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galaxyproject · Jun 1, 2017 · 2f992d9 · 2f992d9
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diff --git a/README.rst b/README.rst
@@ -49,7 +49,7 @@ done in the ``config/galaxy.ini`` file. Tools can be either installed
 from the Tool Shed or added manually. For details please see the Galaxy
 wiki:
 
-https://wiki.galaxyproject.org/Admin/Tools/AddToolFromToolShedTutorial
+https://galaxyproject.org/admin/tools/add-tool-from-toolshed-tutorial/
 
 Not all dependencies are included for the tools provided in the sample
 ``tool_conf.xml``. A full list of external dependencies is available at:

diff --git a/contrib/galaxy.debian-init b/contrib/galaxy.debian-init
@@ -18,7 +18,7 @@ GROUP="nogroup"
 GALAXY_DIR="/home/galaxy/galaxy_dist/"
 # Galaxy releases >= 16.01 installs dependencies by default into a virtualenv in <GALAXY_DIR>/.venv
 # A simple way to activate this virtualenv is to use the python interpreter in <GALAXY_DIR>/.venv
-# See https://wiki.galaxyproject.org/News/2016_01_GalaxyRelease and
+# See https://galaxyproject.org/news/2016-01-galaxy-release/ and
 # https://github.com/galaxyproject/galaxy/blob/dev/doc/source/admin/framework_dependencies.rst
 PYTHON="/home/galaxy/galaxy_dist/.venv/bin/python"
 OPTS="./scripts/paster.py serve --log-file /home/galaxy/galaxy.log config/galaxy.ini"

diff --git a/contrib/galaxy_supervisor.conf b/contrib/galaxy_supervisor.conf
@@ -12,8 +12,8 @@
 # This assumes galaxy is installed in /home/galaxy/galaxy, so change occurences of /home/galaxy/galaxy accordingly.
 # If you want to run galaxy under a different username, change "user = galaxy" to "user = <your user>".
 # You will probably want to proxy uwsgi (you can't connect with a browser to uwsgi port 4001) with nginx or apache, 
-# see https://wiki.galaxyproject.org/Admin/Config/Performance/Scaling#uWSGI-1
-# or https://wiki.galaxyproject.org/Admin/Config/Performance/Scaling#uWSGI-2 . 
+# see https://galaxyproject.org/admin/config/performance/scaling/#apache
+# or https://galaxyproject.org/admin/config/performance/scaling/#nginx
 
 [program:galaxy_web]
 command         = /home/galaxy/galaxy/.venv/bin/uwsgi --virtualenv /home/galaxy/galaxy/.venv --ini-paste /home/galaxy/galaxy/config/galaxy.ini --logdate --master --processes 2 --threads 2 --logto /home/galaxy/galaxy/uwsgi.log --socket 127.0.0.1:4001 --pythonpath lib --stats 127.0.0.1:9191

diff --git a/doc/source/admin/authentication.md b/doc/source/admin/authentication.md
@@ -104,7 +104,7 @@ Smtp server takes care of the email sending and the activation_email email is us
 
 You can also set the instance_resource_url which is shown in the activation emails so you can point users to your wiki or other materials.
 ```
-instance_resource_url = http://wiki.galaxyproject.org/
+instance_resource_url = http://galaxyproject.org/
 ```
 
 

diff --git a/doc/source/admin/special_topics/mulled_containers.rst b/doc/source/admin/special_topics/mulled_containers.rst
@@ -120,7 +120,7 @@ you could do something along these lines.
 
 
 .. _Galaxy Conda documentation: ./conda_faq.rst
-.. _IUC: https://wiki.galaxyproject.org/IUC
+.. _IUC: https://galaxyproject.org/iuc/
 .. _container annotation:  https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/catDocker.xml#L4
 .. _BioContainers: https://github.com/biocontainers
 .. _bioconda: https://github.com/bioconda/bioconda-recipes

diff --git a/doc/source/dev/build_a_job_runner.rst b/doc/source/dev/build_a_job_runner.rst
@@ -11,7 +11,7 @@ components based on their function.
 We assume you are familiar with setting up and managing a local installation of Galaxy.
 
