Commit Graph
280 Commits
Author SHA1 Message Date
Nicola Soranzo 527e332aa3 Fix a bunch of errors reported by Sphinx 2016-10-24 19:42:19 +01:00
Nicola Soranzo 3180b63166 Properly integrate tool XML schema with docs
Generate intermediate rst file instead of html
Move generation to doc/Makefile
Use pandoc to generate table of contents and fragment ids.
Remove nested inline markup (not supported by reStructuredText)
Fix https and other links.
2016-10-24 19:42:19 +01:00
Nicola Soranzo e6d0b69ec8 Add and use local images for build runner doc 2016-10-24 19:40:42 +01:00
Nicola Soranzo 8a17143bc7 Remove unused files 2016-10-24 19:40:42 +01:00
Nicola Soranzo a21ed34efb Move png in the right directory
Broken in #2543.
2016-10-24 19:40:41 +01:00
Dannon Baker a6d52cdbdc Merge remote-tracking branch 'bgruening/feature/plugin-system' into dev 2016-10-23 19:00:43 +02:00
Remi Marenco 3e737c99ea Add Galaxy Architecture slides in .md
+ the plumbing for slides creation

Init of #2244, second part: Python converter md to html + wip on GCC 2015 talk conversion
Add the 2. Galaxy app architecture. Need images
Add the 3. Galaxy components and object model
Add more content in md
Fix linting error by adding newline at the end of build_slideshow.py
Moved the galaxyArchitecture.md into a folder dedicated to it
Add 7th and 17th image + add style.css to have a better management of layout + added first slide as the first in GCC2015 slide
Set properly the CSS used in the whole presentation + add special to p and first slide
Add special orange for regular text and green emphasis (emphasis_2_galaxy)
Changed the font to PT Sans
Add 3. with images + few modifications
Removed the images integrated using background-image by now Markdown imaging (still need work, image's size seems not good by default
Add Makefile target to build architecture slides...
2016 Updates to 2015 architecture talk.
More intro slides for Galaxy architecture.
Update author line.
Progress on architecture slides...
 - Improved styling (use Oxygen - closer to Galaxy font)
 - Add ability to generate SVG diagrams to slide infrastructure
 - Add newer client-server sequence diagram based on that.
Improved logging when there are problems with SQL migrations.
More misc work on architecture talk.
More images, slides, slide formatting, and initial work on an IPython notebook.
Improved styling for architecture slides...
Updates to architecture talk...
- Infrastructure for building class diagrams with plantuml
- Bring in move SVGs from last year's google docs.
- Fill out section on client architecture.
More work on slides for architecture talk.
Add startup_output.
Replace mermaid diagrams with plantuml diagrams.
Fill out these diagrams more and style them for a black background in Galaxy oranges.
2016-10-17 14:02:06 -04:00
Björn Grüning 4bbab51c05 Add note about interface stability. 2016-10-14 12:43:28 +02:00
Björn Grüning 8694356ab7 Adopt help to the latest changes 2016-10-13 23:20:51 +02:00
Bjoern Gruening 6a62dbc91a Merge branch 'dev' into feature/plugin-system 2016-10-13 19:18:13 +02:00
Björn Grüning 2d915a42f6 tense changes 2016-10-13 12:04:43 +02:00
Björn Grüning 4f89528c94 make activation procedure more clear 2016-10-12 23:04:59 +02:00
Evgeny Anatskiy 95d6990cf3 Update webhooks.rst 2016-10-12 22:30:12 +02:00
Evgeny Anatskiy bc51dc3ec7 Update webhooks.rst
escape missing dependencies
2016-10-12 22:29:20 +02:00
Joachim Wolff af8a3f1104 Fixing errors 2016-10-12 17:20:01 +02:00
Joachim Wolff fafeedc286 Fixing errors 2016-10-12 17:18:16 +02:00
Joachim Wolff 6684fd4e26 Fixing errors 2016-10-12 17:15:54 +02:00
