From 2f992d90ae8e0a4efec313fa0064b1576a26c2ba Mon Sep 17 00:00:00 2001 From: E Rasche Date: Thu, 1 Jun 2017 16:43:21 +0000 Subject: [PATCH] Rebase --- README.rst | 2 +- contrib/galaxy.debian-init | 2 +- contrib/galaxy_supervisor.conf | 4 ++-- doc/source/admin/authentication.md | 2 +- .../admin/special_topics/mulled_containers.rst | 2 +- doc/source/dev/build_a_job_runner.rst | 4 ++-- doc/source/releases/13.01_announce.rst | 2 +- doc/source/releases/13.02_announce.rst | 2 +- doc/source/releases/13.04_announce.rst | 2 +- doc/source/releases/13.06_announce.rst | 2 +- doc/source/releases/13.08_announce.rst | 2 +- doc/source/releases/13.11_announce.rst | 2 +- doc/source/releases/14.02_announce.rst | 2 +- doc/source/releases/14.04_announce.rst | 2 +- doc/source/releases/14.06_announce.rst | 2 +- doc/source/releases/14.08_announce.rst | 2 +- doc/source/releases/14.10_announce.rst | 2 +- doc/source/releases/15.01_announce.rst | 2 +- doc/source/releases/15.03_announce.rst | 2 +- doc/source/releases/15.05.rst | 2 +- doc/source/releases/15.05_announce.rst | 2 +- doc/source/releases/15.07_announce.rst | 2 +- doc/source/releases/15.10_announce.rst | 4 ++-- doc/source/releases/16.01_announce.rst | 2 +- doc/source/releases/16.04_announce.rst | 2 +- doc/source/releases/16.07_announce.rst | 4 ++-- doc/source/releases/16.10_announce.rst | 2 +- doc/source/releases/17.01_announce.rst | 2 +- .../architecture/galaxy_architecture.md | 2 +- lib/galaxy/tools/xsd/README.md | 2 +- lib/galaxy/tools/xsd/galaxy.xsd | 16 ++++++++-------- scripts/bootstrap_history.py | 11 ++++------- static/welcome.html.sample | 6 +++--- test/functional/tools/sample_datatypes_conf.xml | 6 +++--- test/qunit/test-data/bootstrapped.js | 6 +++--- test/qunit/tests/galaxy-app-base.js | 6 +++--- 36 files changed, 58 insertions(+), 61 deletions(-) diff --git a/README.rst b/README.rst index 0abd2e598a2..50775f18ff8 100644 --- 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 index edb94128486..1de8ffc83fb 100644 --- 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 /.venv # A simple way to activate this virtualenv is to use the python interpreter in /.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 index e739365581f..ca61fdb6be5 100644 --- 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 = ". # 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 index 81ce814433f..15ed1b5ef89 100644 --- 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 index e0a5b9129b5..6cd0a281d36 100644 --- 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 index 9e8577c87d7..a34c7a0f638 100644 --- 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 `__. +`here `__. 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 index 1f6ad49c71c..37b7cee8ad7 100644 --- 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 index 09a67d50e33..4062939fc0c 100644 --- 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 index e2f93782b34..32d2ce9d223 100644 --- 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 index 58afa3846a1..56ff21ca0cc 100644 --- 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 index 44c8ad154fc..7bfaeb98992 100644 --- 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 index 4fb4c7c48ba..fa53fadd389 100644 --- 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 index 94462d732b6..440dd9decdf 100644 --- 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 index 22e02c8993e..2f2941dd062 100644 --- 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 index 5b690ef3d60..f9ec319cdca 100644 --- 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 index 7052e85c8f1..41ac1a88c87 100644 --- 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 index e6aaf567d39..32b5cc49b8a 100644 --- 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 index f670f3ced21..4712086e356 100644 --- 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 index 7206175f6a1..efc8c185a46 100644 --- 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 index 8e68f3f1989..5de92f86cfc 100644 --- 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 index db98dc32bdc..3617fdd72a7 100644 --- 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 `__ for additional details regarding the source code locations. +See `our wiki `__ 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 index f9cafcb6ce3..ca02d6dc81e 100644 --- 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 `__ for additional details regarding the source code locations. +See `our wiki `__ 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 index 9869f3bdcdf..c46bf09a882 100644 --- 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 `__ for additional details regarding the source code locations. +See `our wiki `__ 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 index 60ea98660f8..387666c4d86 100644 --- 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 `__ for additional details regarding the source code locations. +See `our wiki `__ 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 index e615714a65a..cf97350d0e3 100644 --- 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 `__ for additional details regarding the source code locations. +See `our wiki `__ 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 index 131609e79ad..acde41b5be1 100644 --- 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 `__. + `wiki `__. Implemented in `PR #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 `__ for additional