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Commit Graph
812 Commits
Author SHA1 Message Date
Marius van den Beek ef9698895a Merge pull request #8319 from nsoranzo/lowercase_boolean_yaml 
Use lowercase true/false in config_schema.yml
 2019-07-10 11:18:19 +02:00
Marius van den Beek bc7b48756b Merge pull request #7402 from guerler/activate_toolshed 
Activate api-based Toolshed interface in Admin panel
 2019-07-10 11:06:18 +02:00
Nicola Soranzo d0c28f669b Use lowercase true/false in config_schema.yml 
since these are the only allowed values for booleans in YAML 1.2:
https://yaml.org/spec/1.2/spec.html#id2803629

make config-rebuild
 2019-07-09 18:58:51 +01:00
Dannon Baker 3072975897 Drop mimeparse docs 2019-07-09 14:14:37 +01:00
Marius van den Beek d22d7beaf4 Merge pull request #8305 from jmchilton/axe_log_tempfile 
Remove log_tempfile.
 2019-07-09 14:42:43 +02:00
guerler deaa583890 Merge branch 'dev' into activate_toolshed 2019-07-09 13:58:01 +02:00
Dannon Baker f5f15e2dfc Drop log_tempfile docs 2019-07-08 20:04:03 -04:00
Dannon Baker ae11aaa5ec Drop psyco_full docs 2019-07-08 16:08:20 -04:00
Sergey Golitsynskiy b5f19e8466 Rerun make updaterst 
First rm doc/source/lib/*, then rerun sphinx. Cleans out obsolete files.
 2019-07-06 10:10:56 +02:00
Sergey Golitsynskiy 17beaef624 Update Sphinx RST files for lib/ 
Running sphinx 1.8.5 updates all files (one known update: periods are no
longer escaped)
 2019-07-05 17:21:31 +02:00
guerler d8e089308a Merge branch 'dev' into activate_toolshed 2019-07-05 14:09:08 +02:00
Sergey Golitsynskiy 6f167a2e8d Run make config-rebuild to update config/docs 
This is to update galaxy.yml.sample and galaxy_options.rst to be
consistent with the latest update to config_schema.yml (#5651edc)

(generated with make config-rebuild)
 2019-06-25 00:18:21 -04:00
John Chilton 8564eabb43 Merge branch 'release_19.05' into dev 2019-06-10 15:01:42 -04:00
Enis Afgan 9043dd18c6 [19.05] Add recent merges to release notes 2019-06-10 10:31:59 -04:00
Nicola Soranzo dafe9dd30b Merge branch 'release_19.05' into dev 2019-06-10 14:15:02 +01:00
Martin Cech 8f5a35e584 I love RST 2019-06-07 15:13:14 -04:00
Martin Cech 0a32933e72 fix link to user release notes 2019-06-05 16:59:46 -04:00
Martin Cech 47fd60fcce fix link to user release notes 2019-06-05 16:58:53 -04:00
Martin Cech 20bdd5867a Merge branch 'release_19.05' into dev 2019-06-05 16:35:35 -04:00
Martin Cech 5db219b1d2 add 19.05 RN to index 2019-06-05 15:53:05 -04:00
Martin Cech e8311393e7 minor changes to RN 2019-06-05 15:48:33 -04:00
Enis Afgan 90f56ebc40 Fix link formats for mulled_containers.rst, minor rewording 2019-05-31 15:32:23 -04:00
Helena Rasche 4521614718 Enhance user facing release notes with gifs 2019-05-29 13:03:46 +02:00
John Chilton aa4566e77e First pass at writing 19.05 release notes. 2019-05-24 16:59:32 -04:00
John Chilton 0cf83ef345 Initial bootstrapping of 19.05 release notes... 2019-05-24 16:59:32 -04:00
Nicola Soranzo c82749688e Merge branch 'release_19.05' into dev 2019-05-11 14:05:55 +01:00
Dannon Baker 349ac80412 Include suggestion from Marius to make port specification more clear. 2019-05-10 10:12:27 -04:00
Dannon Baker a1487d733a Fix a few more random typos in config, rebuild 2019-05-10 10:09:10 -04:00
Dannon Baker 6bc802307f Document the modern docker networking special DNS 'host.docker.internal' for use with GIES. Fix another typo I saw. 2019-05-10 10:04:12 -04:00
Nicola Soranzo 8a2abb867f Update instructions on conda upgrade 
Reported by @William-Brown .
 2019-05-08 18:54:55 +01:00
Dannon Baker a9b1a0454d Update documentation for IES 2019-05-08 11:59:16 -04:00
Dannon Baker fd75ce5e43 Standardize (at least a step forward) access to IES lib via bundle 2019-05-08 10:59:34 -04:00
Dannon Baker dfa13efe63 Update doc on NodeJS version compatibility (I updated proxy deps a while back, works with modern node now) 2019-05-08 10:25:26 -04:00
Dannon Baker 38c2a80904 Update IES to use bundleEntries-based JS entrypoint to avoid having to ship an extra file; incremental step towards removing require here, too. 2019-05-07 16:44:15 -04:00
John Chilton f81c41895b Allow YAML configuration of job_conf.xml. 2019-05-07 08:23:30 -04:00
Sergey Golitsynskiy 158fb6b454 Update config_schema + run make config-rebuild 2019-04-27 01:19:57 -04:00
guerler 8b8e14976f Merge branch 'dev' into activate_toolshed 2019-04-18 17:43:30 -04:00
Dannon e95abd4cbf Merge pull request #7707 from martenson/plusone-enough 
[PROCEDURES] relax the vote requirement for fixing bugs in releases
 2019-04-17 17:15:51 -04:00
John Chilton 12b41507a2 Merge pull request #7706 from martenson/procedure-docs 
[PROCEDURES] exempt notes, changelogs, and packages from mandatory review
 2019-04-17 16:11:23 -04:00
Nate Coraor d1d5944387 Mention cookie_path in the nginx/Apache docs just for anyone who had it 
set and might be confused about why it's no longer documented.
 2019-04-16 17:48:36 -04:00
Nate Coraor fed86eb598 Remove cookie_path configuration documentation since it's now set 
automatically.
 2019-04-16 17:48:36 -04:00
Nicola Soranzo 305ca77cc2 Replace `enable_beta_export_format2_default with default_workflow_export_format` 
This allows future different formats to be included.

Also remove promises about next release.
 2019-04-15 20:11:26 +01:00
Martin Cech 7de1255670 relax the vote requirement for fixing bugs 2019-04-09 13:52:43 -04:00
Martin Cech b40ef5ba4c [PROCEDURES] exempt release notes, changelogs, and packages from mandatory review 2019-04-09 13:49:04 -04:00
Martin Cech 1075a0e6bc Merge pull request #7659 from jmchilton/format2_import_default 
Allow import of format2 workflows by default for 19.05.
 2019-04-09 10:50:45 -04:00
guerler 6ee429cdda Remove unused openid config file option 2019-04-06 03:18:25 -04:00
guerler 1308b5f4dc Repack config yaml 2019-04-06 01:50:30 -04:00
guerler 28f34c433e Add OpenID support 2019-04-06 01:20:36 -04:00
John Chilton 4b13917d86 Allow import format2 workflows by default. 
Setup forcing export of format2 workflows by default in next release. There should be a least one release between enabling them to be imported by default and exporting them by default anyway I think - so 19.09 workflows can still be used on slightly older Galaxy instances.
 2019-04-04 09:15:30 -04:00
Dannon Baker 2bb159ef52 Merge remote-tracking branch 'upstream/release_19.01' into dev 2019-03-22 10:49:37 -04:00