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
Sergey Golitsynskiy
03794ce21a
Fix broken links on Job Configuration page
2018-11-08 11:52:31 -05:00
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
pvanheus
a5d794dc4d
Add docs about running jobs in containers
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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
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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
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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
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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
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watchdog notifications.
2018-05-24 13:19:01 -04:00
Nicola Soranzo
41e12f0b9d
Merge branch 'release_18.05' into dev
2018-05-18 10:43:15 +01:00
Martin Cech
fe37996de3
rename the config option to enable_gdpr_beta
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to reflect the information that we do not guarantee compliance
2018-05-16 12:38:46 -05:00
Nicola Soranzo
c3f9e0c2a7
Merge branch 'release_18.05' into dev
2018-05-16 11:41:22 +01:00
Martin Cech
3a9a46f772
Merge pull request #6069 from erasche/gdpr
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[18.05] GDPR Compliance Mode
2018-05-15 20:40:20 -05:00
Martin Cech
f8bfb82169
fix what 🦅 👀 spotted
2018-05-15 20:23:37 -05:00
Martin Cech
1dc4749846
iteration of gdpr compliance docs
2018-05-14 20:30:22 -05:00
Helena Rasche
41e6910df2
document more gdpr stuff :(
2018-05-14 16:15:57 +02:00
Helena Rasche
2f351bf3a7
rebuild configuratoin
2018-05-14 15:33:34 +02:00
Helena Rasche
c122b3f573
better docs
2018-05-14 15:28:09 +02:00
Helena Rasche
6cc20f2634
start writing compliance documentation
2018-05-14 14:02:00 +02:00
Helena Rasche
ee985e6bbc
Update documentation
2018-05-14 11:51:10 +02:00
Helena Rasche
b4bd972b71
update documentation
2018-05-10 17:44:11 +02:00
Dannon Baker
02ffdf0be9
This strips the graphite-specific middleware; statistic functionality is provided by the statsd middleware and we don't need two separate mechanisms to maintain.
2018-04-30 13:50:05 -04:00
Nicola Soranzo
916078beb0
Merge branch 'release_18.01' into release_18.05
2018-04-27 19:22:24 +01:00
Nate Coraor
cbaff1dca2
Correct uWSGI UNIX domain socket syntax.
2018-04-27 10:49:07 -04:00
Nicola Soranzo
7ce49394c3
Merge branch 'release_18.01' into release_18.05
2018-04-26 19:05:38 +01:00
Nicola Soranzo
a3e6963666
Merge branch 'release_17.09' into release_18.01
2018-04-26 19:01:48 +01:00
Sergey Golitsynskiy