diff --git a/doc/source/admin/framework_dependencies.rst b/doc/source/admin/framework_dependencies.rst index 4c4c54d4f24..d0d293a1539 100644 --- a/doc/source/admin/framework_dependencies.rst +++ b/doc/source/admin/framework_dependencies.rst @@ -1,7 +1,7 @@ .. _framework-dependencies: -Galaxy Framework Dependencies -============================= +Framework Dependencies +====================== Galaxy is a large Python application with a long list of `Python module dependencies`_. As a result, the Galaxy developers have made significant effort @@ -84,7 +84,7 @@ live in ``/srv/galaxy/venv`` and the Galaxy source code has been cloned to ``/srv/galaxy/server``. .. code-block:: console - + $ virtualenv /srv/galaxy/venv New python executable in /srv/galaxy/venv/bin/python Installing setuptools, pip, wheel...done. @@ -100,12 +100,12 @@ yourself to set up Galaxy pip and the dependencies without creating a virtualenv using the ``--no-create-venv`` option: .. code-block:: console - + (venv)$ PYTHONPATH= sh /srv/galaxy/server/scripts/common_startup.sh --no-create-venv Ignoring indexes: https://pypi.python.org/simple Collecting pip Downloading https://wheels.galaxyproject.org/packages/pip-8.0.0+gx1-py2.py3-none-any.whl (1.2MB) - 100% |████████████████████████████████| 1.2MB 37.8MB/s + 100% |████████████████████████████████| 1.2MB 37.8MB/s Installing collected packages: pip Found existing installation: pip 7.1.2 Uninstalling pip-7.1.2: @@ -113,13 +113,13 @@ virtualenv using the ``--no-create-venv`` option: Successfully installed pip-8.0.0+gx1 Collecting bx-python==0.7.3 (from -r requirements.txt (line 2)) Downloading https://wheels.galaxyproject.org/packages/bx_python-0.7.3-cp27-cp27mu-linux_x86_64.whl (1.7MB) - 100% |████████████████████████████████| 1.7MB 25.4MB/s + 100% |████████████████████████████████| 1.7MB 25.4MB/s ... Collecting pysam==0.8.3+gx1 (from -r requirements.txt (line 69)) Downloading https://wheels.galaxyproject.org/packages/pysam-0.8.3+gx1-cp27-cp27mu-linux_x86_64.whl (7.4MB) - 100% |████████████████████████████████| 7.4MB 15.1MB/s + 100% |████████████████████████████████| 7.4MB 15.1MB/s Installing collected packages: bx-python, MarkupSafe, PyYAML, SQLAlchemy, mercurial, numpy, pycrypto, six, Paste, PasteDeploy, docutils, wchartype, repoze.lru, Routes, WebOb, WebHelpers, Mako, pytz, Babel, Beaker, @@ -307,48 +307,48 @@ automatic fetching of pinned dependencies. The following NEW packages will be INSTALLED: - babel: 2.1.1-py27_0 - bioblend: 0.7.0-py27_0 - boto: 2.38.0-py27_0 + babel: 2.1.1-py27_0 + bioblend: 0.7.0-py27_0 + boto: 2.38.0-py27_0 bx-python: 0.7.3-np110py27_1 - cheetah: 2.4.4-py27_0 - decorator: 4.0.6-py27_0 - docutils: 0.12-py27_0 - ecdsa: 0.11-py27_0 - fabric: 1.10.2-py27_0 - libgfortran: 1.0-0 - mako: 1.0.3-py27_0 - markupsafe: 0.23-py27_0 - mercurial: 3.4.2-py27_0 - nose: 1.3.7-py27_0 - numpy: 1.10.2-py27_0 - openblas: 0.2.14-3 - openssl: 1.0.2e-0 - paramiko: 1.15.2-py27_0 - paste: 1.7.5.1-py27_0 - pastedeploy: 1.5.2-py27_1 - pip: 7.1.2-py27_0 - pycrypto: 2.6.1-py27_0 - python: 2.7.11-0 - pytz: 2015.7-py27_0 - pyyaml: 3.11-py27_1 - readline: 6.2-2 - repoze.lru: 0.6-py27_0 - requests: 2.9.1-py27_0 - requests-toolbelt: 0.5.0-py27_0 - routes: 2.2-py27_0 - setuptools: 19.2-py27_0 - six: 1.10.0-py27_0 - sqlalchemy: 1.0.11-py27_0 - sqlite: 3.9.2-0 - sqlparse: 0.1.18-py27_0 - tk: 8.5.18-0 - webob: 1.4.1-py27_0 - wheel: 0.26.0-py27_1 - yaml: 0.1.6-0 - zlib: 1.2.8-0 + cheetah: 2.4.4-py27_0 + decorator: 4.0.6-py27_0 + docutils: 0.12-py27_0 + ecdsa: 0.11-py27_0 + fabric: 1.10.2-py27_0 + libgfortran: 1.0-0 + mako: 1.0.3-py27_0 + markupsafe: 0.23-py27_0 + mercurial: 3.4.2-py27_0 + nose: 1.3.7-py27_0 + numpy: 1.10.2-py27_0 + openblas: 0.2.14-3 + openssl: 1.0.2e-0 + paramiko: 1.15.2-py27_0 + paste: 1.7.5.1-py27_0 + pastedeploy: 1.5.2-py27_1 + pip: 7.1.2-py27_0 + pycrypto: 2.6.1-py27_0 + python: 2.7.11-0 + pytz: 2015.7-py27_0 + pyyaml: 3.11-py27_1 + readline: 6.2-2 + repoze.lru: 0.6-py27_0 + requests: 2.9.1-py27_0 + requests-toolbelt: 0.5.0-py27_0 + routes: 2.2-py27_0 + setuptools: 19.2-py27_0 + six: 1.10.0-py27_0 + sqlalchemy: 1.0.11-py27_0 + sqlite: 3.9.2-0 + sqlparse: 0.1.18-py27_0 + tk: 8.5.18-0 + webob: 1.4.1-py27_0 + wheel: 0.26.0-py27_1 + yaml: 0.1.6-0 + zlib: 1.2.8-0 - Proceed ([y]/n)? + Proceed ([y]/n)? Fetching packages ... boto-2.38.0-py 100% |############################################| Time: 0:00:00 3.27 MB/s @@ -397,7 +397,7 @@ automatic fetching of pinned dependencies. Collecting WebHelpers (from -r lib/galaxy/dependencies/requirements.txt (line 15)) Downloading https://wheels.galaxyproject.org/packages/WebHelpers-1.3-py2-none-any.whl (149kB) - 100% |████████████████████████████████| 151kB 55.7MB/s + 100% |████████████████████████████████| 151kB 55.7MB/s ... @@ -425,7 +425,7 @@ install uWSGI into Galaxy virtualenv (by default, ``.venv``) using pip, e.g.: (.venv)$ pip install uwsgi Collecting uwsgi Downloading uwsgi-2.0.12.tar.gz (784kB) - 100% |████████████████████████████████| 786kB 981kB/s + 100% |████████████████████████████████| 786kB 981kB/s Building wheels for collected packages: uwsgi Running setup.py bdist_wheel for uwsgi Stored in directory: /home/nate/.cache/pip/wheels/a4/7b/7c/8cbe2fe2c2b963173361cc18aa726f165dc4803effbb8195fc diff --git a/doc/source/admin/index.rst b/doc/source/admin/index.rst index 572f1cf274f..552103c851b 100644 --- a/doc/source/admin/index.rst +++ b/doc/source/admin/index.rst @@ -11,4 +11,5 @@ This documentation is in the midst of being ported and unified based on resource dependency_resolvers conda_faq framework_dependencies + reports useful_scripts diff --git a/doc/source/admin/reports.md b/doc/source/admin/reports.md new file mode 100644 index 00000000000..dcec7a76bb9 --- /dev/null +++ b/doc/source/admin/reports.md @@ -0,0 +1,21 @@ +# Galaxy Reports + +Galaxy includes a report tool that is separate from the main process but which gives lots of potentially useful information about the usage of a Galaxy instance, for example the numbers of jobs that have been run each month, how much disk space each user is currently consuming and so on. + +## Setup on localhost + +The report tool takes its configuration settings from a file called reports.ini, which is located in the config subdirectory of the Galaxy distribution. + +Configuring the reports for your local setup is a case of: + +* Making a copy of `reports.ini.sample` called `reports.ini`. +* Editing the `database_connection` parameter to match the one in your `galaxy.ini` file +* Optionally, editing the `port` parameter (by default the tool uses port 9001) + +You should also set the 'salt' parameter `session_secret` if you intend to expose the reports via the web proxy (see below). + +Then you can start the report server using `sh run_reports.sh` and view the reports by pointing a web browser running on the same server to http://127.0.0.1:9001. If you'd like the report tool to persist between sessions then use `sh run_reports.sh --daemon` to run it as a background process. As with Galaxy itself, use `--stop-daemon` to halt the background process. (The log file is written to `reports_webapp.log` if you need to try and debug a problem.) + +## Expose Outside + +To make your reports available from outside of the localhost using NGINX proxy server you can check out the [blogpost](http://galacticengineer.blogspot.co.uk/2015/06/exposing-galaxy-reports-via-nginx-in.html) by Peter Briggs. diff --git