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Commit Graph
601 Commits
Author SHA1 Message Date
Nate Coraor b0b313c617 Merge pull request #345 from dannon/metadata_limit 
Metadata size limiting
 2015-06-16 11:11:17 -04:00
Dannon Baker 3b9158acfe Update sample text. 2015-06-16 10:23:46 -04:00
Dannon Baker 286aaba51e Make metadata limit configurable, off by default. 2015-06-15 13:11:18 -04:00
Dannon Baker f472a67e79 Merge pull request #337 from martenson/ts-hide-test-results 
TS hide test results
 2015-06-15 11:34:49 -04:00
John Chilton 19dbf2f780 Allow specifying EDAM format for dynamic subclass datatypes. 
Use this to specify the EDAM format for genbank.
 2015-06-15 11:17:43 -04:00
John Chilton bdf1738885 Merge remote-tracking branch 'jmchilton/dev' into HEAD 
Conflicts:
	config/datatypes_conf.xml.sample
 2015-06-14 17:17:55 -04:00
Martin Cech 353ee2f22a introduce a config option to hide results of install & test framework 2015-06-12 13:16:16 -04:00
Martin Cech 9a3e1f86db refactor TS sample config to follow 80char/line rule 2015-06-12 11:53:15 -04:00
John Chilton 508194f223 Fix sample datatype definition for CSV. 
For me it seems like the viz plugins only detect the datatype if the plugin datatype (e.g. ``tabular.CSV``) is explicitly instantiated by some extension directly. In your sample config you have ``subclass="True"`` so ``tabular.CSV`` wasn't working. This is probably a bug with the datatype code - but nonetheless I think dropping subclass from the sample is an okay workaround - because it does seem to be a direct mapping.
 2015-06-03 10:52:59 -04:00
John Chilton 884e824d72 Merge remote-tracking branch 'vavrusa/table-datatype' into dev. 
Conflicts:
	lib/galaxy/datatypes/tabular.py
 2015-06-03 10:52:42 -04:00
Dannon Baker c69945ff95 Merge new workflow editor. 2015-06-02 18:44:56 -04:00
Nicola Soranzo 30872e72bb Improve auth_conf.xml.sample documentation. 2015-06-01 11:58:08 +01:00
Renato Alves 253493c393 Allow passing advanced options to the LDAP connection 
Useful to configure the connection if ldap.conf and/or ldaprc cannot be used

auth_conf.xml.sample includes an example to connect to LDAPS using
self-signed certificates.
 2015-05-29 13:56:48 +01:00
carlfeberhard 3c12d90730 Merge pull request #290 from guerler/charts_000 
Fix load order of require and d3
 2015-05-27 11:27:02 -04:00
guerler cc1f56a118 Fix load order of require and d3 2015-05-27 11:18:04 -04:00
guerler 229577b5c2 Merge branch 'dev' of https://github.com/galaxyproject/galaxy into workflow_form_000 2015-05-24 15:38:50 -04:00
John Chilton bb88dcb059 Make the data manager JSON datatype's class more specific. 
Use Json base class instead of text - fixes data manager type for PR #80.
 2015-05-22 10:20:48 -04:00
guerler 44739c6457 Merge branch 'dev' of https://github.com/galaxyproject/galaxy into workflow_form_000 2015-05-20 23:20:06 -04:00
Nicola Soranzo 6b2f01a5ca Explain how to remove the mailing list subscription option from the user registration form. 2015-05-20 11:30:12 +01:00
guerler 70fab5c319 Enable new workflow editor form by default 2015-05-20 01:19:27 -04:00
Eric Rasche 21368266ce Implement XMFA Datatype 
This is used with Mauve/ProgressiveMauve.

Additionally a bug is fixed in the Stockholm datatype which
would have prevented proper sequence count autodetection.
 2015-05-18 12:58:42 -05:00
Nicola Soranzo 48023ed374 Remove outdated sentence. 2015-05-15 12:45:16 +01:00
Daniel Blankenberg f52bbbf50e Add display for Interval files at IGV via bedstrict. 2015-05-14 14:51:43 -04:00
John Chilton ed8112b422 Fix problems introduced in IE refactorings. 2015-05-14 14:32:49 -04:00
John Chilton 998d0e8a8c IE: Move IPython-specific password hashing out of framework into plugin. 
