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1d19fd535ab39a89f7a957e28116c8f83fdcc241
Commit Graph
737 Commits
Author SHA1 Message Date
Nicola Soranzo 1d19fd535a Add note about HTTP Range also to Apache docs 2019-02-08 00:55:47 +00:00
pvanheus 041152bd14 Add note about Range support 
Add note explaining that nginx sendfile support is required for Range (and thus IGV/JBrowse) to work.
 2019-02-07 20:53:05 +02:00
Nicola Soranzo e97634739d Build tool XML schema docs using `sphinx_markdown_tables` 
instead of converting the Markdown to reStructuredText with pandoc.

Fix the broken tables, but code inside tables is not coloured as
in the rest of the document.
 2019-02-06 17:27:48 +00:00
Nicola Soranzo e725f8423a Disable auto toctree for Markdown docs. Doc syntax fixes 
recommonmark allows now to use the `.md` extension for cross referencing
other documents, which also works on GitHub.
 2019-02-06 17:12:06 +00:00
Nicola Soranzo 8acd07a50f Remove architecture slides 
Now available at

https://galaxyproject.github.io/training-material/topics/dev/tutorials/architecture/slides.html
 2019-02-06 17:12:05 +00:00
Nicola Soranzo 03463f4b05 Merge branch 'release_19.01' into dev 2019-02-05 13:30:34 +00:00
Daniel Blankenberg 49cbad5deb Merge pull request #7191 from natefoo/admin-docs-19.01 
[19.01] Properly document handler assignment method configuration and fix logging configuration docs
 2019-02-02 10:02:07 -05:00
Nate Coraor 74fcf12fa0 Incorporate suggestions from @nsoranzo 2019-02-01 21:47:48 -05:00
Nicola Soranzoandnatefoo 9a133e91f8 Remove spurious characters 
Co-Authored-By: natefoo <nate@bx.psu.edu>
 2019-02-01 21:34:04 -05:00
Nicola Soranzo 79fe787037 Fixes for the cluster documentation 
Fix https://github.com/galaxyproject/galaxy/issues/5319
 2019-01-30 10:27:17 +00:00
Nicola Soranzo d9dd2e3cf1 Merge branch 'release_19.01' into dev 2019-01-29 15:51:44 +00:00
Nicola Soranzo 152e0012c7 Merge branch 'release_18.09' into release_19.01 2019-01-29 15:50:39 +00:00
John Chilton d83db6a537 Stop with tool migrations by default, they are not needed in modern Galaxies... 
... and even problematic in some ways.
 2019-01-27 15:48:16 -05:00
Nicola Soranzo d5b306dd21 Remove OpenID auth from docs 
Follow-up on https://github.com/galaxyproject/galaxy/pull/7028 .
 2019-01-21 17:44:34 +00:00
Nicola Soranzo d0373c6a95 `make config-rebuild` 
Follow-up on https://github.com/galaxyproject/galaxy/pull/7028 .
 2019-01-21 17:43:14 +00:00
Nicola Soranzo 1befc38810 Update `use_interactive` default in docs 
This was never enabled by default in the code, but it was explicitly set
to True in `config/galaxy.ini.sample` . Since we moved to
`galaxy.yml.sample`, this has defaulted to False in practice.
 2019-01-15 20:41:14 +00:00
Nicola Soranzo 8915766275 Do not exclude releases docs when using `GALAXY_DOCS_SKIP_SOURCE` 
They are quite fast to build.
 2019-01-14 22:45:34 +00:00
Nicola Soranzo 46b3539a35 Fix doc bugs 
Use proper cross-referencing with `:doc:`.
 2019-01-14 22:45:34 +00:00
Nicola Soranzo 4bb6f18b30 Do not build rst files starting with '_' 2019-01-14 22:45:34 +00:00
Nicola Soranzo ce5895f585 Update recommonmark configuration in Sphinx 
See https://github.com/rtfd/recommonmark/pull/113
 2019-01-14 22:45:34 +00:00
John Chilton b0bc39261d Merge pull request #7154 from jmchilton/objectstore_uuid 
Allow storing objects in the object store by UUID.
 2019-01-11 15:27:39 -05:00
Nate Coraor 35c60489e8 Fixed link to proxy_package_layout in proxy docs 2019-01-09 11:59:00 -05:00
Dannon Baker e9773f1733 Minor spello 2019-01-09 11:56:44 -05:00
Nate Coraor 79672df452 Update documentation for handler assignment method configurability and 
remove some legacy stuff.
 2019-01-09 11:56:36 -05:00
Nate Coraor 37a9f2bcea Update logging config docs: 
- The example for split file logging was invalid (referenced the
  nonexistent "generic" formatter)

