mode 100644 index 00000000000..a37900b0aa5 --- /dev/null +++ b/doc/source/lib/galaxy.web.base.controllers.rst @@ -0,0 +1,11 @@ +controllers Package +=================== + +:mod:`admin` Module +------------------- + +.. automodule:: galaxy.web.base.controllers.admin + :members: + :undoc-members: + :show-inheritance: + diff --git a/doc/source/lib/galaxy.web.base.rst b/doc/source/lib/galaxy.web.base.rst index 4a54561dc91..3f1078c6b3a 100644 --- a/doc/source/lib/galaxy.web.base.rst +++ b/doc/source/lib/galaxy.web.base.rst @@ -9,3 +9,10 @@ base Package :undoc-members: :show-inheritance: +Subpackages +----------- + +.. toctree:: + + galaxy.web.base.controllers + diff --git a/doc/source/lib/galaxy.web.rst b/doc/source/lib/galaxy.web.rst index 5d0d5428e7a..c929ad6a40e 100644 --- a/doc/source/lib/galaxy.web.rst +++ b/doc/source/lib/galaxy.web.rst @@ -38,9 +38,7 @@ Subpackages .. toctree:: - galaxy.web.api galaxy.web.base - galaxy.web.controllers galaxy.web.framework galaxy.web.security diff --git a/doc/source/lib/galaxy.webapps.community.controllers.rst b/doc/source/lib/galaxy.webapps.community.controllers.rst index 244b3b84186..848ae12f98e 100644 --- a/doc/source/lib/galaxy.webapps.community.controllers.rst +++ b/doc/source/lib/galaxy.webapps.community.controllers.rst @@ -41,6 +41,14 @@ controllers Package :undoc-members: :show-inheritance: +:mod:`repository_review` Module +------------------------------- + +.. automodule:: galaxy.webapps.community.controllers.repository_review + :members: + :undoc-members: + :show-inheritance: + :mod:`upload` Module -------------------- @@ -49,6 +57,14 @@ controllers Package :undoc-members: :show-inheritance: +:mod:`user` Module +------------------ + +.. automodule:: galaxy.webapps.community.controllers.user + :members: + :undoc-members: + :show-inheritance: + :mod:`workflow` Module ---------------------- diff --git a/doc/source/lib/galaxy.webapps.community.framework.middleware.rst b/doc/source/lib/galaxy.webapps.community.framework.middleware.rst index e1cd48898c2..5bb9965acf6 100644 --- a/doc/source/lib/galaxy.webapps.community.framework.middleware.rst +++ b/doc/source/lib/galaxy.webapps.community.framework.middleware.rst @@ -17,3 +17,11 @@ middleware Package :undoc-members: :show-inheritance: +:mod:`remoteuser` Module +------------------------ + +.. automodule:: galaxy.webapps.community.framework.middleware.remoteuser + :members: + :undoc-members: + :show-inheritance: + diff --git a/doc/source/lib/galaxy.web.api.rst b/doc/source/lib/galaxy.webapps.galaxy.api.rst similarity index 85% rename from doc/source/lib/galaxy.web.api.rst rename to doc/source/lib/galaxy.webapps.galaxy.api.rst index 8294518db0d..a55878f8adb 100644 --- a/doc/source/lib/galaxy.web.api.rst +++ b/doc/source/lib/galaxy.webapps.galaxy.api.rst @@ -216,7 +216,23 @@ API Controllers :mod:`datasets` Module ---------------------- -.. automodule:: galaxy.web.api.datasets +.. automodule:: galaxy.webapps.galaxy.api.datasets + :members: + :undoc-members: + :show-inheritance: + +:mod:`folder_contents` Module +----------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.folder_contents + :members: + :undoc-members: + :show-inheritance: + +:mod:`folders` Module +--------------------- + +.. automodule:: galaxy.webapps.galaxy.api.folders :members: :undoc-members: :show-inheritance: @@ -224,7 +240,7 @@ API Controllers :mod:`forms` Module ------------------- -.. automodule:: galaxy.web.api.forms +.. automodule:: galaxy.webapps.galaxy.api.forms :members: :undoc-members: :show-inheritance: @@ -232,7 +248,31 @@ API Controllers :mod:`genomes` Module --------------------- -.. automodule:: galaxy.web.api.genomes +.. automodule:: galaxy.webapps.galaxy.api.genomes + :members: + :undoc-members: + :show-inheritance: + +:mod:`group_roles` Module +------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.group_roles + :members: + :undoc-members: + :show-inheritance: + +:mod:`group_users` Module +------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.group_users + :members: + :undoc-members: + :show-inheritance: + +:mod:`groups` Module +-------------------- + +.. automodule:: galaxy.webapps.galaxy.api.groups :members: :undoc-members: :show-inheritance: @@ -240,7 +280,7 @@ API Controllers :mod:`histories` Module ----------------------- -.. automodule:: galaxy.web.api.histories +.. automodule:: galaxy.webapps.galaxy.api.histories :members: :undoc-members: :show-inheritance: @@ -248,7 +288,7 @@ API Controllers :mod:`history_contents` Module ------------------------------ -.. automodule:: galaxy.web.api.history_contents +.. automodule:: galaxy.webapps.galaxy.api.history_contents :members: :undoc-members: :show-inheritance: @@ -256,7 +296,7 @@ API Controllers :mod:`libraries` Module ----------------------- -.. automodule:: galaxy.web.api.libraries +.. automodule:: galaxy.webapps.galaxy.api.libraries :members: :undoc-members: :show-inheritance: @@ -264,7 +304,7 @@ API Controllers :mod:`library_contents` Module ------------------------------ -.. automodule:: galaxy.web.api.library_contents +.. automodule:: galaxy.webapps.galaxy.api.library_contents :members: :undoc-members: :show-inheritance: @@ -272,7 +312,7 @@ API Controllers :mod:`permissions` Module ------------------------- -.. automodule:: galaxy.web.api.permissions +.. automodule:: galaxy.webapps.galaxy.api.permissions :members: :undoc-members: :show-inheritance: @@ -280,7 +320,7 @@ API Controllers :mod:`quotas` Module -------------------- -.. automodule:: galaxy.web.api.quotas +.. automodule:: galaxy.webapps.galaxy.api.quotas :members: :undoc-members: :show-inheritance: @@ -288,7 +328,7 @@ API Controllers :mod:`request_types` Module --------------------------- -.. automodule:: galaxy.web.api.request_types +.. automodule:: galaxy.webapps.galaxy.api.request_types :members: :undoc-members: :show-inheritance: @@ -296,7 +336,7 @@ API Controllers :mod:`requests` Module ---------------------- -.. automodule:: galaxy.web.api.requests +.. automodule:: galaxy.webapps.galaxy.api.requests :members: :undoc-members: :show-inheritance: @@ -304,7 +344,7 @@ API Controllers :mod:`roles` Module ------------------- -.. automodule:: galaxy.web.api.roles +.. automodule:: galaxy.webapps.galaxy.api.roles :members: :undoc-members: :show-inheritance: @@ -312,7 +352,7 @@ API Controllers :mod:`samples` Module --------------------- -.. automodule:: galaxy.web.api.samples +.. automodule:: galaxy.webapps.galaxy.api.samples :members: :undoc-members: :show-inheritance: @@ -320,7 +360,7 @@ API Controllers :mod:`tools` Module ------------------- -.. automodule:: galaxy.web.api.tools +.. automodule:: galaxy.webapps.galaxy.api.tools :members: :undoc-members: :show-inheritance: @@ -328,7 +368,7 @@ API Controllers :mod:`users` Module ------------------- -.. automodule:: galaxy.web.api.users +.. automodule:: galaxy.webapps.galaxy.api.users :members: :undoc-members: :show-inheritance: @@ -336,7 +376,7 @@ API Controllers :mod:`visualizations` Module ---------------------------- -.. automodule:: galaxy.web.api.visualizations +.. automodule:: galaxy.webapps.galaxy.api.visualizations :members: :undoc-members: :show-inheritance: @@ -344,9 +384,8 @@ API Controllers :mod:`workflows` Module ----------------------- -.. automodule:: galaxy.web.api.workflows +.. automodule:: galaxy.webapps.galaxy.api.workflows :members: :undoc-members: :show-inheritance: - diff --git a/doc/source/lib/galaxy.webapps.galaxy.api.rst~ b/doc/source/lib/galaxy.webapps.galaxy.api.rst~ new file mode 100644 index 00000000000..3f6f5a1c5d5 --- /dev/null +++ b/doc/source/lib/galaxy.webapps.galaxy.api.rst~ @@ -0,0 +1,179 @@ +api Package +=========== + +:mod:`datasets` Module +---------------------- + +.. automodule:: galaxy.webapps.galaxy.api.datasets + :members: + :undoc-members: + :show-inheritance: + +:mod:`folder_contents` Module +----------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.folder_contents + :members: + :undoc-members: + :show-inheritance: + +:mod:`folders` Module +--------------------- + +.. automodule:: galaxy.webapps.galaxy.api.folders + :members: + :undoc-members: + :show-inheritance: + +:mod:`forms` Module +------------------- + +.. automodule:: galaxy.webapps.galaxy.api.forms + :members: + :undoc-members: + :show-inheritance: + +:mod:`genomes` Module +--------------------- + +.. automodule:: galaxy.webapps.galaxy.api.genomes + :members: + :undoc-members: + :show-inheritance: + +:mod:`group_roles` Module +------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.group_roles + :members: + :undoc-members: + :show-inheritance: + +:mod:`group_users` Module +------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.group_users + :members: + :undoc-members: + :show-inheritance: + +:mod:`groups` Module +-------------------- + +.. automodule:: galaxy.webapps.galaxy.api.groups + :members: + :undoc-members: + :show-inheritance: + +:mod:`histories` Module +----------------------- + +.. automodule:: galaxy.webapps.galaxy.api.histories + :members: + :undoc-members: + :show-inheritance: + +:mod:`history_contents` Module +------------------------------ + +.. automodule:: galaxy.webapps.galaxy.api.history_contents + :members: + :undoc-members: + :show-inheritance: + +:mod:`libraries` Module +----------------------- + +.. automodule:: galaxy.webapps.galaxy.api.libraries + :members: + :undoc-members: + :show-inheritance: + +:mod:`library_contents` Module +------------------------------ + +.. automodule:: galaxy.webapps.galaxy.api.library_contents + :members: + :undoc-members: + :show-inheritance: + +:mod:`permissions` Module +------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.permissions + :members: + :undoc-members: + :show-inheritance: + +:mod:`quotas` Module +-------------------- + +.. automodule:: galaxy.webapps.galaxy.api.quotas + :members: + :undoc-members: + :show-inheritance: + +:mod:`request_types` Module +--------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.request_types + :members: + :undoc-members: + :show-inheritance: + +:mod:`requests` Module +---------------------- + +.. automodule:: galaxy.webapps.galaxy.api.requests + :members: + :undoc-members: + :show-inheritance: + +:mod:`roles` Module +------------------- + +.. automodule:: galaxy.webapps.galaxy.api.roles + :members: + :undoc-members: + :show-inheritance: + +:mod:`samples` Module +--------------------- + +.. automodule:: galaxy.webapps.galaxy.api.samples + :members: + :undoc-members: + :show-inheritance: + +:mod:`tools` Module +------------------- + +.. automodule:: galaxy.webapps.galaxy.api.tools + :members: + :undoc-members: + :show-inheritance: + +:mod:`users` Module +------------------- + +.. automodule:: galaxy.webapps.galaxy.api.users + :members: + :undoc-members: + :show-inheritance: + +:mod:`visualizations` Module +---------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.visualizations + :members: + :undoc-members: + :show-inheritance: + +:mod:`workflows` Module +----------------------- + +.. automodule:: galaxy.webapps.galaxy.api.workflows + :members: + :undoc-members: + :show-inheritance: + diff --git a/doc/source/lib/galaxy.web.controllers.rst b/doc/source/lib/galaxy.webapps.galaxy.controllers.rst similarity index 63% rename from doc/source/lib/galaxy.web.controllers.rst rename to doc/source/lib/galaxy.webapps.galaxy.controllers.rst index cf170ea777b..4517fc2ba37 100644 --- a/doc/source/lib/galaxy.web.controllers.rst +++ b/doc/source/lib/galaxy.webapps.galaxy.controllers.rst @@ -4,7 +4,7 @@ controllers Package :mod:`controllers` Package -------------------------- -.. automodule:: galaxy.web.controllers +.. automodule:: galaxy.webapps.galaxy.controllers :members: :undoc-members: :show-inheritance: @@ -12,7 +12,7 @@ controllers Package :mod:`admin` Module ------------------- -.. automodule:: galaxy.web.controllers.admin +.. automodule:: galaxy.webapps.galaxy.controllers.admin :members: :undoc-members: :show-inheritance: @@ -20,7 +20,7 @@ controllers Package :mod:`admin_toolshed` Module ---------------------------- -.. automodule:: galaxy.web.controllers.admin_toolshed +.. automodule:: galaxy.webapps.galaxy.controllers.admin_toolshed :members: :undoc-members: :show-inheritance: @@ -28,15 +28,15 @@ controllers Package :mod:`async` Module ------------------- -.. automodule:: galaxy.web.controllers.async +.. automodule:: galaxy.webapps.galaxy.controllers.async :members: :undoc-members: :show-inheritance: -:mod:`cloud` Module -------------------- +:mod:`cloudlaunch` Module +------------------------- -.. automodule:: galaxy.web.controllers.cloud +.. automodule:: galaxy.webapps.galaxy.controllers.cloudlaunch :members: :undoc-members: :show-inheritance: @@ -44,7 +44,7 @@ controllers Package :mod:`data_admin` Module ------------------------ -.. automodule:: galaxy.web.controllers.data_admin +.. automodule:: galaxy.webapps.galaxy.controllers.data_admin :members: :undoc-members: :show-inheritance: @@ -52,7 +52,7 @@ controllers Package :mod:`dataset` Module --------------------- -.. automodule:: galaxy.web.controllers.dataset +.. automodule:: galaxy.webapps.galaxy.controllers.dataset :members: :undoc-members: :show-inheritance: @@ -60,7 +60,7 @@ controllers Package :mod:`error` Module ------------------- -.. automodule:: galaxy.web.controllers.error +.. automodule:: galaxy.webapps.galaxy.controllers.error :members: :undoc-members: :show-inheritance: @@ -68,7 +68,7 @@ controllers Package :mod:`external_service` Module ------------------------------ -.. automodule:: galaxy.web.controllers.external_service +.. automodule:: galaxy.webapps.galaxy.controllers.external_service :members: :undoc-members: :show-inheritance: @@ -76,7 +76,7 @@ controllers Package :mod:`external_services` Module ------------------------------- -.. automodule:: galaxy.web.controllers.external_services +.. automodule:: galaxy.webapps.galaxy.controllers.external_services :members: :undoc-members: :show-inheritance: @@ -84,7 +84,7 @@ controllers Package :mod:`forms` Module ------------------- -.. automodule:: galaxy.web.controllers.forms +.. automodule:: galaxy.webapps.galaxy.controllers.forms :members: :undoc-members: :show-inheritance: @@ -92,7 +92,7 @@ controllers Package :mod:`history` Module --------------------- -.. automodule:: galaxy.web.controllers.history +.. automodule:: galaxy.webapps.galaxy.controllers.history :members: :undoc-members: :show-inheritance: @@ -100,7 +100,7 @@ controllers Package :mod:`library` Module --------------------- -.. automodule:: galaxy.web.controllers.library +.. automodule:: galaxy.webapps.galaxy.controllers.library :members: :undoc-members: :show-inheritance: @@ -108,7 +108,7 @@ controllers Package :mod:`library_admin` Module --------------------------- -.. automodule:: galaxy.web.controllers.library_admin +.. automodule:: galaxy.webapps.galaxy.controllers.library_admin :members: :undoc-members: :show-inheritance: @@ -116,7 +116,7 @@ controllers Package :mod:`library_common` Module ---------------------------- -.. automodule:: galaxy.web.controllers.library_common +.. automodule:: galaxy.webapps.galaxy.controllers.library_common :members: :undoc-members: :show-inheritance: @@ -124,7 +124,7 @@ controllers Package :mod:`mobile` Module -------------------- -.. automodule:: galaxy.web.controllers.mobile +.. automodule:: galaxy.webapps.galaxy.controllers.mobile :members: :undoc-members: :show-inheritance: @@ -132,7 +132,7 @@ controllers