1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/changeset/c0f9edeb7ab1/ changeset: c0f9edeb7ab1 user: clem...@galaxyproject.org date: 2012-10-31 23:41:13 summary: Bringing Sphinx RST files up to date; changing generated doc so all modules are documented, not just galaxy.* affected #: 27 files

diff -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/index.rst --- a/doc/source/index.rst +++ b/doc/source/index.rst @@ -3,22 +3,19 @@

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 <lib/galaxy.web.api> + API Documentation <lib/galaxy.webapps.galaxy.api>

- Application Documentation <lib/galaxy> + Application Documentation <lib/modules>

Indices and tables ==================

diff -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.datatypes.converters.rst --- a/doc/source/lib/galaxy.datatypes.converters.rst +++ b/doc/source/lib/galaxy.datatypes.converters.rst @@ -113,6 +113,14 @@ :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 -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.jobs.deferred.rst --- a/doc/source/lib/galaxy.jobs.deferred.rst +++ b/doc/source/lib/galaxy.jobs.deferred.rst @@ -17,6 +17,14 @@ :undoc-members: :show-inheritance:

+:mod:`genome_index` Module +-------------------------- + +.. automodule:: galaxy.jobs.deferred.genome_index + :members: + :undoc-members: + :show-inheritance: + :mod:`genome_transfer` Module -----------------------------

diff -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.jobs.rst --- a/doc/source/lib/galaxy.jobs.rst +++ b/doc/source/lib/galaxy.jobs.rst @@ -25,6 +25,14 @@ :undoc-members: :show-inheritance:

+:mod:`mapper` Module +-------------------- + +.. automodule:: galaxy.jobs.mapper + :members: + :undoc-members: + :show-inheritance: + :mod:`transfer_manager` Module ------------------------------

@@ -40,6 +48,7 @@

galaxy.jobs.actions galaxy.jobs.deferred + galaxy.jobs.rules galaxy.jobs.runners galaxy.jobs.splitters

diff -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.jobs.runners.cli_job.rst --- /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 -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.jobs.runners.cli_shell.rst --- /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 -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.jobs.runners.rst --- a/doc/source/lib/galaxy.jobs.runners.rst +++ b/doc/source/lib/galaxy.jobs.runners.rst @@ -9,6 +9,22 @@ :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 @@ :undoc-members: :show-inheritance:

+Subpackages +----------- + +.. toctree:: + + galaxy.jobs.runners.cli_job + galaxy.jobs.runners.cli_shell +

diff -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.util.backports.importlib.rst --- /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 -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.util.backports.rst --- /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 -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.util.rst --- a/doc/source/lib/galaxy.util.rst +++ b/doc/source/lib/galaxy.util.rst @@ -137,3 +137,10 @@ :undoc-members: :show-inheritance:

+Subpackages +----------- + +.. toctree:: + + galaxy.util.backports +

diff -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.visualization.data_providers.phyloviz.rst --- /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 -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.visualization.data_providers.rst --- /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 -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.visualization.genome.rst --- /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 -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.visualization.rst --- a/doc/source/lib/galaxy.visualization.rst +++ b/doc/source/lib/galaxy.visualization.rst @@ -22,5 +22,7 @@

.. toctree::

+ galaxy.visualization.data_providers + galaxy.visualization.genome galaxy.visualization.tracks

diff -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.visualization.tracks.rst --- a/doc/source/lib/galaxy.visualization.tracks.rst +++ b/doc/source/lib/galaxy.visualization.tracks.rst @@ -9,14 +9,6 @@ :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 @@ :undoc-members: :show-inheritance:

