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
d72f82de98
remove Paste config option, reword URL prefix
2019-02-19 10:37:34 -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
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
Nate Coraor
c3dfdb0dc7
Default shed tool installation to database/shed_tools instead of
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../shed_tools
2018-10-29 12:15:42 -04:00
Nate Coraor
7c6b184557
Clarify that maximum job runner worker shutdown time is a multiple of
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`monitor_thread_join_timeout` based on the configured number of runner
plugins.
2018-10-25 15:10:08 -04:00
Nate Coraor
33c3b74bf5
Increase the value of monitor_thread_join_timeout to 30 now that it is
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the total wait time. Add more documentation about it and the uWSGI and
supervisord options that changing it will have an effect upon.
2018-10-25 14:52:10 -04:00
John Chilton
096fe9b7b9
Merge pull request #6909 from nsoranzo/error_reports
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Update Bug Reports docs to use YAML syntax
2018-10-23 18:51:33 -04:00
Nicola Soranzo
02c71e2429
Merge branch 'release_18.09' into dev
2018-10-23 14:37:09 +01:00
Nicola Soranzo
cbf8a6658d
Update Bug Reports docs to use YAML syntax
2018-10-23 12:43:13 +01:00
Nicola Soranzo
4dd2ecb13f
Fix `make config-validate`
2018-10-23 12:28:47 +01:00
Nicola Soranzo
4e0f814f61
Add documentation for `conda_use_local` config directive
2018-10-12 09:57:53 +01:00
Martin Cech
c9b0379230
Merge pull request #6846 from thobalose/docs
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Updated GIE docs
2018-10-10 13:15:15 -04:00
thobalose
2cacb69d97
en-US spelling
2018-10-10 17:56:03 +02:00
thobalose
292197386b
Added NVM to manage multiple node versions.
2018-10-10 15:06:32 +02:00
Nicola Soranzo
afa7299705
Merge branch 'release_18.09' into dev
2018-10-10 10:11:13 +01:00
Nicola Soranzo
9b6833b5a0
make config-rebuild
2018-10-08 11:03:46 +01:00
Nicola Soranzo
c83c5cb784
Change conda channel priority: conda-forge > bioconda
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xref. https://github.com/bioconda/bioconda-utils/issues/330
2018-10-08 11:02:23 +01:00
Nicola Soranzo