 To learn more about the basics, please refer to:
-https://wiki.galaxyproject.org/Admin/GetGalaxy
+https://galaxyproject.org/admin/get-galaxy/
 
 To explore existing runners, please refer to:
 https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/jobs/runners
@@ -81,7 +81,7 @@ The input params are read from job\_conf.xml and passed to the runner by
 the Galaxy framework. Configuration of where to run jobs and external
 runner configuration is performed in the job\_conf.xml file. More
 information about job\_conf.xml is available
-`here <https://wiki.galaxyproject.org/Admin/Config/Jobs>`__.
+`here <https://galaxyproject.org/admin/config/jobs/>`__.
 
 Have a look at the sample job\_conf.xml:
 

diff --git a/doc/source/releases/13.01_announce.rst b/doc/source/releases/13.01_announce.rst
@@ -6,6 +6,6 @@ January 2013 Galaxy Release (v 13.01)
 
 Please see the `Galaxy wiki`_ for announcement and release notes.
 
-.. _Galaxy wiki: https://wiki.galaxyproject.org/News/2013_01_11_DistributionNewsBrief
+.. _Galaxy wiki: https://galaxyproject.org/news/2013-01-11-distribution-news-brief/
 
 .. include:: _thanks.rst
diff --git a/doc/source/releases/13.02_announce.rst b/doc/source/releases/13.02_announce.rst
@@ -6,6 +6,6 @@ February 2013 Galaxy Release (v 13.02)
 
 Please see the `Galaxy wiki`_ for announcement and release notes.
 
-.. _Galaxy wiki: https://wiki.galaxyproject.org/News/2013_02_08_GalaxyNewsBrief
+.. _Galaxy wiki: https://galaxyproject.org/news/2013-02-08-galaxy-news-brief/
 
 .. include:: _thanks.rst
diff --git a/doc/source/releases/13.04_announce.rst b/doc/source/releases/13.04_announce.rst
@@ -6,6 +6,6 @@ April 2013 Galaxy Release (v 13.04)
 
 Please see the `Galaxy wiki`_ for announcement and release notes.
 
-.. _Galaxy wiki: https://wiki.galaxyproject.org/News/2013_04_01_Galaxy_Distribution
+.. _Galaxy wiki: https://galaxyproject.org/news/2013-04-01-galaxy-distribution/
 
 .. include:: _thanks.rst
diff --git a/doc/source/releases/13.06_announce.rst b/doc/source/releases/13.06_announce.rst
@@ -6,6 +6,6 @@ June 2013 Galaxy Release (v 13.06)
 
 Please see the `Galaxy wiki`_ for announcement and release notes.
 
-.. _Galaxy wiki: https://wiki.galaxyproject.org/News/2013_06_03_Galaxy_Distribution
+.. _Galaxy wiki: https://galaxyproject.org/news/2013-06-03-galaxy-distribution/
 
 .. include:: _thanks.rst
diff --git a/doc/source/releases/13.08_announce.rst b/doc/source/releases/13.08_announce.rst
@@ -6,6 +6,6 @@ August 2013 Galaxy Release (v 13.08)
 
 Please see the `Galaxy wiki`_ for announcement and release notes.
 
-.. _Galaxy wiki: https://wiki.galaxyproject.org/News/2013_08_12_Galaxy_Distribution
+.. _Galaxy wiki: https://galaxyproject.org/news/2013-08-12-galaxy-distribution/
 
 .. include:: _thanks.rst
diff --git a/doc/source/releases/13.11_announce.rst b/doc/source/releases/13.11_announce.rst
@@ -6,6 +6,6 @@ November 2013 Galaxy Release (v 13.11)
 
 Please see the `Galaxy wiki`_ for announcement and release notes.
 
