opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-09-24 16:30:27 +08:00
Code Issues Packages Projects Releases Wiki Activity
38,133 Commits 69 Branches 243 Tags
79672df45221e4417d2c363bb262c19a2eb48b1f
Commit Graph
284 Commits
Author SHA1 Message Date
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 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
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
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
Nate Coraor c3dfdb0dc7 Default shed tool installation to database/shed_tools instead of 
../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 
`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 
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 
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 
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 
xref. https://github.com/bioconda/bioconda-utils/issues/330
 2018-10-08 11:02:23 +01:00
pvanheus a5d794dc4d Add docs about running jobs in containers 
Explain how jobs can be run in containers (something currently documented in the `job_conf.xml.sample_advanced` file)
 2018-10-05 15:49:47 +02:00
Nicola Soranzo 64bb339a31 Merge pull request #6641 from martenson/rename-and-document-config-value 
document config for sniffing compressed files, enable by default
 2018-09-08 00:32:08 +01:00
Nicola Soranzo 59c1ed2266 Various doc fixes 2018-09-03 14:34:13 +01:00
Nicola Soranzo ad02c53154 Fix many links 2018-09-03 14:34:13 +01:00
Martin Cech b34414adc8 switch the default to sniff compressed datatypes 2018-08-28 13:38:44 -04:00
Martin Cech e0d1208834 document the sniff_compressed_dynamic_datatypes_default config and include in sample 2018-08-28 10:09:27 -04:00
Nicola Soranzo f5bd245faa Merge branch 'release_18.05' into dev 2018-08-17 16:39:29 +01:00
Matthew Spelchak 6cbb574553 Fix Location of Plugin Static Content 2018-08-14 13:15:39 -05:00
Enis Afgan 4f3cd889f1 Typo and wording fixes for dependency resolvers docs 2018-08-07 19:13:29 -04:00
Dannon Baker c9d17545d8 Config rebuild, and a few typos. 2018-08-06 10:01:20 -04:00
Nicola Soranzo 6e02c9aff7 Merge branch 'release_18.05' into dev 2018-06-17 13:11:47 +01:00
Nicola Soranzo e8beea0d60 Merge branch 'release_18.01' into release_18.05 2018-06-17 12:05:50 +01:00
mvdbeek 9ac0161891 Update description for installing pbs-python 2018-06-15 18:11:50 +02:00
Nicola Soranzo d66a63012a Replace unmaintained pycrypto dependency with pycryptodome 
Minimum secret key length for Blowfish was increased from 4 to 5 bytes.

First argument to Blowfish.new() must be a bytestring, and the `mode`
argument is no more optional.

Remove unused `encode_id` function from `scripts/api/common.py` .

Documentation updated, then rebuilt with `make config-rebuild` .
 2018-06-13 03:07:04 +01:00
Dannon 5ba71f580f Merge pull request #6215 from natefoo/dynamic-rule-dynamic-reload 
Enable automatic reload of dynamic job rules on change
 2018-06-01 11:38:24 -04:00
Katrin Leinweber f99f8667bc Hyperlink DOIs against preferred resolver 2018-05-30 16:49:21 +01:00
Nate Coraor 30b5e50ba0 Enable dynamic reload of dynamic job rules when configured, using 
watchdog notifications.
 2018-05-24 13:19:01 -04:00