-:mod:`visual_analytics` Module ------------------------------- - -.. automodule:: galaxy.visualization.tracks.visual_analytics - :members: - :undoc-members: - :show-inheritance: -

diff -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.web.api.rst --- a/doc/source/lib/galaxy.web.api.rst +++ /dev/null @@ -1,352 +0,0 @@ -Galaxy API Documentation -************************ - -Background -========== -In addition to being accessible through a web interface, Galaxy can now also be -accessed programmatically, through shell scripts and other programs. The web -interface is appropriate for things like exploratory analysis, visualization, -construction of workflows, and rerunning workflows on new datasets. - -The web interface is less suitable for things like - - Connecting a Galaxy instance directly to your sequencer and running - workflows whenever data is ready - - Running a workflow against multiple datasets (which can be done with the - web interface, but is tedious) - - When the analysis involves complex control, such as looping and - branching. - -The Galaxy API addresses these and other situations by exposing Galaxy -internals through an additional interface, known as an Application Programming -Interface, or API. - -Quickstart -========== - -Set the following option in universe_wsgi.ini and start the server:: - - enable_api = True - -Log in as your user, navigate to the API Keys page in the User menu, and -generate a new API key. Make a note of the API key, and then pull up a -terminal. Now we'll use the display.py script in your galaxy/scripts/api -directory for a short example:: - - % ./display.py my_key http://localhost:4096/api/histories - Collection Members - ------------------ - #1: /api/histories/8c49be448cfe29bc - name: Unnamed history - id: 8c49be448cfe29bc - #2: /api/histories/33b43b4e7093c91f - name: output test - id: 33b43b4e7093c91f - -The result is a Collection of the histories of the user specified by the API -key (you). To look at the details of a particular history, say #1 above, do -the following:: - - % ./display.py my_key http://localhost:4096/api/histories/8c49be448cfe29bc - Member Information - ------------------ - state_details: {'ok': 1, 'failed_metadata': 0, 'upload': 0, 'discarded': 0, 'running': 0, 'setting_metadata': 0, 'error': 0, 'new': 0, 'queued': 0, 'empty': 0} - state: ok - contents_url: /api/histories/8c49be448cfe29bc/contents - id: 8c49be448cfe29bc - name: Unnamed history - -This gives detailed information about the specific member in question, in this -case the History. To view history contents, do the following:: - - - % ./display.py my_key http://localhost:4096/api/histories/8c49be448cfe29bc/contents - Collection Members - ------------------ - #1: /api/histories/8c49be448cfe29bc/contents/6f91353f3eb0fa4a - name: Pasted Entry - type: file - id: 6f91353f3eb0fa4a - -What we have here is another Collection of items containing all of the datasets -in this particular history. Finally, to view details of a particular dataset -in this collection, execute the following:: - - % ./display.py my_key http://localhost:4096/api/histories/8c49be448cfe29bc/contents/6f91353f3eb0fa... - Member Information - ------------------ - misc_blurb: 1 line - name: Pasted Entry - data_type: txt - deleted: False - file_name: /Users/yoplait/work/galaxy-stock/database/files/000/dataset_82.dat - state: ok - download_url: /datasets/6f91353f3eb0fa4a/display?to_ext=txt - visible: True - genome_build: ? - model_class: HistoryDatasetAssociation - file_size: 17 - metadata_data_lines: 1 - id: 6f91353f3eb0fa4a - misc_info: uploaded txt file - metadata_dbkey: ? - -And now you've successfully used the API to request and select a history, -browse the contents of that history, and then look at detailed information -about a particular dataset. - -For a more comprehensive Data Library example, set the following option in your -universe_wsgi.ini as well, and restart galaxy again:: - - admin_users = you@example.org - library_import_dir = /path/to/some/directory - -In the directory you specified for 'library_import_dir', create some -subdirectories, and put (or symlink) files to import into Galaxy into those -subdirectories. - -In Galaxy, create an account that matches the address you put in 'admin_users', -then browse to that user's preferences and generate a new API Key. Copy the -key to your clipboard and then use these scripts:: - - % ./display.py my_key http://localhost:4096/api/libraries - Collection Members - ------------------ - - 0 elements in collection - - % ./library_create_library.py my_key http://localhost:4096/api/libraries api_test 'API Test Library' - Response - -------- - /api/libraries/f3f73e481f432006 - name: api_test - id: f3f73e481f432006 - - % ./display.py my_key http://localhost:4096/api/libraries - Collection Members - ------------------ - /api/libraries/f3f73e481f432006 - name: api_test - id: f3f73e481f432006 - - % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006 - Member Information - ------------------ - synopsis: None - contents_url: /api/libraries/f3f73e481f432006/contents - description: API Test Library - name: api_test - - % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents - Collection Members - ------------------ - /api/libraries/f3f73e481f432006/contents/28202595c0d2591f61ddda595d2c3670 - name: / - type: folder - id: 28202595c0d2591f61ddda595d2c3670 - - % ./library_create_folder.