-.. _Galaxy wiki: https://wiki.galaxyproject.org/News/2013_11_04_Galaxy_Distribution
+.. _Galaxy wiki: https://galaxyproject.org/news/2013-11-04-galaxy-distribution/
 
 .. include:: _thanks.rst
diff --git a/doc/source/releases/14.02_announce.rst b/doc/source/releases/14.02_announce.rst
@@ -6,6 +6,6 @@ February 2014 Galaxy Release (v 14.02)
 
 Please see the `Galaxy wiki`_ for announcement and release notes.
 
-.. _Galaxy wiki: https://wiki.galaxyproject.org/News/2014_02_10_Galaxy_Distribution
+.. _Galaxy wiki: https://galaxyproject.org/news/2014-02-10-galaxy-distribution/
 
 .. include:: _thanks.rst
diff --git a/doc/source/releases/14.04_announce.rst b/doc/source/releases/14.04_announce.rst
@@ -6,6 +6,6 @@ April 2014 Galaxy Release (v 14.04)
 
 Please see the `Galaxy wiki`_ for announcement and release notes.
 
-.. _Galaxy wiki: https://wiki.galaxyproject.org/News/2014_04_14_Galaxy_Distribution
+.. _Galaxy wiki: https://galaxyproject.org/news/2014-04-14-galaxy-distribution/
 
 .. include:: _thanks.rst
diff --git a/doc/source/releases/14.06_announce.rst b/doc/source/releases/14.06_announce.rst
@@ -6,6 +6,6 @@ June 2014 Galaxy Release (v 14.06)
 
 Please see the `Galaxy wiki`_ for announcement and release notes.
 
-.. _Galaxy wiki: https://wiki.galaxyproject.org/News/2014_06_02_Galaxy_Distribution
+.. _Galaxy wiki: https://galaxyproject.org/news/2014-06-02-galaxy-distribution/
 
 .. include:: _thanks.rst
diff --git a/doc/source/releases/14.08_announce.rst b/doc/source/releases/14.08_announce.rst
@@ -6,6 +6,6 @@ August 2014 Galaxy Release (v 14.08)
 
 Please see the `Galaxy wiki`_ for announcement and release notes.
 
-.. _Galaxy wiki: https://wiki.galaxyproject.org/News/2014_08_11_Galaxy_Distribution
+.. _Galaxy wiki: https://galaxyproject.org/news/2014-08-11-galaxy-distribution/
 
 .. include:: _thanks.rst
diff --git a/doc/source/releases/14.10_announce.rst b/doc/source/releases/14.10_announce.rst
@@ -6,6 +6,6 @@ October 2014 Galaxy Release (v 14.10)
 
 Please see the `Galaxy wiki`_ for announcement and release notes.
 
-.. _Galaxy wiki: https://wiki.galaxyproject.org/News/2014_10_06_Galaxy_Distribution
+.. _Galaxy wiki: https://galaxyproject.org/news/2014-10-06-galaxy-distribution/
 
 .. include:: _thanks.rst
diff --git a/doc/source/releases/15.01_announce.rst b/doc/source/releases/15.01_announce.rst
@@ -6,6 +6,6 @@ January 2015 Galaxy Release (v 15.01)
 
 Please see the `Galaxy wiki`_ for announcement and release notes.
 
-.. _Galaxy wiki: https://wiki.galaxyproject.org/News/2015_01_13_Galaxy_Distribution
+.. _Galaxy wiki: https://galaxyproject.org/news/2015-01-13-galaxy-distribution/
 
 .. include:: _thanks.rst
diff --git a/doc/source/releases/15.03_announce.rst b/doc/source/releases/15.03_announce.rst
@@ -6,6 +6,6 @@ March 2015 Galaxy Release (v 15.03)
 
 Please see the `Galaxy wiki`_ for announcement and release notes.
 
