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637 Commits
Author SHA1 Message Date
Dannon Baker 9b0ee0589a Resolve sample merge conflict. 2015-07-08 12:30:39 +01:00
youri 534d7b8b50 Added datatype definition for ConnectivityTable (*.ct) - RNA 2D structure file format 2015-07-07 17:30:54 +02:00
Jim Johnson ab4dc39a67 Add datatype: galaxy.datatypes.proteomics:MzSQlite extension: mz.sqlite 
This is a SQLite schema for representing Peptide Spectral Matches from mzid and mzML datatypes.
 2015-07-05 04:33:39 -05:00
John Chilton 235f432c43 Merge pull request #366 from yhoogstrate/dev 
Datatype definition for Dot-Bracket notation (dbn)
 2015-07-02 08:23:59 -05:00
Dannon Baker 79562cf8d2 Merge branch 'master' into dev 2015-07-01 14:29:13 -04:00
John Chilton f12bb33e0c Merge pull request #411 from guerler/fix_charts_config 
[15.05] Disable custom tooltips for histograms in charts, repack scripts
 2015-07-01 09:59:12 -05:00
guerler 8b7a455b01 Disable custome tooltips for histograms 2015-06-30 13:46:12 -04:00
Eric Rasche fcc706e8d0 Whitespace/other small fixes 2015-06-30 11:50:27 -05:00
Dannon Baker 1387ae1e3e Merge pull request #354 from charz/fixed_object_store_path 
Fixed object store path ('job_work')
 2015-06-30 10:43:21 -04:00
John Chilton 3deaf2f103 Merge pull request #389 from iracooke/dev 
Proteomics Datatypes
 2015-06-27 07:18:20 -05:00
Ira Cooke 089cd474d0 Change raw to thermo.raw 2015-06-27 08:42:45 +10:00
Ira Cooke cca245c62c Change RAW to ThermoRAW and add to sniffers 2015-06-26 06:24:18 +10:00
Ira Cooke c2cf786e76 Remove trailing spaces on line 46 2015-06-25 09:06:42 +10:00
Ira Cooke 031b4e01c0 Back out trailing space removal 2015-06-25 09:06:02 +10:00
guerler 53d13e9284 Merge branch 'dev' of https://github.com/galaxyproject/galaxy into workflow_form_002 2015-06-24 12:58:53 -04:00
Ira Cooke 3593d9c45c Remove trailing spaces 2015-06-24 09:10:14 +10:00
Dannon Baker d1179ebd14 Merge pull request #362 from jmchilton/xml_macros_3 
More, Better XML Macros
 2015-06-23 09:22:37 -04:00
Ira Cooke 734a429d3c Add Proteomics Sniffers above GenericXML 2015-06-23 10:00:03 +10:00
Ira Cooke b16d224fce Add proteomics datatypes 2015-06-23 09:33:27 +10:00
John Chilton a5a474fd40 Add example and test case for job configuration expansion. 
First suggestion by @nsoranzo and second was easy once example was added to advanced config.
 2015-06-22 13:09:23 -04:00
guerler cc1db3543e Merge branch 'dev' of https://github.com/galaxyproject/galaxy into workflow_form_002 
Conflicts:
	templates/webapps/galaxy/workflow/editor_tool_form.mako
 2015-06-22 08:53:28 -04:00
Martin Cech 1bb4e99e27 make field boosts for TS search configurable 2015-06-19 17:25:53 -04:00
youri 486899c021 DotBracket datatype definition is in line with Datatype description at Galaxy wiki 2015-06-19 09:19:16 +02:00
guerler cc979583ce Merge branch 'dev' of https://github.com/galaxyproject/galaxy into workflow_form_002 2015-06-17 16:04:37 -04:00
Bjoern Gruening 43b2b7929b change docker_host to docker_hostname to be more explicit 2015-06-17 15:54:18 +02:00
y.hoogstrate@erasmusmc.nl 4e5338d24e updates to DotBracket 2015-06-17 13:31:27 +02:00
y.hoogstrate@erasmusmc.nl 41e346adfe Added support for DotBracket notation 2015-06-17 11:11:14 +02:00
Bjoern Gruening 77169a2078 add docker_host as configurable option 2015-06-16 17:23:58 +02:00
Dannon Baker 6423454857 Update sample text. 2015-06-16 11:12:56 -04:00
Dannon Baker 1d5d322a15 Make metadata limit configurable, off by default. 2015-06-16 11:12:44 -04:00
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
guerler 4de4aecea2 Merge branch 'dev' of https://github.com/galaxyproject/galaxy into workflow_form_002 2015-06-15 13:34:44 -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
Charles 521b287b13 Add extra_dir options for S3/Swift ObjectStore. 2015-06-15 09:17:59 +00:00
guerler 614b35e3a9 Merge branch 'dev' of https://github.com/galaxyproject/galaxy into workflow_form_002 
Conflicts:
	client/galaxy/scripts/galaxy.workflows.js
	static/maps/galaxy.workflows.js.map
	static/scripts/galaxy.workflows.js
 2015-06-15 04:01:26 -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
guerler e466bcbc44 Merge branch 'dev' of https://github.com/galaxyproject/galaxy into workflow_form_002 2015-06-07 22:17:25 -04:00
guerler a00461eaf6 Merge workflow_001 2015-06-04 02:42:53 -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