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2303 Commits
Author SHA1 Message Date
Mark Einon d6d8e5ef86 upload.py: Remove unused function parameter 2015-11-13 11:33:56 +00:00
Daniel Blankenberg 39ff0e9d76 Merge pull request #1044 from jmchilton/release_15.10_to_dev 
Bring 15.10 (and 15.07) fixes into dev.
 2015-11-10 10:42:02 -05:00
John Chilton 2934c2f3bd Lint fix for 15.10 to dev merge. 2015-11-09 15:33:05 +00:00
John Chilton dc534bb258 Merge branch 'release_15.10' into dev 
Conflicts:
	client/galaxy/scripts/mvc/grid/grid-view.js
	static/maps/mvc/collection/list-of-pairs-collection-creator.js.map
	static/scripts/mvc/collection/list-of-pairs-collection-creator.js
 2015-11-09 15:19:02 +00:00
John Chilton 57d6c9872c Merge remote-tracking branch 'jmchilton/release_15.07' into release_15.10 2015-11-09 15:13:12 +00:00
Nicola Soranzo f69c06b6cf Merge pull request #1033 from scholtalbers/wig_to_bigwig_error_msg 
wig_to_bigwig: Add error message for wrongly formatted data
 2015-11-05 18:37:35 +00:00
Jelle Scholtalbers 4908a5bab6 wig_to_bigwig: Add error message for wrongly formatted data 2015-11-05 19:15:51 +01:00
Nicola Soranzo 69cda48690 Remove remaining references to galaxy.eggs . flake8 some files in tools/ . 2015-10-26 19:29:13 +00:00
Daniel Blankenberg a02e0f19c8 Set <options sanitize="False"> for genomespace_importer.xml 2015-10-21 11:33:45 -04:00
Daniel Blankenberg 120ec61264 Fix command quoting and remove size from text input for Cut tool. 2015-10-14 10:11:21 -04:00
Eric Enns 0ec1b17794 Update list comprehension to go through headings instead of summary so that we output in the order we want. 2015-10-14 08:28:30 -05:00
Eric Enns ad4458a458 Revert to previous changes if using rpy2 2015-10-09 10:34:20 -05:00
Eric Enns ad20452340 Fix output to print values and not hash key 2015-10-09 10:08:48 -05:00
Daniel Blankenberg 092fc17ec0 Merge pull request #846 from jmchilton/ucsc_cleanup 
UCSC Tool Cleanup
 2015-10-05 17:05:56 -04:00
Martin Cech f90c49e270 Merge pull request #847 from jmchilton/citations_5 
Add more distribution tool citations.
 2015-10-05 17:01:18 -04:00
John Chilton 4cd4dac0a0 Merge pull request #848 from jmchilton/echo_remove 
Remove unused echo tool
 2015-10-05 20:44:56 +01:00
Martin Cech bb43ace509 Merge pull request #842 from bgruening/filter_by_attribute 
Update documentation for the gff_filter_by_attribute tool
 2015-10-05 14:55:30 -04:00
Björn Grüning 6430b9c4e8 Update documentation for the gff_filter_by_attribute tool 2015-10-05 18:43:36 +02:00
John Chilton a6f9e62c1a Add citations to ucsc browser tools. 2015-10-05 15:55:21 +01:00
John Chilton 1aebbc3f68 Remove likely broken UCSC proxy and associated tools. 
Unused for many, many years and likely no longer works.
 2015-10-05 15:55:21 +01:00
Eric Rasche f50702f962 Remove unused echo tool 2015-10-05 15:21:39 +01:00
John Chilton 88239abf5c Add more distribution tool citations. 
xref #361.
 2015-10-05 15:16:50 +01:00
John Chilton 591519009b Add citations to a few more tools. 2015-10-05 15:12:46 +01:00
Daniel Blankenberg 54d4c266bd Have GenomeSpace tools report the GS tool name (for their internal metrics). Default is "Galaxy", but can be overridden by setting "GENOMESPACE_TOOLNAME" environment variable. 2015-09-10 14:45:40 -04:00
yhoogstrate 6a38e0bda7 Update liftOver_wrapper.xml 
version++
 2015-08-12 10:57:42 +02:00
youri 83bc5b74ff liftOver.loc was not accessible from local data 2015-08-11 10:58:06 +02:00
y.hoogstrate@erasmusmc.nl 6ce94ce7e6 Fixed comments 2015-07-30 13:12:51 +02:00
y.hoogstrate@erasmusmc.nl 91a29d8a6a extract_genomic_dna support for 2bit files from Local data 2015-07-30 12:06:07 +02:00
Nicola Soranzo cc9b0bed85 Fix all E712 errors. Standardize sqlalchemy imports. 2015-07-14 20:49:34 +01:00
Nicola Soranzo 34d9388456 Use os.pardir everywhere instead of '..' . 2015-07-14 16:20:29 +01:00
Nate Coraor 6eafa52f41 Remove superflous assignment left over from 
647fcf1f60, thanks @nsoranzo.
 2015-07-13 14:55:33 -04:00
Nate Coraor 647fcf1f60 Only make the Group tool's return value an integer if rounding is 
selected, as pointed out by @nsoranzo.
 2015-07-13 11:01:55 -04:00
Oleksandr Moskalenko 58091b4b5b Make the Group tool return integer values when 'round to nearest integer' is selected 2015-07-04 17:58:07 +01:00
Nicola Soranzo 1830adfb30 Fixes for @jmchilton and @dannon. 2015-06-17 19:37:45 +01:00
Nicola Soranzo 7830bc62e0 Another fix for 3c40f32fa2 . 2015-06-17 19:21:13 +01:00
Nicola Soranzo 3c40f32fa2 PEP-8 and pylint fixes. 2015-06-16 16:53:49 +01:00
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
John Chilton 1a39b6aa79 Merge remote-tracking branch 'jmchilton/release_15.05' into dev 2015-05-20 15:48:25 -04:00
Daniel Blankenberg af6172d14d Update default dbkey for worm_modencode.xml and bump version. 
ce10 is UCSC for WS220
 2015-05-20 12:42:05 -04:00
Daniel Blankenberg 93c51fa259 Update default dbkey for fly_modencode.xml and bump version. 
dm3 is UCSC for release 5
 2015-05-20 12:39:59 -04:00
Martin Cech 182fbd1bc6 fix the data source tools for modendcode with proper URLs 2015-05-19 16:53:25 -04:00
Nicola Soranzo 341a6cf760 Use requirements of type="package" instead of deprecated "binary". 2015-05-15 12:43:15 +01:00
Nicola Soranzo 224d8f3fc4 Remove numpy requirement, not used since commit 09ce7a9b17 . 2015-05-15 12:41:08 +01:00
Nicola Soranzo 22d4a1d8c3 dos2unix of tools/ directory. Some whitespace and PEP-8 fixes. 2015-05-15 12:40:52 +01:00
Marek Vavrusa bc8bdadca8 datatypes: extracted TabularData superclass from Tabular, CSV subclass 2015-04-30 17:20:32 +02:00
Björn Grüning 1dde01220c Remove plain R dependency 2015-04-29 21:49:04 +02:00
Marek Vavrusa e5aa966f1d stats/gsummary: RPy is deprecated, use RPy2/classic as an alternative 2015-04-29 17:24:22 +02:00
Björn Grüning 6f13a4be45 drop python-module 2015-04-29 16:47:37 +02:00
Björn Grüning e11e1864ef Update gsummary dependencies. 2015-04-29 12:14:07 +02:00
Dannon Baker 66ef2fc90e Merge over and resolve conflicts release->dev 2015-04-22 10:08:53 -04:00