-.. _Galaxy wiki: https://wiki.galaxyproject.org/News/2015_03_GalaxyRelease
+.. _Galaxy wiki: https://galaxyproject.org/news/2015-03-galaxy-release/
 
 .. include:: _thanks.rst
diff --git a/doc/source/releases/15.05.rst b/doc/source/releases/15.05.rst
@@ -192,7 +192,7 @@ Fixes
 
 .. _IGV: https://www.broadinstitute.org/igv/
 .. _External Display Application: https://wiki.galaxyproject.org/Admin/Tools/External%20Display%20Applications%20Tutorial
-.. _Interactive Environments: https://wiki.galaxyproject.org/Admin/IEs
+.. _Interactive Environments: https://galaxyproject.org/Admin/IEs
 .. _TravisCI: https://travis-ci.org/
 .. _Tox: https://testrun.org/tox/latest/
 .. _Source Maps: https://developer.chrome.com/devtools/docs/javascript-debugging#source-maps

diff --git a/doc/source/releases/15.05_announce.rst b/doc/source/releases/15.05_announce.rst
@@ -47,7 +47,7 @@ Upgrade
       % hg update latest_15.05
 
 
-See `our wiki <https://wiki.galaxyproject.org/Develop/SourceCode>`__ for additional details regarding the source code locations.
+See `our wiki <https://galaxyproject.org/develop/source-code/>`__ for additional details regarding the source code locations.
 
 Release Notes
 ===========================================================

diff --git a/doc/source/releases/15.07_announce.rst b/doc/source/releases/15.07_announce.rst
@@ -52,7 +52,7 @@ Upgrade
       % hg update latest_15.07
 
 
-See `our wiki <https://wiki.galaxyproject.org/Develop/SourceCode>`__ for additional details regarding the source code locations.
+See `our wiki <https://galaxyproject.org/develop/source-code/>`__ for additional details regarding the source code locations.
 
 Deprecation Notice
 ===========================================================

diff --git a/doc/source/releases/15.10_announce.rst b/doc/source/releases/15.10_announce.rst
@@ -52,7 +52,7 @@ Upgrade
       % hg update latest_15.10
 
 
-See `our wiki <https://wiki.galaxyproject.org/Develop/SourceCode>`__ for additional details regarding the source code locations.
+See `our wiki <https://galaxyproject.org/develop/source-code/>`__ for additional details regarding the source code locations.
 
 
 Deprecation Notices
@@ -61,7 +61,7 @@ Deprecation Notices
 The Mercurial repository at https://bitbucket.org/galaxy/galaxy-dist is deprecated.
 **We recommend deployers to switch their instances to git** and follow the `master`
 branch of GitHub repository https://github.com/galaxyproject/galaxy
-Details are available at https://wiki.galaxyproject.org/Develop/SourceCode
+Details are available at https://galaxyproject.org/develop/source-code/
 *The next few releases will still be available on Bitbucket, but they may be
 less up to date than the corresponding GitHub branches.*
 

diff --git a/doc/source/releases/16.01_announce.rst b/doc/source/releases/16.01_announce.rst
@@ -63,7 +63,7 @@ Upgrade
       % hg update latest_16.01
 
 
-See `our wiki <https://wiki.galaxyproject.org/Develop/SourceCode>`__ for additional details regarding the source code locations.
+See `our wiki <https://galaxyproject.org/develop/source-code/>`__ for additional details regarding the source code locations.
 
 Deprecation Notices
 ===========================================================

diff --git a/doc/source/releases/16.04_announce.rst b/doc/source/releases/16.04_announce.rst
@@ -61,7 +61,7 @@ Upgrade
       % hg update latest_16.04
 
 
-See `our wiki <https://wiki.galaxyproject.org/Develop/SourceCode>`__ for additional details regarding the source code locations.
+See `our wiki <https://galaxyproject.org/develop/source-code/>`__ for additional details regarding the source code locations.
 