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents 28202595c0d2591f61ddda595d2c3670 api_test_folder1 'API Test Folder 1' - Response - -------- - /api/libraries/f3f73e481f432006/contents/28202595c0d2591fa4f9089d2303fd89 - name: api_test_folder1 - id: 28202595c0d2591fa4f9089d2303fd89 - - % ./library_upload_from_import_dir.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents 28202595c0d2591fa4f9089d2303fd89 bed bed hg19 - Response - -------- - /api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b - name: 2.bed - id: e9ef7fdb2db87d7b - /api/libraries/f3f73e481f432006/contents/3b7f6a31f80a5018 - name: 3.bed - id: 3b7f6a31f80a5018 - - % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents - Collection Members - ------------------ - /api/libraries/f3f73e481f432006/contents/28202595c0d2591f61ddda595d2c3670 - name: / - type: folder - id: 28202595c0d2591f61ddda595d2c3670 - /api/libraries/f3f73e481f432006/contents/28202595c0d2591fa4f9089d2303fd89 - name: /api_test_folder1 - type: folder - id: 28202595c0d2591fa4f9089d2303fd89 - /api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b - name: /api_test_folder1/2.bed - type: file - id: e9ef7fdb2db87d7b - /api/libraries/f3f73e481f432006/contents/3b7f6a31f80a5018 - name: /api_test_folder1/3.bed - type: file - id: 3b7f6a31f80a5018 - - % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d... - Member Information - ------------------ - misc_blurb: 68 regions - metadata_endCol: 3 - data_type: bed - metadata_columns: 6 - metadata_nameCol: 4 - uploaded_by: nate@... - metadata_strandCol: 6 - name: 2.bed - genome_build: hg19 - metadata_comment_lines: None - metadata_startCol: 2 - metadata_chromCol: 1 - file_size: 4272 - metadata_data_lines: 68 - message: - metadata_dbkey: hg19 - misc_info: uploaded bed file - date_uploaded: 2010-06-22T17:01:51.266119 - metadata_column_types: str, int, int, str, int, str - -Other parameters are valid when uploading, they are the same parameters as are -used in the web form, like 'link_data_only' and etc. - -The request and response format should be considered alpha and are subject to change. - - -API Controllers -=============== - -:mod:`datasets` Module ----------------------- - -.. automodule:: galaxy.web.api.datasets - :members: - :undoc-members: - :show-inheritance: - -:mod:`forms` Module -------------------- - -.. automodule:: galaxy.web.api.forms - :members: - :undoc-members: - :show-inheritance: - -:mod:`genomes` Module ---------------------- - -.. automodule:: galaxy.web.api.genomes - :members: - :undoc-members: - :show-inheritance: - -:mod:`histories` Module ------------------------ - -.. automodule:: galaxy.web.api.histories - :members: - :undoc-members: - :show-inheritance: - -:mod:`history_contents` Module ------------------------------- - -.. automodule:: galaxy.web.api.history_contents - :members: - :undoc-members: - :show-inheritance: - -:mod:`libraries` Module ------------------------ - -.. automodule:: galaxy.web.api.libraries - :members: - :undoc-members: - :show-inheritance: - -:mod:`library_contents` Module ------------------------------- - -.. automodule:: galaxy.web.api.library_contents - :members: - :undoc-members: - :show-inheritance: - -:mod:`permissions` Module -------------------------- - -.. automodule:: galaxy.web.api.permissions - :members: - :undoc-members: - :show-inheritance: - -:mod:`quotas` Module --------------------- - -.. automodule:: galaxy.web.api.quotas - :members: - :undoc-members: - :show-inheritance: - -:mod:`request_types` Module ---------------------------- - -.. automodule:: galaxy.web.api.request_types - :members: - :undoc-members: - :show-inheritance: - -:mod:`requests` Module ----------------------- - -.. automodule:: galaxy.web.api.requests - :members: - :undoc-members: - :show-inheritance: - -:mod:`roles` Module -------------------- - -.. automodule:: galaxy.web.api.roles - :members: - :undoc-members: - :show-inheritance: - -:mod:`samples` Module ---------------------- - -.. automodule:: galaxy.web.api.samples - :members: - :undoc-members: - :show-inheritance: - -:mod:`tools` Module -------------------- - -.. automodule:: galaxy.web.api.tools - :members: - :undoc-members: - :show-inheritance: - -:mod:`users` Module -------------------- - -.. automodule:: galaxy.web.api.users - :members: - :undoc-members: - :show-inheritance: - -:mod:`visualizations` Module ----------------------------- - -.. automodule:: galaxy.web.api.visualizations - :members: - :undoc-members: - :show-inheritance: - -:mod:`workflows` Module ------------------------ - -.. automodule:: galaxy.web.api.workflows - :members: - :undoc-members: - :show-inheritance: - -

