opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-09-24 16:30:27 +08:00
Code Issues Packages Projects Releases Wiki Activity
21,434 Commits 69 Branches 243 Tags
68f718d53bc6bcc44c8ccbe14c79a9fb79c3b9fc
Commit Graph
2306 Commits
Author SHA1 Message Date
pavanvidem bf4e736c3c Update david identifier types 
David identifier types seem to be changed. Some of them are no more available on david web server.
 2016-02-09 09:54:12 +00:00
John Chilton 50e531aa59 Refactor galaxy.datatypes.checkers into galaxy.util.checkers. 
- Primary reason is because it is used all over the place in contexts that have nothing to do with Galaxy datatype classes or datatype registery or sniffing, most importantly by the code in the tool shed for determining if something is a tool or not.
 - This code has no dependencies on the datatypes module or any hard dependencies on things not in the Python standard library.
 2015-12-17 15:41:06 +00:00
John Chilton 83f57c56c1 Refactor is_multi_byte out of galaxy.util. 
It introduces a fairly esoteric dependency in galaxy.util for just a couple uses in Galaxy. Separating it out like this will allow reuse of the entire galaxy.util with only one external dependency (docutils, which planemo for instance already depends on).
 2015-12-16 21:36:16 +00:00
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