 Security
 ===========================================================

diff --git a/doc/source/releases/16.07_announce.rst b/doc/source/releases/16.07_announce.rst
@@ -18,7 +18,7 @@ Highlights
   Our friends from Canada National Microbiology Laboratory enhanced
   Galaxy with feature that allows dynamic mapping of tools to destinations
   based on finer grained admin-specified rules. Please see the
-  `wiki <https://wiki.galaxyproject.org/Admin/Config/Jobs#Dynamic_Destination_Mapping>`__.
+  `wiki <https://galaxyproject.org/admin/config/jobs/#Dynamic_Destination_Mapping>`__.
   Implemented in `PR #2579 <https://github.com/galaxyproject/galaxy/pull/2579>`__
 
 **Galaxy chat**
@@ -41,7 +41,7 @@ Update of existing Galaxy repository
 
       $ git checkout release_16.07 && git pull --ff-only origin release_16.07
 
-See `our wiki <https://wiki.galaxyproject.org/Develop/SourceCode>`__ for additional details regarding the source code locations.
+See `our wiki <https://galaxyproject.org/develop/source-code/>`__ for additional details regarding the source code locations.
 
 Deprecation Notices
 ===========================================================

diff --git a/doc/source/releases/16.10_announce.rst b/doc/source/releases/16.10_announce.rst
@@ -41,7 +41,7 @@ To update an existing Galaxy repository run:
 
       $ git checkout release_16.10 && git pull --ff-only origin release_16.10
 
-See `our wiki <https://wiki.galaxyproject.org/Develop/SourceCode>`__ for additional details regarding the source code location.
+See `our wiki <https://galaxyproject.org/develop/source-code/>`__ for additional details regarding the source code location.
 
 Deprecation Notices
 ===================

diff --git a/doc/source/releases/17.01_announce.rst b/doc/source/releases/17.01_announce.rst
@@ -44,7 +44,7 @@ To update an existing Galaxy repository run:
 
       $ git checkout release_17.01 && git pull --ff-only origin release_17.01
 
-See `our wiki <https://wiki.galaxyproject.org/Develop/SourceCode>`__ for additional details regarding the source code locations.
+See `our wiki <https://galaxyproject.org/develop/source-code/>`__ for additional details regarding the source code locations.
 
 Deprecation Notices
 ===================

diff --git a/doc/source/slideshow/architecture/galaxy_architecture.md b/doc/source/slideshow/architecture/galaxy_architecture.md
@@ -443,7 +443,7 @@ def handle_request(self, environ, start_response):
 
 ### Database Diagram
 
-https://wiki.galaxyproject.org/Admin/Internals/DataModel
+https://galaxyproject.org/admin/internals/data-model/
 
 ---
 

diff --git a/lib/galaxy/tools/xsd/README.md b/lib/galaxy/tools/xsd/README.md
@@ -41,5 +41,5 @@ This code is free software released under the terms of the MIT license.
 # See also:
 
 * Galaxy https://usegalaxy.org/
-* Galaxy Tool XML File https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax
+* Galaxy Tool XML File https://galaxyproject.org/admin/tools/tool-config-syntax/
 
