From f174358b9542610ffa4c00588096a4e80583ae0a Mon Sep 17 00:00:00 2001 From: Martin Cech Date: Thu, 16 Mar 2017 15:54:22 -0400 Subject: [PATCH 1/5] fix link to galaxy logo --- doc/source/releases/_header.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) 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 From 85093dc13ad06eb8d4896f01d934846cd57c1473 Mon Sep 17 00:00:00 2001 From: Martin Cech Date: Thu, 16 Mar 2017 13:15:15 -0400 Subject: [PATCH 2/5] reword topic --- doc/source/admin/useful_scripts.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) 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. From e02e2cb09e245ab5cbbe48d532e4f3ffe9a1612a Mon Sep 17 00:00:00 2001 From: Martin Cech Date: Thu, 16 Mar 2017 14:55:07 -0400 Subject: [PATCH 3/5] improve doc-build-urself docs --- doc/source/index.rst | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/doc/source/index.rst b/doc/source/index.rst index dc176f71ec1..9882c7fee58 100644 --- a/doc/source/index.rst +++ b/doc/source/index.rst @@ -58,10 +58,10 @@ Indices and tables 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 From b4feb85f11280935b0ce13ea5d3693122f4319e8 Mon Sep 17 00:00:00 2001 From: Martin Cech Date: Mon, 27 Mar 2017 15:21:37 -0400 Subject: [PATCH 4/5] improve accessibility of API docs for both Galaxy and TS --- doc/source/api/api.rst | 209 +++++++++++ doc/source/api/ts_api.rst | 44 +++ doc/source/api_doc.rst | 13 +- doc/source/conf.py | 4 +- doc/source/index.rst | 3 +- doc/source/lib/galaxy.webapps.galaxy.api.rst | 324 ------------------ .../lib/galaxy.webapps.tool_shed.api.rst | 76 ---- doc/source/ts_api_doc.rst | 6 +- 8 files changed, 269 insertions(+), 410 deletions(-) create mode 100644 doc/source/api/api.rst create mode 100644 doc/source/api/ts_api.rst delete mode 100644 doc/source/lib/galaxy.webapps.galaxy.api.rst delete mode 100644 doc/source/lib/galaxy.webapps.tool_shed.api.rst 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 9882c7fee58..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 @@ -53,7 +53,6 @@ Indices and tables * :ref:`genindex` * :ref:`modindex` -* :ref:`search` Building this Documentation =========================== 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/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 From bdcf4807ce5f2d3c1f12cd23120f4f5ec55f0067 Mon Sep 17 00:00:00 2001 From: Martin Cech Date: Mon, 27 Mar 2017 15:39:54 -0400 Subject: [PATCH 5/5] add basic Reports documentation --- doc/source/admin/framework_dependencies.rst | 98 ++++++++++----------- doc/source/admin/index.rst | 1 + doc/source/admin/reports.md | 21 +++++ 3 files changed, 71 insertions(+), 49 deletions(-) create mode 100644 doc/source/admin/reports.md 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.