a/doc/source/admin/useful_scripts.rst b/doc/source/admin/useful_scripts.rst index 5c17ddbcda8..933c846aae2 100644 --- a/doc/source/admin/useful_scripts.rst +++ b/doc/source/admin/useful_scripts.rst @@ -1,5 +1,5 @@ -Useful Scripts and Administration Tricks -======================================== +Scripts & Tricks +================ This page aims to help ease the burden of administration with some easy to use scripts and documentation on what is available for admins to use. diff --git a/doc/source/api/api.rst b/doc/source/api/api.rst new file mode 100644 index 00000000000..7dcd5a50a30 --- /dev/null +++ b/doc/source/api/api.rst @@ -0,0 +1,209 @@ +Galaxy API +========== + +annotations +----------- + +.. automodule:: galaxy.webapps.galaxy.api.annotations + +authenticate +------------ + +.. automodule:: galaxy.webapps.galaxy.api.authenticate + +configuration +------------- + +.. automodule:: galaxy.webapps.galaxy.api.configuration + +dataset_collections +------------------- + +.. automodule:: galaxy.webapps.galaxy.api.dataset_collections + +datasets +-------- + +.. automodule:: galaxy.webapps.galaxy.api.datasets + +datatypes +--------- + +.. automodule:: galaxy.webapps.galaxy.api.datatypes + +extended_metadata +----------------- + +.. automodule:: galaxy.webapps.galaxy.api.extended_metadata + +folder_contents +--------------- + +.. automodule:: galaxy.webapps.galaxy.api.folder_contents + +folders +------- + +.. automodule:: galaxy.webapps.galaxy.api.folders + +forms +----- + +.. automodule:: galaxy.webapps.galaxy.api.forms + +genomes +------- + +.. automodule:: galaxy.webapps.galaxy.api.genomes + +group_roles +----------- + +.. automodule:: galaxy.webapps.galaxy.api.group_roles + +group_users +----------- + +.. automodule:: galaxy.webapps.galaxy.api.group_users + +groups +------ + +.. automodule:: galaxy.webapps.galaxy.api.groups + +histories +--------- + +.. automodule:: galaxy.webapps.galaxy.api.histories + +history_contents +---------------- + +.. automodule:: galaxy.webapps.galaxy.api.history_contents + +item_tags +--------- + +.. automodule:: galaxy.webapps.galaxy.api.item_tags + +job_files +--------- + +.. automodule:: galaxy.webapps.galaxy.api.job_files + +jobs +---- + +.. automodule:: galaxy.webapps.galaxy.api.jobs + +lda_datasets +------------ + +.. automodule:: galaxy.webapps.galaxy.api.lda_datasets + +libraries +--------- + +.. automodule:: galaxy.webapps.galaxy.api.libraries + +library_contents +---------------- + +.. automodule:: galaxy.webapps.galaxy.api.library_contents + +metrics +------- + +.. automodule:: galaxy.webapps.galaxy.api.metrics + +page_revisions +-------------- + +.. automodule:: galaxy.webapps.galaxy.api.page_revisions + +pages +----- + +.. automodule:: galaxy.webapps.galaxy.api.pages + +provenance +---------- + +.. automodule:: galaxy.webapps.galaxy.api.provenance + +quotas +------ + +.. automodule:: galaxy.webapps.galaxy.api.quotas + +remote_files +------------ + +.. automodule:: galaxy.webapps.galaxy.api.remote_files + +request_types +------------- + +.. automodule:: galaxy.webapps.galaxy.api.request_types + +requests +-------- + +.. automodule:: galaxy.webapps.galaxy.api.requests + +roles +----- + +.. automodule:: galaxy.webapps.galaxy.api.roles + +samples +------- + +.. automodule:: galaxy.webapps.galaxy.api.samples + +search +------ + +.. automodule:: galaxy.webapps.galaxy.api.search + +tool_data +--------- + +.. automodule:: galaxy.webapps.galaxy.api.tool_data + +tool_shed_repositories +---------------------- + +.. automodule:: galaxy.webapps.galaxy.api.tool_shed_repositories + +tools +----- + +.. automodule:: galaxy.webapps.galaxy.api.tools + +tours +----- + +.. automodule:: galaxy.webapps.galaxy.api.tours + +users +----- + +.. automodule:: galaxy.webapps.galaxy.api.users + +visualizations +-------------- + +.. automodule:: galaxy.webapps.galaxy.api.visualizations + +webhooks +-------------- + +.. automodule:: galaxy.webapps.galaxy.api.webhooks + +workflows +--------- + +.. automodule:: galaxy.webapps.galaxy.api.workflows + + diff --git a/doc/source/api/ts_api.rst b/doc/source/api/ts_api.rst new file mode 100644 index 00000000000..24d9c983623 --- /dev/null +++ b/doc/source/api/ts_api.rst @@ -0,0 +1,44 @@ +Tool Shed API +============= + +authenticate +------------ + +.. automodule:: galaxy.webapps.tool_shed.api.authenticate + +categories +---------- + +.. automodule:: galaxy.webapps.tool_shed.api.categories + +configuration +------------- + +.. automodule:: galaxy.webapps.tool_shed.api.configuration + +groups +------ + +.. automodule:: galaxy.webapps.tool_shed.api.groups + +repositories +------------ + +.. automodule:: galaxy.webapps.tool_shed.api.repositories + +repository_revisions +-------------------- + +.. automodule:: galaxy.webapps.tool_shed.api.repository_revisions + +tools +----- + +.. automodule:: galaxy.webapps.tool_shed.api.tools + +users +----- + +.. automodule:: galaxy.webapps.tool_shed.api.users + + diff --git a/doc/source/api_doc.rst b/doc/source/api_doc.rst index b8acafaac48..86d50d94740 100644 --- a/doc/source/api_doc.rst +++ b/doc/source/api_doc.rst @@ -18,12 +18,17 @@ The Galaxy API addresses these and other situations by exposing Galaxy internals through an additional interface, known as an Application Programming Interface, or API. +Various language specific bindings for interfacing with the Galaxy API have been developed by the Galaxy community including `Python `__, `PHP `__, `Java `__, and `JavaScript `__. + +Overview of available API resources is available at https://galaxyproject.org/develop/api/. + .. toctree:: - :maxdepth: 3 + :maxdepth: 2 - Galaxy API Quickstart + Quickstart - Galaxy API Guidelines + Development Guidelines + + Documentation - Galaxy API Documentation diff --git a/doc/source/conf.py b/doc/source/conf.py index 04b5df1160b..c9cad61ce92 100644 --- a/doc/source/conf.py +++ b/doc/source/conf.py @@ -46,8 +46,10 @@ extensions = ['sphinx.ext.autodoc', 'sphinx.ext.doctest', 'sphinx.ext.todo', 'sp templates_path = ['_templates'] # Configure default autodoc's action -autodoc_default_flags = [ 'members', 'undoc-members', 'show-inheritance' ] +autodoc_default_flags = [ 'members', 'undoc-members' ] +# Prevent alphabetical reordering of module members. +autodoc_member_order = 'bysource' def dont_skip_init(app, what, name, obj, skip, options): if name == "__init__": diff --git a/doc/source/index.rst b/doc/source/index.rst index dc176f71ec1..87bd0f9da02 100644 --- a/doc/source/index.rst +++ b/doc/source/index.rst @@ -31,7 +31,7 @@ For more information on the Galaxy Project, please visit the https://galaxyproje .. _dev-docs: .. toctree:: - :maxdepth: 1 + :maxdepth: 2 :caption: Developer Documentation Development @@ -53,15 +53,14 @@ Indices and tables * :ref:`genindex` * :ref:`modindex` -* :ref:`search` Building this Documentation =========================== -If you have your own copy of the Galaxy source code, you can also generate your own version of this documentation: +If you have your own copy of the Galaxy source code, you can also generate your own version of this documentation. Run the following command from the Galaxy's root: :: - $ make -C doc/ html + $ make docs -The generated documentation will be in ``doc/build/html/`` and can be viewed with a web browser. Note that you will need to install Sphinx and a fair number of module dependencies before this will produce output. \ No newline at end of file +The generated documentation will be in ``doc/build/html/`` and can be viewed with a web browser. Note that you will need to install Sphinx and a other module dependencies which are listed in the Makefile in the Galaxy root folder. \ No newline at end of file diff --git a/doc/source/lib/galaxy.webapps.galaxy.api.rst b/doc/source/lib/galaxy.webapps.galaxy.api.rst deleted file mode 100644 index 657035ef368..00000000000 --- a/doc/source/lib/galaxy.webapps.galaxy.api.rst +++ /dev/null @@ -1,324 +0,0 @@ -galaxy.webapps.galaxy.api package -================================= - -.. automodule:: galaxy.webapps.galaxy.api - :members: - :undoc-members: - :show-inheritance: - -Submodules ----------- - -galaxy.webapps.galaxy.api.annotations module --------------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.annotations - :members: - :undoc-members: - :show-inheritance: - -galaxy.webapps.galaxy.api.authenticate module ---------------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.authenticate - :members: - :undoc-members: - :show-inheritance: - -galaxy.webapps.galaxy.api.configuration module ----------------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.configuration - :members: - :undoc-members: - :show-inheritance: - -galaxy.webapps.galaxy.api.dataset_collections module ----------------------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.dataset_collections - :members: - :undoc-members: - :show-inheritance: - -galaxy.webapps.galaxy.api.datasets module ------------------------------------------ - -.. automodule:: galaxy.webapps.galaxy.api.datasets - :members: - :undoc-members: - :show-inheritance: - -galaxy.webapps.galaxy.api.datatypes module ------------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.datatypes - :members: - :undoc-members: - :show-inheritance: - -galaxy.webapps.galaxy.api.extended_metadata module --------------------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.extended_metadata - :members: - :undoc-members: - :show-inheritance: - -galaxy.webapps.galaxy.api.folder_contents module ------------------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.folder_contents - :members: - :undoc-members: - :show-inheritance: - -galaxy.webapps.galaxy.api.folders module ----------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.folders - :members: - :undoc-members: - :show-inheritance: - -galaxy.webapps.galaxy.api.forms module --------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.forms - :members: - :undoc-members: - :show-inheritance: - -galaxy.webapps.galaxy.api.genomes module ----------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.genomes - :members: - :undoc-members: - :show-inheritance: - -galaxy.webapps.galaxy.api.group_roles module --------------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.group_roles - :members: - :undoc-members: - :show-inheritance: - -galaxy.webapps.galaxy.api.group_users module --------------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.group_users - :members: - :undoc-members: - :show-inheritance: - -galaxy.webapps.galaxy.api.groups module ---------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.groups - :members: - :undoc-members: - :show-inheritance: - -galaxy.webapps.galaxy.api.histories module ------------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.histories - :members: - :undoc-members: - :show-inheritance: - -galaxy.webapps.galaxy.api.history_contents module -------------------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.history_contents - :members: - :undoc-members: - :show-inheritance: - -galaxy.webapps.galaxy.api.item_tags module ------------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.item_tags - :members: - :undoc-members: - :show-inheritance: - -galaxy.webapps.galaxy.api.job_files module ------------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.job_files - :members: - :undoc-members: - :show-inheritance: - -galaxy.webapps.galaxy.api.jobs module -------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.jobs - :members: - :undoc-members: - :show-inheritance: - -galaxy.webapps.galaxy.api.lda_datasets module ---------------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.lda_datasets - :members: - :undoc-members: - :show-inheritance: - -galaxy.webapps.galaxy.api.libraries module ------------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.libraries - :members: - :undoc-members: - :show-inheritance: - -galaxy.webapps.galaxy.api.library_contents module -------------------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.library_contents - :members: - :undoc-members: - :show-inheritance: - -galaxy.webapps.galaxy.api.metrics module ----------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.metrics - :members: - :undoc-members: - :show-inheritance: - -galaxy.webapps.galaxy.api.page_revisions module ------------------------------------------------ - -.. automodule:: galaxy.webapps.galaxy.api.page_revisions - :members: - :undoc-members: - :show-inheritance: - -galaxy.webapps.galaxy.api.pages module --------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.pages - :members: - :undoc-members: - :show-inheritance: - -galaxy.webapps.galaxy.api.provenance module -------------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.provenance - :members: - :undoc-members: - :show-inheritance: - -galaxy.webapps.galaxy.api.quotas module ---------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.quotas - :members: - :undoc-members: - :show-inheritance: - -galaxy.webapps.galaxy.api.remote_files module ---------------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.remote_files - :members: - :undoc-members: - :show-inheritance: - -galaxy.webapps.galaxy.api.request_types module ----------------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.request_types - :members: - :undoc-members: - :show-inheritance: - -galaxy.webapps.galaxy.api.requests module ------------------------------------------ - -.. automodule:: galaxy.webapps.galaxy.api.requests - :members: - :undoc-members: - :show-inheritance: - -galaxy.webapps.galaxy.api.roles module --------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.roles - :members: - :undoc-members: - :show-inheritance: - -galaxy.webapps.galaxy.api.samples module ----------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.samples - :members: - :undoc-members: - :show-inheritance: - -galaxy.webapps.galaxy.api.search module ---------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.search - :members: - :undoc-members: - :show-inheritance: - -galaxy.webapps.galaxy.api.tool_data module ------------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.tool_data - :members: - :undoc-members: - :show-inheritance: - -galaxy.webapps.galaxy.api.tool_shed_repositories module -------------------------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.tool_shed_repositories - :members: - :undoc-members: - :show-inheritance: - -galaxy.webapps.galaxy.api.tools module --------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.tools - :members: - :undoc-members: - :show-inheritance: - -galaxy.webapps.galaxy.api.users module --------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.users - :members: - :undoc-members: - :show-inheritance: - -galaxy.webapps.galaxy.api.visualizations module ------------------------------------------------ - -.. automodule:: galaxy.webapps.galaxy.api.visualizations - :members: - :undoc-members: - :show-inheritance: - -galaxy.webapps.galaxy.api.workflows module ------------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.api.workflows - :members: - :undoc-members: - :show-inheritance: - - diff --git a/doc/source/lib/galaxy.webapps.tool_shed.api.rst b/doc/source/lib/galaxy.webapps.tool_shed.api.rst deleted file mode 100644 index 16a54648a2a..00000000000 --- a/doc/source/lib/galaxy.webapps.tool_shed.api.rst +++ /dev/null @@ -1,76 +0,0 @@ -galaxy.webapps.tool_shed.api package -==================================== - -.. automodule:: galaxy.webapps.tool_shed.api - :members: - :undoc-members: - :show-inheritance: - -Submodules ----------- - -galaxy.webapps.tool_shed.api.authenticate module ------------------------------------------------- - -.. automodule:: galaxy.webapps.tool_shed.api.authenticate - :members: - :undoc-members: - :show-inheritance: - -galaxy.webapps.tool_shed.api.categories module ----------------------------------------------- - -.. automodule:: galaxy.webapps.tool_shed.api.categories - :members: - :undoc-members: - :show-inheritance: - -galaxy.webapps.tool_shed.api.configuration module -------------------------------------------------- - -.. automodule:: galaxy.webapps.tool_shed.api.configuration - :members: - :undoc-members: - :show-inheritance: - -galaxy.webapps.tool_shed.api.groups module ------------------------------------------- - -.. automodule:: galaxy.webapps.tool_shed.api.groups - :members: - :undoc-members: - :show-inheritance: - -galaxy.webapps.tool_shed.api.repositories module ------------------------------------------------- - -.. automodule:: galaxy.webapps.tool_shed.api.repositories - :members: - :undoc-members: - :show-inheritance: - -galaxy.webapps.tool_shed.api.repository_revisions module --------------------------------------------------------- - -.. automodule:: galaxy.webapps.tool_shed.api.repository_revisions - :members: - :undoc-members: - :show-inheritance: - -galaxy.webapps.tool_shed.api.tools module ------------------------------------------ - -.. automodule:: galaxy.webapps.tool_shed.api.tools - :members: - :undoc-members: - :show-inheritance: - -galaxy.webapps.tool_shed.api.users module ------------------------------------------ - -.. automodule:: galaxy.webapps.tool_shed.api.users - :members: - :undoc-members: - :show-inheritance: - - diff --git a/doc/source/releases/_header.rst b/doc/source/releases/_header.rst index ddaf966e0c9..08b00e3dd05 100644 --- a/doc/source/releases/_header.rst +++ b/doc/source/releases/_header.rst @@ -1,3 +1,3 @@ -.. image:: https://wiki.galaxyproject.org/Images/GalaxyLogos?action=AttachFile&do=get&target=galaxy_logo_25percent_transparent.png - :alt: Get the Galaxy Release Your Way +.. image:: https://galaxyproject.org/images/galaxy-logos/galaxy_logo_25percent_transparent.png + :alt: Get Galaxy :target: http://getgalaxy.org diff --git a/doc/source/ts_api_doc.rst b/doc/source/ts_api_doc.rst index 99b6c8c1be6..2d1373ce5aa 100644 --- a/doc/source/ts_api_doc.rst +++ b/doc/source/ts_api_doc.rst @@ -3,7 +3,7 @@ Tool Shed API Documentation The Galaxy Tool Shed can be accessed programmatically using API described here via shell scripts and other programs. -To interact with the API you first need to log in as your user, navigate +To interact with the API you first need to obtain API key e.g.: log in as your user, navigate to the API Keys page in the User menu, and generate a new API key. This key you have to attach to every request as a parameter. Example: @@ -12,6 +12,6 @@ key you have to attach to every request as a parameter. Example: GET https://toolshed.g2.bx.psu.edu/api/repositories?q=fastq?key=SOME_KEY_HERE .. toctree:: - :maxdepth: 3 + :maxdepth: 2 - Toolshed API Documentation + API Documentation