diff --git a/lib/galaxy/tools/xsd/galaxy.xsd b/lib/galaxy/tools/xsd/galaxy.xsd
@@ -166,8 +166,8 @@ graphical tool form by setting this to ``false``.</xs:documentation>
           <xs:documentation xml:lang="en">Allows for certain framework
 functionality to be performed on certain types of tools. Normal tools that execute
 typical command-line jobs do not need to specify this, special kinds of tools such
-as [Data Source](https://wiki.galaxyproject.org/Admin/Internals/DataSources) and
-[Data Manager](https://wiki.galaxyproject.org/Admin/Tools/DataManagers) tools should
+as [Data Source](https://galaxyproject.org/admin/internals/data-sources/) and
+[Data Manager](https://galaxyproject.org/admin/tools/data-managers/) tools should
 set this to have values such as ``data_source`` or ``manage_data``.</xs:documentation>
         </xs:annotation>
       </xs:attribute>
@@ -237,7 +237,7 @@ programs or modules that the tool depends upon are included in this tag set.
 When a tool runs, Galaxy attempts to *resolve* these requirements (also called
 dependencies). ``requirement``s are meant to be abstract and resolvable by
 multiple different systems (e.g. [conda](http://conda.pydata.org/docs/), the
-[Galaxy Tool Shed dependency management system](https://wiki.galaxyproject.org/ToolShedToolFeatures#Automatic_third-party_tool_dependency_installation_and_compilation_with_installed_repositories),
+[Galaxy Tool Shed dependency management system](https://galaxyproject.org/toolshed/tool-features/#Automatic_third-party_tool_dependency_installation_and_compilation_with_installed_repositories),
 or [environment modules](http://modules.sourceforge.net/)).
 
 Read more about dependency resolvers in Galaxy on
@@ -251,7 +251,7 @@ discussed in greater detail
 This example shows a tool that requires the samtools 0.0.18 package.
 
 This package is available via the Tool Shed (see
-[Tool Shed dependency management](https://wiki.galaxyproject.org/ToolShedToolFeatures#Automatic_third-party_tool_dependency_installation_and_compilation_with_installed_repositories)
+[Tool Shed dependency management](https://galaxyproject.org/toolshed/tool-features/#Automatic_third-party_tool_dependency_installation_and_compilation_with_installed_repositories)
 ) as well as [Conda](https://docs.galaxyproject.org/en/master/admin/conda_faq.html)
 and can be configured locally to adapt to any other package management system.
 
@@ -301,7 +301,7 @@ this tag allows the tool to suggest possible valid Docker containers for this
 tool.
 
 Read more about configuring Galaxy to run Docker jobs
-[here](https://wiki.galaxyproject.org/Admin/Tools/Docker).
+[here](https://galaxyproject.org/admin/tools/docker/).
 
 ]]></xs:documentation>
     </xs:annotation>
@@ -593,7 +593,7 @@ The documentation contained here is mostly reference documentation, for
 tutorials on writing tool tests please check out Planemo's
 [Test-Driven Development](https://planemo.readthedocs.io/en/latest/writing_advanced.html#test-driven-development)
 documentation or the much older wiki content for
-[WritingTests](https://wiki.galaxyproject.org/Admin/Tools/WritingTests).
+[WritingTests](https://galaxyproject.org/admin/tools/writing-tests/).
 
 ]]></xs:documentation>
     </xs:annotation>
@@ -1717,7 +1717,7 @@ conditionally reference ``${input_type.process_obs_metadata}`` with a Cheetah
 
 A common use of the conditional wrapper is to select between reference data
 managed by the Galaxy admins (for instance via
-[data managers](https://wiki.galaxyproject.org/Admin/Tools/DataManagers)
+[data managers](https://galaxyproject.org/admin/tools/data-managers/)
 ) and
 history files. A good example tool that demonstrates this is
 the [Bowtie 2](https://github.com/galaxyproject/tools-devteam/blob/master/tools/bowtie2/bowtie2_wrapper.xml) wrapper.
@@ -3103,7 +3103,7 @@ specified by the ``skip`` attribute.</xs:documentation>
             <xs:documentation xml:lang="en">Tool data table name to check against
 if ``type`` is ``dataset_metadata_in_tool_data``. See the documentation for
 [tool data tables](https://wiki.galaxyproject.org/Admin/Tools/Data%20Tables)
-and [data managers](https://wiki.galaxyproject.org/Admin/Tools/DataManagers) for
+and [data managers](https://galaxyproject.org/admin/tools/data-managers/) for
 more information.</xs:documentation>
           </xs:annotation>
         </xs:attribute>