diff -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.web.base.controllers.rst --- /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 -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.web.base.rst --- a/doc/source/lib/galaxy.web.base.rst +++ b/doc/source/lib/galaxy.web.base.rst @@ -9,3 +9,10 @@ :undoc-members: :show-inheritance:

+Subpackages +----------- + +.. toctree:: + + galaxy.web.base.controllers +

diff -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.web.controllers.rst --- a/doc/source/lib/galaxy.web.controllers.rst +++ /dev/null @@ -1,235 +0,0 @@ -controllers Package -=================== - -:mod:`controllers` Package --------------------------- - -.. automodule:: galaxy.web.controllers - :members: - :undoc-members: - :show-inheritance: - -:mod:`admin` Module -------------------- - -.. automodule:: galaxy.web.controllers.admin - :members: - :undoc-members: - :show-inheritance: - -:mod:`admin_toolshed` Module ----------------------------- - -.. automodule:: galaxy.web.controllers.admin_toolshed - :members: - :undoc-members: - :show-inheritance: - -:mod:`async` Module -------------------- - -.. automodule:: galaxy.web.controllers.async - :members: - :undoc-members: - :show-inheritance: - -:mod:`cloud` Module -------------------- - -.. automodule:: galaxy.web.controllers.cloud - :members: - :undoc-members: - :show-inheritance: - -:mod:`data_admin` Module ------------------------- - -.. automodule:: galaxy.web.controllers.data_admin - :members: - :undoc-members: - :show-inheritance: - -:mod:`dataset` Module ---------------------- - -.. automodule:: galaxy.web.controllers.dataset - :members: - :undoc-members: - :show-inheritance: - -:mod:`error` Module -------------------- - -.. automodule:: galaxy.web.controllers.error - :members: - :undoc-members: - :show-inheritance: - -:mod:`external_service` Module ------------------------------- - -.. automodule:: galaxy.web.controllers.external_service - :members: - :undoc-members: - :show-inheritance: - -:mod:`external_services` Module -------------------------------- - -.. automodule:: galaxy.web.controllers.external_services - :members: - :undoc-members: - :show-inheritance: - -:mod:`forms` Module -------------------- - -.. automodule:: galaxy.web.controllers.forms - :members: - :undoc-members: - :show-inheritance: - -:mod:`history` Module ---------------------- - -.. automodule:: galaxy.web.controllers.history - :members: - :undoc-members: - :show-inheritance: - -:mod:`library` Module ---------------------- - -.. automodule:: galaxy.web.controllers.library - :members: - :undoc-members: - :show-inheritance: - -:mod:`library_admin` Module ---------------------------- - -.. automodule:: galaxy.web.controllers.library_admin - :members: - :undoc-members: - :show-inheritance: - -:mod:`library_common` Module ----------------------------- - -.. automodule:: galaxy.web.controllers.library_common - :members: - :undoc-members: - :show-inheritance: - -:mod:`mobile` Module --------------------- - -.. automodule:: galaxy.web.controllers.mobile - :members: - :undoc-members: - :show-inheritance: - -:mod:`page` Module ------------------- - -.. automodule:: galaxy.web.controllers.page - :members: - :undoc-members: - :show-inheritance: - -:mod:`request_type` Module --------------------------- - -.. automodule:: galaxy.web.controllers.request_type - :members: - :undoc-members: - :show-inheritance: - -:mod:`requests` Module ----------------------- - -.. automodule:: galaxy.web.controllers.requests - :members: - :undoc-members: - :show-inheritance: - -:mod:`requests_admin` Module ----------------------------- - -.. automodule:: galaxy.web.controllers.requests_admin - :members: - :undoc-members: - :show-inheritance: - -:mod:`requests_common` Module ------------------------------ - -.. automodule:: galaxy.web.controllers.requests_common - :members: - :undoc-members: - :show-inheritance: - -:mod:`root` Module ------------------- - -.. automodule:: galaxy.web.controllers.root - :members: - :undoc-members: - :show-inheritance: - -:mod:`tag` Module ------------------ - -.. automodule:: galaxy.web.controllers.tag - :members: - :undoc-members: - :show-inheritance: - -:mod:`tool_runner` Module -------------------------- - -.. automodule:: galaxy.web.controllers.tool_runner - :members: - :undoc-members: - :show-inheritance: - -:mod:`tracks` Module --------------------- - -.. automodule:: galaxy.web.controllers.tracks - :members: - :undoc-members: - :show-inheritance: - -:mod:`ucsc_proxy` Module ------------------------- - -.. automodule:: galaxy.web.controllers.ucsc_proxy - :members: - :undoc-members: - :show-inheritance: - -:mod:`user` Module ------------------- - -.. automodule:: galaxy.web.controllers.user - :members: - :undoc-members: - :show-inheritance: - -:mod:`visualization` Module ---------------------------- - -.. automodule:: galaxy.web.controllers.visualization - :members: - :undoc-members: - :show-inheritance: - -:mod:`workflow` Module ----------------------- - -.. automodule:: galaxy.web.controllers.workflow - :members: - :undoc-members: - :show-inheritance: -

