Nicola Soranzo
91e49acf37
Merge branch 'release_18.09' into release_19.01
2019-03-03 15:52:13 +00:00
mvdbeek
bc8cf37d09
Remove broken tool_submission_burst
2019-03-02 16:53:36 +01:00
Nate Coraor
808aa5bef7
Merge remote-tracking branch 'upstream/release_18.09' into release_19.01
2019-02-22 13:23:16 -05:00
Nicola Soranzo
9b72f5a880
Merge pull request #7216 from mvdbeek/fix_galaxy_yml_prefix_comments
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[18.09] Update configuration samples
2019-02-22 18:16:25 +00:00
Nate Coraor
a83eb67775
Slight rewording of the cookie_path option description, and corrections
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to file_path and new_file_path descriptions.
2019-02-22 11:31:44 -05:00
Nicola Soranzo
351c188830
Remove `filter-with and update cookie_path` options also for Tool Shed and Reports
2019-02-22 12:07:16 +00:00
Martin Cech
1a0f067590
change config schema to reflect removing paste options
2019-02-21 12:26:31 -05:00
mvdbeek
8c9c27b7f6
Drop filter-with from docs / .sample
2019-02-21 17:45:56 +01:00
Martin Cech
015ce5cedc
Merge pull request #7308 from jmchilton/19.01_release_notes
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[19.01] Release notes for 19.01.
2019-02-20 11:52:47 -05:00
Martin Cech
d72f82de98
remove Paste config option, reword URL prefix
2019-02-19 10:37:34 -05:00
Nicola Soranzo
37a93972d5
Fix PR link
2019-02-18 13:36:45 +00:00
Nicola Soranzo
ca4acf78df
Sort PR numbers
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Small fixes.
2019-02-18 13:29:42 +00:00
John Chilton
94bcb8d00f
More fixes to 19.01 release notes.
2019-02-18 08:01:50 -05:00
John Chilton
2a3555d9d7
Better Singularity summary thanks to @mvdbeek.
2019-02-18 07:52:09 -05:00
Marius van den Beek and jmchilton
072b8d73ec
Update doc/source/releases/19.01.rst
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Co-Authored-By: jmchilton <jmchilton@gmail.com >
2019-02-18 07:47:35 -05:00
Marius van den Beek and jmchilton
16af73423f
Update doc/source/releases/19.01.rst
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Co-Authored-By: jmchilton <jmchilton@gmail.com >
2019-02-18 07:47:28 -05:00
John Chilton
b5713ca170
Progress on 19.01 release notes...
2019-02-05 15:47:11 -05:00
John Chilton
ae8bf6f793
Release notes raw.
2019-02-05 09:35:07 -05:00
Daniel Blankenberg
49cbad5deb
Merge pull request #7191 from natefoo/admin-docs-19.01
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[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 Soranzo and natefoo
9a133e91f8
Remove spurious characters
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Co-Authored-By: natefoo <nate@bx.psu.edu >
2019-02-01 21:34:04 -05:00
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...
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... and even problematic in some ways.
2019-01-27 15:48:16 -05:00
mvdbeek
b6d5675f5d
Update galaxy.yml.sample for prefix config
2019-01-15 12:32:41 +01:00
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
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remove some legacy stuff.
2019-01-09 11:56:36 -05:00
Nate Coraor
37a9f2bcea
Update logging config docs:
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- 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
03b363a1ef
Merge pull request #7125 from mvdbeek/MulledSingularityContainerResolver
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Use singularity build / exec with biocontainers
2019-01-07 08:35:44 -05:00
Nicola Soranzo
7ca7394c7d
Document `message_box_class` option
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Reported by @vazovn
2019-01-07 09:45:07 +00:00
Nicola Soranzo and mvdbeek
5f389dd11e
Fix spelling in resolver docs
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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
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
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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
Nate Coraor
1fb8203a0c
Handler assignment documentation.
2018-12-10 17:29:11 -05:00
John Chilton
c679b64272
Merge pull request #7065 from ic4f/dev
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Fix link to requirements.txt
2018-12-02 21:54:12 -05:00
Sergey Golitsynskiy
6703584714
Fix link to requirements.txt
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Dependency files rearranged (commit 1b0ccf6
2018-11-30 19:26:41 -05:00
Nicola Soranzo
2a3b22cf49
Update galaxy.yml.sample and galaxy_options.rst
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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
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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
mvdbeek
9f8c29520d
Use virtualenv when conda is on PATH
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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
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Default shed tool installation to database/shed_tools
2018-11-01 10:22:05 -04:00
Martin Cech
31905f1402
Merge pull request #6917 from dannon/unified_webpack4
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Unified webpack4
2018-10-31 14:52:32 -04:00
Nicola Soranzo
b47efd4ade
Merge branch 'release_18.09' into dev
2018-10-31 09:38:34 +01:00
Nicola Soranzo