Package :mod:`page` Module ------------------ -.. automodule:: galaxy.web.controllers.page +.. automodule:: galaxy.webapps.galaxy.controllers.page :members: :undoc-members: :show-inheritance: @@ -140,7 +140,7 @@ controllers Package :mod:`request_type` Module -------------------------- -.. automodule:: galaxy.web.controllers.request_type +.. automodule:: galaxy.webapps.galaxy.controllers.request_type :members: :undoc-members: :show-inheritance: @@ -148,7 +148,7 @@ controllers Package :mod:`requests` Module ---------------------- -.. automodule:: galaxy.web.controllers.requests +.. automodule:: galaxy.webapps.galaxy.controllers.requests :members: :undoc-members: :show-inheritance: @@ -156,7 +156,7 @@ controllers Package :mod:`requests_admin` Module ---------------------------- -.. automodule:: galaxy.web.controllers.requests_admin +.. automodule:: galaxy.webapps.galaxy.controllers.requests_admin :members: :undoc-members: :show-inheritance: @@ -164,7 +164,7 @@ controllers Package :mod:`requests_common` Module ----------------------------- -.. automodule:: galaxy.web.controllers.requests_common +.. automodule:: galaxy.webapps.galaxy.controllers.requests_common :members: :undoc-members: :show-inheritance: @@ -172,7 +172,7 @@ controllers Package :mod:`root` Module ------------------ -.. automodule:: galaxy.web.controllers.root +.. automodule:: galaxy.webapps.galaxy.controllers.root :members: :undoc-members: :show-inheritance: @@ -180,7 +180,7 @@ controllers Package :mod:`tag` Module ----------------- -.. automodule:: galaxy.web.controllers.tag +.. automodule:: galaxy.webapps.galaxy.controllers.tag :members: :undoc-members: :show-inheritance: @@ -188,15 +188,7 @@ controllers Package :mod:`tool_runner` Module ------------------------- -.. automodule:: galaxy.web.controllers.tool_runner - :members: - :undoc-members: - :show-inheritance: - -:mod:`tracks` Module --------------------- - -.. automodule:: galaxy.web.controllers.tracks +.. automodule:: galaxy.webapps.galaxy.controllers.tool_runner :members: :undoc-members: :show-inheritance: @@ -204,7 +196,7 @@ controllers Package :mod:`ucsc_proxy` Module ------------------------ -.. automodule:: galaxy.web.controllers.ucsc_proxy +.. automodule:: galaxy.webapps.galaxy.controllers.ucsc_proxy :members: :undoc-members: :show-inheritance: @@ -212,7 +204,7 @@ controllers Package :mod:`user` Module ------------------ -.. automodule:: galaxy.web.controllers.user +.. automodule:: galaxy.webapps.galaxy.controllers.user :members: :undoc-members: :show-inheritance: @@ -220,7 +212,7 @@ controllers Package :mod:`visualization` Module --------------------------- -.. automodule:: galaxy.web.controllers.visualization +.. automodule:: galaxy.webapps.galaxy.controllers.visualization :members: :undoc-members: :show-inheritance: @@ -228,7 +220,7 @@ controllers Package :mod:`workflow` Module ---------------------- -.. automodule:: galaxy.web.controllers.workflow +.. automodule:: galaxy.webapps.galaxy.controllers.workflow :members: :undoc-members: :show-inheritance: diff --git a/doc/source/lib/galaxy.webapps.galaxy.rst b/doc/source/lib/galaxy.webapps.galaxy.rst new file mode 100644 index 00000000000..42642bec26c --- /dev/null +++ b/doc/source/lib/galaxy.webapps.galaxy.rst @@ -0,0 +1,19 @@ +galaxy Package +============== + +:mod:`buildapp` Module +---------------------- + +.. automodule:: galaxy.webapps.galaxy.buildapp + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + + galaxy.webapps.galaxy.api + galaxy.webapps.galaxy.controllers + diff --git a/doc/source/lib/galaxy.webapps.rst b/doc/source/lib/galaxy.webapps.rst index 823d6521c46..5b702392115 100644 --- a/doc/source/lib/galaxy.webapps.rst +++ b/doc/source/lib/galaxy.webapps.rst @@ -16,5 +16,6 @@ Subpackages galaxy.webapps.community galaxy.webapps.demo_sequencer + galaxy.webapps.galaxy galaxy.webapps.reports