- Switch YAML dicts from 4- to 2-space indent to match the indentation
  style in galaxy.yml.sample

- Document setting the message format with the YAML config

- Reword a few things to hopefully be a bit clearer
 2019-01-07 16:16:32 -05:00
John Chilton 681225bc9c Merge pull request #7144 from jmchilton/remove_collect_outputs_from 
Remove collect_outputs_from option.
 2019-01-07 10:42:40 -05:00
John Chilton 03b363a1ef Merge pull request #7125 from mvdbeek/MulledSingularityContainerResolver 
Use singularity build / exec with biocontainers
 2019-01-07 08:35:44 -05:00
Nicola Soranzo 7ca7394c7d Document `message_box_class` option 
Reported by @vazovn
 2019-01-07 09:45:07 +00:00
Nicola Soranzoandmvdbeek 5f389dd11e Fix spelling in resolver docs 
Co-Authored-By: mvdbeek <m.vandenbeek@gmail.com>
 2019-01-06 15:11:10 +01:00
mvdbeek a056f17460 Document and use mulled_channels option 2019-01-06 15:01:31 +01:00
M Bernt 0eb96a63f5 doc: added missing docs for new UNIVA runner 2019-01-02 11:36:01 +01:00
John Chilton fa77f62051 Allow storing objects in the object store by UUID. 
This is the most obvious way to allow creating new datasets during a job creation or finish context without a database available.
 2019-01-01 14:33:20 -05:00
Sergey Golitsynskiy 0bd861aec7 Code style improvement to previous commit 2018-12-21 13:23:41 -05:00
Sergey Golitsynskiy 5d8e0bb049 Correct code error in 'build job runner' tutorial 
When  __init__ is called, **kwargs (most likely) will not contain
the 'runner_param_specs' key. And if so, calling update() on
kwargs['runner_param_specs'] will cause an error. Check if key exists,
then update or create.
 2018-12-21 12:42:25 -05:00
John Chilton d91a666d5c Remove collect_outputs_from option. 
And just disable dynamic discovery of outputs from new_file_path for legacy profile tools.

This is part of an ongoing effort to kill new_file_path and simplify output discovery.

This option was added by @natefoo 10 years ago and he switched main to disable new_file_path discovery and noone ever complained. So lets just do this for all Galaxies - if main hasn't run tools that require this functionality in a decade - I very much doubt any Galaxies require this.
 2018-12-20 10:45:42 -05:00
Nate Coraor 1fb8203a0c Handler assignment documentation. 2018-12-10 17:29:11 -05:00
John Chilton c679b64272 Merge pull request #7065 from ic4f/dev 
Fix link to requirements.txt
 2018-12-02 21:54:12 -05:00
Sergey Golitsynskiy 6703584714 Fix link to requirements.txt 
Dependency files rearranged (commit 1b0ccf6, Nov. 1, 2017)
 2018-11-30 19:26:41 -05:00
Nicola Soranzo 2a3b22cf49 Update galaxy.yml.sample and galaxy_options.rst 
with `make config-rebuild` .
Follow-up on https://github.com/galaxyproject/galaxy/pull/6776 .
 2018-11-30 18:10:56 +00:00
Nicola Soranzo 7183a17efc Merge branch 'release_18.09' into dev 2018-11-30 18:05:40 +00:00
Martin Cech 247fd01810 make the transition non-instrusive 2018-11-29 11:28:15 -05:00
Martin Cech 6fa0c8f932 add new item to the help menu 2018-11-28 12:50:18 -05:00
Dannon Baker e9ab7add6e Another typo in admin/nginx 2018-11-09 16:29:12 -05:00
Dannon Baker 35bc1b387a Typos in admin docs. 2018-11-09 16:26:33 -05:00
Dannon 3ed0ce862b Merge pull request #6975 from mvdbeek/conda_run_sh 
Use virtualenv when conda is on PATH
 2018-11-09 15:45:54 -05:00
Sergey Golitsynskiy 03794ce21a Fix broken links on Job Configuration page 2018-11-08 11:52:31 -05:00
Nicola Soranzo e4c00af38d Merge branch 'release_18.09' into dev 2018-11-08 09:32:30 +00:00
mvdbeek 5e098857e5 Display test collection input in documentation 2018-11-07 20:08:21 +01:00
mvdbeek 9f8c29520d Use virtualenv when conda is on PATH 
This uses our proper pinned requirements and is sginificantly easier
to set up and maintain.
 2018-11-07 14:20:05 +01:00
John Chilton c312c1014d Merge pull request #6937 from natefoo/shed-tools-relocate 
Default shed tool installation to database/shed_tools
 2018-11-01 10:22:05 -04:00