Joachim Wolff acd99f76fc Fixing errors 2016-10-12 17:14:39 +02:00
Joachim Wolff 8030d2025d Fixing errors 2016-10-12 17:08:35 +02:00
Joachim Wolff 76b9e004d2 Fixing errors 2016-10-12 17:06:27 +02:00
Joachim Wolff d1737110bf Fixing errors 2016-10-12 17:01:54 +02:00
Joachim Wolff eb32ad229f Fixed formatting errors 2016-10-12 16:55:37 +02:00
Joachim Wolff 95c1f18693 Fixed formatting errors 2016-10-12 16:52:35 +02:00
Joachim Wolff f29b003a8c Added images directory for webhooks documentation 2016-10-12 16:03:25 +02:00
Joachim Wolff 0ad7c99ea2 Extended the documentation of webhooks and added an images directory. 2016-10-12 16:02:40 +02:00
Björn Grüning cd92be8802 Include a section about plugin dependencies. 2016-10-12 13:45:06 +02:00
Evgeny Anatskiy 5f9154a617 tiny fixes 2016-10-12 13:00:24 +02:00
Nicola Soranzo 1156006733 Merge branch 'release_16.07' into dev
Conflicts:
	lib/galaxy/tools/deps/__init__.py
2016-10-11 16:50:37 +01:00
John Chilton 7d642c063f Merge pull request #3032 from martenson/link-mulled-docs
add muled docs to admin index
2016-10-10 21:20:51 -04:00
Martin Cech 1a2d75fade add muled docs to admin index 2016-10-10 20:54:26 -04:00
Martin Cech bcabbd8707 minor changes to mulled admin docs 2016-10-10 19:26:36 -04:00
Björn Grüning 2cc133f325 Add initial docs 2016-10-09 21:32:08 +02:00
Björn Grüning 654b5e9322 Add initial documentation about the new mulled features. 2016-10-09 12:40:50 +02:00
John Chilton 89278b0ec7 Fix for bioconda recipes depending on conda-forge.
Some bioconda recipes now depend on conda forge, this fix is needed for them to work properly.
2016-10-07 15:11:00 -04:00
Martin Cech 59a6d07b7b Merge pull request #3010 from nsoranzo/merge_release_16.07
Merge release_16.07 into dev
2016-10-06 12:10:11 -04:00
John Chilton 2b9034d597 Update some old information in API guideline docs. 2016-10-05 21:37:11 -04:00
Nicola Soranzo a2ee8d10af Merge branch 'release_16.07' into dev
Conflicts:
	doc/source/admin/conda_faq.rst
	static/maps/mvc/ui/ui-modal.js.map
	static/scripts/bundled/libs.bundled.js
	static/scripts/bundled/libs.bundled.js.map
	static/scripts/mvc/ui/ui-modal.js
2016-10-05 20:34:50 +01:00
Nicola Soranzo 2899372791 Update conda_faq.rst 2016-10-03 19:46:27 +01:00
Martin Cech ba274e37f2 describe the conda installation behavior a bit better 2016-10-03 14:31:46 -04:00
Martin Cech 375ed8cc81 polish resolvers section in conda faq docs 2016-10-03 13:20:15 -04:00
Martin Cech 8054da9fb4 Update issues.rst 2016-09-27 15:16:43 -04:00
Enis Afgan 97b748c73a Shorten Conda environment naming as per https://github.com/galaxyproject/galaxy/commit/e9d81500caa3526200b204270aca175839f36f56
Thanks @lparsons.
2016-09-02 10:34:56 -04:00
Enis Afgan ecdbf4d0b5 Address PR #2891 comments 2016-09-01 17:01:56 -04:00
Enis Afgan 07cf96c260 Update Conda FAQ 2016-09-01 15:55:54 -04:00
Marius van den Beek e645036973 Merge pull request #2871 from remimarenco/patch-8
Add the <conda_prefix> in 12. and fix typo
2016-08-30 13:18:33 +02:00
Rémi Marenco 579ea41085 Update Marius advice 2016-08-30 05:08:26 -04:00
Rémi Marenco 040dd33980 Fix typo 2016-08-29 19:42:10 -04:00
Rémi Marenco d86ee37060 Add the <conda_prefix> in 12. and fix typo
I am adding the ``<conda_prefix>/envs`` to check for the package to have been properly installed (if people have brought their own Conda).

And fixing ``conda_prefix`` to stay consistent in the doc (``<conda_prefix>``).
2016-08-29 19:20:04 -04:00
Nate Coraor 4ad0bee552 Merge branch 'release_16.07' into dev 2016-08-26 13:40:03 -04:00
Martin Cech 3e65a165b7 fix inclusion of release notes in announcement 2016-08-25 14:32:10 -04:00