John Chilton
e67506802d
Implement config.single_user = <email> option.
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Let Planemo and other such applications serve a full-fledged Galaxy instance without having to worry about logins, etc....
2016-04-14 12:41:18 -04:00
Nate Coraor
a919e98be3
Merge branch 'release_16.04' into dev
2016-04-14 11:15:43 -04:00
Nicola Soranzo
148d4ee88d
Merge pull request #2145 from mvdbeek/pbs_ncpu
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Use "$NCPUS" if defined to set GALAXY_SLOTS
2016-04-14 15:50:06 +01:00
Nate Coraor
84ef4fd99f
Update pulsar-galaxy-lib in pinned-requirements.txt (it was already
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updated in requirements.txt).
2016-04-14 10:09:26 -04:00
Nate Coraor
9bb5978d53
Merge pull request #2156 from guerler/fix_data_001
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[16.04] Add tool parameters back to parameters and expose for certain tools
2016-04-14 09:56:29 -04:00
guerler
a889e19af7
Fix parameter wrapping
2016-04-14 07:23:06 -04:00
Eric Rasche
3d5663e97f
Remove double escaping
2016-04-13 21:35:50 +00:00
guerler
ac14139714
Add blank line
2016-04-13 15:50:44 -04:00
guerler
82e9ce827c
Add tool parameters back to parameters
2016-04-13 15:34:11 -04:00
Eric Rasche
dd05f0ab24
Escape everything
2016-04-13 18:36:36 +00:00
Eric Rasche
6ce9bd8220
Minor touch up for consistency
2016-04-13 18:21:19 +00:00
Eric Rasche
4d729ff890
Typo
2016-04-13 17:27:14 +00:00
Eric Rasche
a3e925cc1b
Fix second nitpick
2016-04-13 17:24:26 +00:00
Eric Rasche
cba10c812b
Fix nitpick
2016-04-13 17:23:32 +00:00
Eric Rasche
df481dabe0
Remove unused import
2016-04-13 16:34:26 +00:00
Eric Rasche
a6d95d0909
Fix flake8 by reverting a previous commit
2016-04-13 16:32:37 +00:00
Marius van den Beek
3c97d30cd6
Use "$NCPUS" if defined to set GALAXY_SLOTS
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On our PBS cluster we do not have $PBS_NCPUS, and $PBS_NODEFILE contains the
hostname of the nodes the task runs on. But we do have "$NCPUS" with the
correct number of CPUS.
2016-04-13 10:39:43 +02:00
Eric Rasche
5923a67301
Fix sanitization completely
2016-04-13 00:48:09 +00:00
Eric Rasche
c2cff25826
Use CGI for escaping
2016-04-13 00:38:25 +00:00
Eric Rasche
e9823573e3
Add HTML Template
2016-04-13 00:25:31 +00:00
Eric Rasche
024ae7a286
bail earlier if no SMTP server is configured
2016-04-12 23:40:39 +00:00
Nicola Soranzo
408827e251
Merge branch 'release_16.04' into dev
2016-04-12 14:35:37 +01:00
Nate Coraor
f03c037556
Merge pull request #2122 from jmchilton/pulsar_metadata
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[16.04] Rev Pulsar to 0.7.0.dev3.
2016-04-12 09:01:27 -04:00
Nicola Soranzo
baf1bd639f
Merge branch 'release_16.04' into dev
2016-04-11 20:26:42 +01:00
Nicola Soranzo
6317297cad
Merge branch 'release_16.01' into release_16.04
2016-04-11 20:24:46 +01:00
Martin Cech
f759961a29
mention planemo in the error message for disabled TS pushing
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rephrase to Norwegian
2016-04-11 12:56:42 -04:00
carlfeberhard
99c2a6b623
API: add server_starttime to api/configuration
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Adds key server_starttime to the JSON returned from api/configuration.
This is the epoch time since the last server restart and may be
convenient for use in client-side caching.