details regarding the source code locations. +See `our wiki `__ 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 index de1e4a3a997..49ce02e21b6 100644 --- 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 `__ for additional details regarding the source code location. +See `our wiki `__ 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 index 199dbbd68f4..6abf8ac34ee 100644 --- 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 `__ for additional details regarding the source code locations. +See `our wiki `__ 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 index 8aa0c9b922b..a7a17877e07 100644 --- 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 index 60274d37b3b..9cf7855f26f 100644 --- 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 index 36e92c2226f..3dc11bcf1fb 100644 --- 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``. 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``. @@ -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/). ]]> @@ -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/). ]]> @@ -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. 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. diff --git a/scripts/bootstrap_history.py b/scripts/bootstrap_history.py index 3a39708a0ef..766226ecebf 100644 --- a/scripts/bootstrap_history.py +++ b/scripts/bootstrap_history.py @@ -114,7 +114,7 @@ To update an existing Galaxy repository run: $$ git checkout release_${release} && git pull --ff-only origin release_${release} -See our community `hub `__ for additional details regarding the source code locations. +See `our wiki `__ for additional details regarding the source code locations. Release Notes =========================================================== @@ -174,7 +174,7 @@ RELEASE_ISSUE_TEMPLATE = string.Template(""" - [ ] **Create Release Notes** - - [ ] Review merged PRs and ensure they all have a milestones attached. [Link](https://github.com/galaxyproject/galaxy/pulls?q=is%3Apr+is%3Amerged+no%3Amilestone%20-label%3Amerge) + - [ ] Review merged PRs and ensure they all have a milestones attached. [Link](https://github.com/galaxyproject/galaxy/pulls?q=is%3Apr+is%3Amerged+no%3Amilestone) - [ ] Checkout release branch git checkout release_${version} -b ${version}_release_notes @@ -185,9 +185,6 @@ RELEASE_ISSUE_TEMPLATE = string.Template(""" make release-bootstrap-history RELEASE_CURR=${version} - [ ] Open newly created files and manually curate major topics and release notes. - - [ ] Check ``diff`` of ``galaxy.ini.sample`` against last release and include any important changes. - - [ ] Check ``diff`` of ``datatypes_conf.xml.sample`` against last release and include any important changes. - - [ ] Check if there were database migrations and include a high-profile note about it if so. - [ ] Commit release notes. git add docs/; git commit -m "Release notes for $version"; git push upstream ${version}_release_notes @@ -207,7 +204,7 @@ RELEASE_ISSUE_TEMPLATE = string.Template(""" make release-create RELEASE_CURR=${version} - - [ ] Switch Jenkins documentation build [branch specifier](https://jenkins.galaxyproject.org/job/Sphinx-Docs/configure) to `*/release_${version}`. + - [ ] Switch Jenkins documentation build [branch specifier](https://jenkins.galaxyproject.org/job/Sphinx-Docs/configure) to `*/release_{version}`. - [ ] Trigger the documentation build. - [ ] **Do Docker Release** @@ -225,7 +222,7 @@ RELEASE_ISSUE_TEMPLATE = string.Template(""" - [ ] Verify release included in https://docs.galaxyproject.org/en/master/releases/index.html - [ ] Review announcement in https://github.com/galaxyproject/galaxy/blob/dev/doc/source/releases/${version}_announce.rst - [ ] Stage annoucement content (Wiki, Biostars, Bit.ly link) on annouce date to capture date tags. Note: all final content does not need to be completed to do this. - - [ ] Create wiki *highlights* and post to http://galaxyproject.org News (w/ RSS) and NewsBriefs. [An Example](https://wiki.galaxyproject.org/News/2016_04_GalaxyRelease). + - [ ] Create wiki *highlights* and post to http://galaxyproject.org News (w/ RSS) and NewsBriefs. [An Example](https://galaxyproject.org/news/2016-04-galaxy-release). - [ ] Tweet docs news *highlights* via bit.ly link to https://twitter.com/galaxyproject/ (As user ``galaxyproject``, password in Galaxy password store under ``twitter.com / galaxyproject`` ). [An Example](https://twitter.com/galaxyproject/status/733029921316986881). - [ ] Post *highlights* type News to Galaxy Biostars https://biostar.usegalaxy.org. [An Example](https://biostar.usegalaxy.org/p/17712/). - [ ] Email *highlights* to [galaxy-dev](http://dev.list.galaxyproject.org/) and [galaxy-announce](http://announce.list.galaxyproject.org/) @lists.galaxyproject.org. [An Example](http://dev.list.galaxyproject.org/The-Galaxy-release-16-04-is-out-tp4669419.html) diff --git a/static/welcome.html.sample b/static/welcome.html.sample index 7fc590a3548..821bc836a45 100644 --- a/static/welcome.html.sample +++ b/static/welcome.html.sample @@ -10,8 +10,8 @@

Hello, Galaxy is running!

To customize this page edit static/welcome.html
- Configuring Galaxy » - Installing Tools » + Configuring Galaxy » + Installing Tools »
@@ -26,7 +26,7 @@

Galaxy is an open platform for supporting data intensive - research. Galaxy is developed by The Galaxy Team + research. Galaxy is developed by The Galaxy Team with the support of many contributors.