diff -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.web.rst --- a/doc/source/lib/galaxy.web.rst +++ b/doc/source/lib/galaxy.web.rst @@ -38,9 +38,7 @@

.. toctree::

- galaxy.web.api galaxy.web.base - galaxy.web.controllers galaxy.web.framework galaxy.web.security

diff -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.webapps.community.controllers.rst --- a/doc/source/lib/galaxy.webapps.community.controllers.rst +++ b/doc/source/lib/galaxy.webapps.community.controllers.rst @@ -41,6 +41,14 @@ :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 @@ :undoc-members: :show-inheritance:

+:mod:`user` Module +------------------ + +.. automodule:: galaxy.webapps.community.controllers.user + :members: + :undoc-members: + :show-inheritance: + :mod:`workflow` Module ----------------------

diff -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.webapps.community.framework.middleware.rst --- a/doc/source/lib/galaxy.webapps.community.framework.middleware.rst +++ b/doc/source/lib/galaxy.webapps.community.framework.middleware.rst @@ -17,3 +17,11 @@ :undoc-members: :show-inheritance:

+:mod:`remoteuser` Module +------------------------ + +.. automodule:: galaxy.webapps.community.framework.middleware.remoteuser + :members: + :undoc-members: + :show-inheritance: +

diff -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.webapps.galaxy.api.rst --- /dev/null +++ b/doc/source/lib/galaxy.webapps.galaxy.api.rst @@ -0,0 +1,391 @@ +Galaxy API Documentation +************************ + +Background +========== +In addition to being accessible through a web interface, Galaxy can now also be +accessed programmatically, through shell scripts and other programs. The web +interface is appropriate for things like exploratory analysis, visualization, +construction of workflows, and rerunning workflows on new datasets. + +The web interface is less suitable for things like + - Connecting a Galaxy instance directly to your sequencer and running + workflows whenever data is ready + - Running a workflow against multiple datasets (which can be done with the + web interface, but is tedious) + - When the analysis involves complex control, such as looping and + branching. + +The Galaxy API addresses these and other situations by exposing Galaxy +internals through an additional interface, known as an Application Programming +Interface, or API. + +Quickstart +========== + +Set the following option in universe_wsgi.ini and start the server:: + + enable_api = True + +Log in as your user, navigate to the API Keys page in the User menu, and +generate a new API key. Make a note of the API key, and then pull up a +terminal. Now we'll use the display.py script in your galaxy/scripts/api +directory for a short example:: + + % ./display.py my_key http://localhost:4096/api/histories + Collection Members + ------------------ + #1: /api/histories/8c49be448cfe29bc + name: Unnamed history + id: 8c49be448cfe29bc + #2: /api/histories/33b43b4e7093c91f + name: output test + id: 33b43b4e7093c91f + +The result is a Collection of the histories of the user specified by the API +key (you). To look at the details of a particular history, say #1 above, do +the following:: + + % ./display.py my_key http://localhost:4096/api/histories/8c49be448cfe29bc + Member Information + ------------------ + state_details: {'ok': 1, 'failed_metadata': 0, 'upload': 0, 'discarded': 0, 'running': 0, 'setting_metadata': 0, 'error': 0, 'new': 0, 'queued': 0, 'empty': 0} + state: ok + contents_url: /api/histories/8c49be448cfe29bc/contents + id: 8c49be448cfe29bc + name: Unnamed history + +This gives detailed information about the specific member in question, in this +case the History. To view history contents, do the following:: + + + % ./display.py my_key http://localhost:4096/api/histories/8c49be448cfe29bc/contents + Collection Members + ------------------ + #1: /api/histories/8c49be448cfe29bc/contents/6f91353f3eb0fa4a + name: Pasted Entry + type: file + id: 6f91353f3eb0fa4a + +What we have here is another Collection of items containing all of the datasets +in this particular history. Finally, to view details of a particular dataset +in this collection, execute the following:: + + % ./display.py my_key http://localhost:4096/api/histories/8c49be448cfe29bc/contents/6f91353f3eb0fa... + Member Information + ------------------ + misc_blurb: 1 line + name: Pasted Entry + data_type: txt + deleted: False + file_name: /Users/yoplait/work/galaxy-stock/database/files/000/dataset_82.dat + state: ok + download_url: /datasets/6f91353f3eb0fa4a/display?to_ext=txt + visible: True + genome_build: ? + model_class: HistoryDatasetAssociation + file_size: 17 + metadata_data_lines: 1 + id: 6f91353f3eb0fa4a + misc_info: uploaded txt file + metadata_dbkey: ? + +And now you've successfully used the API to request and select a history, +browse the contents of that history, and then look at detailed information +about a particular dataset. + +For a more comprehensive Data Library example, set the following option in your +universe_wsgi.ini as well, and restart galaxy again:: + + admin_users = you@example.org + library_import_dir = /path/to/some/directory + +In the directory you specified for 'library_import_dir', create some +subdirectories, and put (or symlink) files to import into Galaxy into those +subdirectories. + +In Galaxy, create an account that matches the address you put in 'admin_users', +then browse to that user's preferences and generate a new API Key. Copy the +key to your clipboard and then use these scripts:: + + % ./display.py my_key http://localhost:4096/api/libraries + Collection Members + ------------------ + + 0 elements in collection + + % ./library_create_library.py my_key http://localhost:4096/api/libraries api_test 'API Test Library' + Response + -------- + /api/libraries/f3f73e481f432006 + name: api_test + id: f3f73e481f432006 + + % ./display.py my_key http://localhost:4096/api/libraries + Collection Members + ------------------ + /api/libraries/f3f73e481f432006 + name: api_test + id: f3f73e481f432006 + + % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006 + Member Information + ------------------ + synopsis: None + contents_url: /api/libraries/f3f73e481f432006/contents + description: API Test Library + name: api_test + + % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents + Collection Members + ------------------ + /api/libraries/f3f73e481f432006/contents/28202595c0d2591f61ddda595d2c3670 + name: / + type: folder + id: 28202595c0d2591f61ddda595d2c3670 + + % ./library_create_folder.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents 28202595c0d2591f61ddda595d2c3670 api_test_folder1 'API Test Folder 1' + Response + -------- + /api/libraries/f3f73e481f432006/contents/28202595c0d2591fa4f9089d2303fd89 + name: api_test_folder1 + id: 28202595c0d2591fa4f9089d2303fd89 + + % ./library_upload_from_import_dir.