This moves server_starttime from web/framework/helpers/__init__.py
(for use in script cache-busting) to web/framework/base.py.
On the client, this should be available to all pages as:
Galaxy.config.server_starttime.
2016-04-11 10:38:20 -04:00
John Chilton
84ad9c2ee2
Rev Pulsar to 0.7.0.dev3.
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- Fixes numerous problems mostly notably fixes external metadata generation and job metrics collection for recent Pulsar. This was broken when tools were given clean working directory.
- Produce a new message if an older Pulsar version is targetted via REST of library (should help with upgrading to Galaxy 16.04).
- Newer pulsar lib allows more flexible configuration of managers - update documntation to reflect this.
2016-04-10 23:54:02 -04:00
John Chilton
5739f25003
Update version to 16.07.dev
2016-04-08 14:00:47 -04:00
John Chilton
579846fdfb
Update version to 16.04.rc1
2016-04-08 13:59:37 -04:00
John Chilton
0945809099
Merge remote-tracking branch 'upstream/release_16.01' into dev
2016-04-08 13:22:03 -04:00
John Chilton
ce27863086
Merge pull request #2099 from davebx/shed_model_trim
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Consolidate duplicated method in tool_shed/model.
2016-04-08 13:21:59 -04:00
John Chilton
0d616af28a
Merge pull request #2106 from davebx/hg_middleware
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Workaround for the toolshed's hgweb.
2016-04-08 13:20:22 -04:00
John Chilton
6f6554ea8c
Merge pull request #2104 from Christian-B/unlinked_depenency_resolver_update_to_new_dependency
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Updated to Dependency change in b167a741a4
2016-04-08 13:18:26 -04:00
Dave Bouvier
5ead1c089f
Remove refactoring that belongs in a different PR.
2016-04-08 12:38:56 -04:00
John Chilton
be10253b69
Remove stray print statements.
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Not Python 3 compat.
2016-04-08 10:28:09 -04:00
John Chilton
2744d5541f
Merge pull request #2093 from davebx/move_scripts
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Move scripts out of lib/tool_shed.
2016-04-08 09:54:44 -04:00
John Chilton
ef604a75e5
Merge pull request #2102 from natefoo/global-drmaa-session
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Convert the DRMAA runner to use Pulsar's DRMAA session wrapper
2016-04-08 09:47:24 -04:00
John Chilton
40953369e6
Merge pull request #2107 from ThomasWollmann/master
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Fix cli runner: use embed_metadata_in_job parameter
2016-04-08 09:44:53 -04:00
Thomas Wollmann
fb26d27b97
fixed lint error
2016-04-08 13:48:13 +02:00
Thomas Wollmann
bf8292ecc1
fixed lint error
2016-04-08 12:30:56 +02:00
Thomas Wollmann
0548e8ed30
added missing import
2016-04-08 12:20:50 +02:00
Thomas Wollmann
4e15dc4e74
typo
2016-04-08 12:17:36 +02:00
Thomas Wollmann
91c4ccfc90
added default DEFAULT_EMBED_METADATA_IN_JOB value
2016-04-08 12:09:58 +02:00
Thomas Wollmann
987aac34bb
removed comment
2016-04-08 11:00:34 +02:00
Thomas Wollmann
ab242a84b1
fixed bug with cli runner analogous to https://github.com/dpryan79/galaxy/commit/3536ff923cf736b2dbefab3e04b7fcd79b909d22
2016-04-08 11:00:13 +02:00
Dave Bouvier
2a76eb19c1
Remove unused import, restore used import.
2016-04-07 20:38:11 -04:00
Martin Cech
50268cb8ca
fix missing call; add docs and refactor a bit
2016-04-07 18:22:42 -04:00
Dave Bouvier
b4e768b828
Workaround for the toolshed's hgweb.
2016-04-07 16:54:43 -04:00
Nate Coraor
edd23f7c7a
Bump pulsar-galaxy-lib version
2016-04-07 12:31:41 -04:00
John Chilton