See dicussion here - https://github.com/erasche/galaxy/commit/23459f318507255a2bb1d1fb647e1581bd2090e1.
 2015-05-14 10:15:49 -04:00
John Chilton 624d540c04 IEs: Move temp dir handling into ie_request to simplify interface. 2015-05-13 23:08:21 -04:00
John Chilton 55e523ea63 Introduce new IE launch abstraction. 
In addition to reducing duplication between IPython and RStudio - it also shields them from low-level details and creates an interface we could more reasonably generalize to something like qsubing the docker commands or using Docker Swarm.
 2015-05-13 23:08:20 -04:00
John Chilton 23459f3185 Expose and cache raw IE password to simplify RStudio plugin. 2015-05-13 23:08:20 -04:00
John Chilton 0a5ec3e8d3 Merge remote-tracking branch 'jmchilton/dev' into rstudio 2015-05-13 21:06:21 -04:00
Eric Rasche a9fb12a146 Update RStudio to new IE infrastructure 2015-05-11 17:11:04 -05:00
Eric Rasche 285eece97a Update RStudio to new IE infrastructure 2015-05-11 17:07:33 -05:00
John Chilton f3e81f148f Eliminate potential boilerplate code in new IE env stuff. 2015-05-11 09:07:45 -04:00
John Chilton eb2034ac6e Merge remote-tracking branch 'erasche/ie-updates2' into pr229 
Conflicts:
	config/plugins/interactive_environments/ipython/config/ipython.ini.sample
 2015-05-10 23:17:17 -04:00
Eric Rasche 213f21f890 Updates to take advantage of #229 infrastructure 2015-05-10 21:52:04 -05:00
Eric Rasche 201f2db184 Pin to :dev 2015-05-08 17:07:04 -05:00
John Chilton f7af19b82c Merge pull request #239 from erasche/rdata2 
Add RData and RData.gz formats
 2015-05-08 17:00:50 -05:00
Nate Coraor a85eadfb74 Merge pull request #243 from carlfeberhard/vis.remove-template 
Visualizations registry: switch to entry_point config definition for …
 2015-05-08 10:26:29 -04:00
Carl Eberhard 11b2fbcb3b Visualizations registry: switch to entry_point config definition for built-in visualizations 2015-05-07 16:04:25 -04:00
Eric Rasche a940f19e15 Merged down datatypes 2015-05-07 12:27:22 -05:00
Martin Cech d28ea45556 Merge branch 'release_15.05' into dev 
Conflicts:
	config/plugins/visualizations/common/templates/script_entry_point.mako
 2015-05-07 13:09:24 -04:00
Eric Rasche 148acf0ddc Add RData and RData.gz formats 2015-05-07 11:59:01 -05:00
Eric Rasche 2c04d1a768 Pin to :dev 2015-05-07 11:12:02 -05:00
Nate Coraor 049e9e8024 Merge remote-tracking branch 'upstream/release_15.03' into release_15.05 
Conflicts:
	config/plugins/interactive_environments/ipython/config/ipython.ini.sample
 2015-05-07 11:57:59 -04:00
Dannon Baker 7a936f824a Merge pull request #222 from jmchilton/tox_switch_and_fixes 
[15.05] Switch Travis testing to tox and associated fixes.
 2015-05-07 11:41:46 -04:00
John Chilton 76821247c8 Merge pull request #218 from erasche/hmmer 
Hmmer & Stockholm Datatypes
 2015-05-07 07:25:08 -05:00
John Chilton 0aabdd4048 Merge remote-tracking branch 'jmchilton/release_15.05' into dev 2015-05-06 20:56:43 -04:00
Eric Rasche 7e9df4714a Migrated to correct location 2015-05-06 16:31:28 -05:00
Eric Rasche c9623c16ae Merge remote-tracking branch 'rstudio/master' into rstudio 2015-05-06 16:30:49 -05:00
John Chilton a15a2bd2b2 Fix Python 2.6 incompat in script_entry_point.mako. 2015-05-06 14:06:16 -04:00
Eric Rasche b2b25f595b Update documentation on the get() function 2015-05-06 11:48:37 -05:00