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents 28202595c0d2591fa4f9089d2303fd89 bed bed hg19 + Response + -------- + /api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b + name: 2.bed + id: e9ef7fdb2db87d7b + /api/libraries/f3f73e481f432006/contents/3b7f6a31f80a5018 + name: 3.bed + id: 3b7f6a31f80a5018 + + % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents + Collection Members + ------------------ + /api/libraries/f3f73e481f432006/contents/28202595c0d2591f61ddda595d2c3670 + name: / + type: folder + id: 28202595c0d2591f61ddda595d2c3670 + /api/libraries/f3f73e481f432006/contents/28202595c0d2591fa4f9089d2303fd89 + name: /api_test_folder1 + type: folder + id: 28202595c0d2591fa4f9089d2303fd89 + /api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b + name: /api_test_folder1/2.bed + type: file + id: e9ef7fdb2db87d7b + /api/libraries/f3f73e481f432006/contents/3b7f6a31f80a5018 + name: /api_test_folder1/3.bed + type: file + id: 3b7f6a31f80a5018 + + % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d... + Member Information + ------------------ + misc_blurb: 68 regions + metadata_endCol: 3 + data_type: bed + metadata_columns: 6 + metadata_nameCol: 4 + uploaded_by: nate@... + metadata_strandCol: 6 + name: 2.bed + genome_build: hg19 + metadata_comment_lines: None + metadata_startCol: 2 + metadata_chromCol: 1 + file_size: 4272 + metadata_data_lines: 68 + message: + metadata_dbkey: hg19 + misc_info: uploaded bed file + date_uploaded: 2010-06-22T17:01:51.266119 + metadata_column_types: str, int, int, str, int, str + +Other parameters are valid when uploading, they are the same parameters as are +used in the web form, like 'link_data_only' and etc. + +The request and response format should be considered alpha and are subject to change. + + +API Controllers +=============== + +: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 -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.webapps.galaxy.api.rst~ --- /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 -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.webapps.galaxy.controllers.rst --- /dev/null +++ b/doc/source/lib/galaxy.webapps.galaxy.controllers.rst @@ -0,0 +1,227 @@ +controllers Package +=================== + +:mod:`controllers` Package +-------------------------- + +.. automodule:: galaxy.webapps.galaxy.controllers + :members: + :undoc-members: + :show-inheritance: + +:mod:`admin` Module +------------------- + +.. automodule:: galaxy.webapps.galaxy.controllers.admin + :members: + :undoc-members: + :show-inheritance: + +:mod:`admin_toolshed` Module +---------------------------- + +.. automodule:: galaxy.webapps.galaxy.controllers.admin_toolshed + :members: + :undoc-members: + :show-inheritance: + +:mod:`async` Module +------------------- + +.. automodule:: galaxy.webapps.galaxy.controllers.async + :members: + :undoc-members: + :show-inheritance: + +:mod:`cloudlaunch` Module +------------------------- + +.. automodule:: galaxy.webapps.galaxy.controllers.cloudlaunch + :members: + :undoc-members: + :show-inheritance: + +:mod:`data_admin` Module +------------------------ + +.. automodule:: galaxy.webapps.galaxy.controllers.data_admin + :members: + :undoc-members: + :show-inheritance: + +:mod:`dataset` Module +--------------------- + +.. automodule:: galaxy.webapps.galaxy.controllers.dataset + :members: + :undoc-members: + :show-inheritance: + +:mod:`error` Module +------------------- + +.. automodule:: galaxy.webapps.galaxy.controllers.error + :members: + :undoc-members: + :show-inheritance: + +:mod:`external_service` Module +------------------------------ + +.. automodule:: galaxy.webapps.galaxy.controllers.external_service + :members: + :undoc-members: + :show-inheritance: + +:mod:`external_services` Module +------------------------------- + +.. automodule:: galaxy.webapps.galaxy.controllers.external_services + :members: + :undoc-members: + :show-inheritance: + +:mod:`forms` Module +------------------- + +.. automodule:: galaxy.webapps.galaxy.controllers.forms + :members: + :undoc-members: + :show-inheritance: + +:mod:`history` Module +--------------------- + +.. automodule:: galaxy.webapps.galaxy.controllers.history + :members: + :undoc-members: + :show-inheritance: + +:mod:`library` Module +--------------------- + +.. automodule:: galaxy.webapps.galaxy.controllers.library + :members: + :undoc-members: + :show-inheritance: + +:mod:`library_admin` Module +--------------------------- + +.. automodule:: galaxy.webapps.galaxy.controllers.library_admin + :members: + :undoc-members: + :show-inheritance: + +:mod:`library_common` Module +---------------------------- + +.. automodule:: galaxy.webapps.galaxy.controllers.library_common + :members: + :undoc-members: + :show-inheritance: + +:mod:`mobile` Module +-------------------- + +.. automodule:: galaxy.webapps.galaxy.controllers.mobile + :members: + :undoc-members: + :show-inheritance: + +:mod:`page` Module +------------------ + +.. automodule:: galaxy.webapps.galaxy.controllers.page + :members: + :undoc-members: + :show-inheritance: + +:mod:`request_type` Module +-------------------------- + +.. automodule:: galaxy.webapps.galaxy.controllers.request_type + :members: + :undoc-members: + :show-inheritance: + +:mod:`requests` Module +---------------------- + +.. automodule:: galaxy.webapps.galaxy.controllers.requests + :members: + :undoc-members: + :show-inheritance: + +:mod:`requests_admin` Module +---------------------------- + +.. automodule:: galaxy.webapps.galaxy.controllers.requests_admin + :members: + :undoc-members: + :show-inheritance: + +:mod:`requests_common` Module +----------------------------- + +.. automodule:: galaxy.webapps.galaxy.controllers.requests_common + :members: + :undoc-members: + :show-inheritance: + +:mod:`root` Module +------------------ + +.. automodule:: galaxy.webapps.galaxy.controllers.root + :members: + :undoc-members: + :show-inheritance: + +:mod:`tag` Module +----------------- + +.. automodule:: galaxy.webapps.galaxy.controllers.tag + :members: + :undoc-members: + :show-inheritance: + +:mod:`tool_runner` Module +------------------------- + +.. automodule:: galaxy.webapps.galaxy.controllers.tool_runner + :members: + :undoc-members: + :show-inheritance: + +:mod:`ucsc_proxy` Module +------------------------ + +.. automodule:: galaxy.webapps.galaxy.controllers.ucsc_proxy + :members: + :undoc-members: + :show-inheritance: + +:mod:`user` Module +------------------ + +.. automodule:: galaxy.webapps.galaxy.controllers.user + :members: + :undoc-members: + :show-inheritance: + +:mod:`visualization` Module +--------------------------- + +.. automodule:: galaxy.webapps.galaxy.controllers.visualization + :members: + :undoc-members: + :show-inheritance: + +:mod:`workflow` Module +---------------------- + +.. automodule:: galaxy.webapps.galaxy.controllers.workflow + :members: + :undoc-members: + :show-inheritance: +

diff -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.webapps.galaxy.rst --- /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 -r 86f05ee5dedbb1f21bdb8f7e4e823fc760a4d674 -r c0f9edeb7ab137bf7adf76478eccb7fc32557cef doc/source/lib/galaxy.webapps.rst --- a/doc/source/lib/galaxy.webapps.rst +++ b/doc/source/lib/galaxy.webapps.rst @@ -16,5 +16,6 @@

galaxy.webapps.community galaxy.webapps.demo_sequencer + galaxy.webapps.galaxy galaxy.webapps.reports

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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