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2337 Commits
Author SHA1 Message Date
nturaga 4fabf51f4b typo in summary statistics tool 2016-07-20 15:27:24 -04:00
Gildas Le Corguillé f951249c79 Update gsummary.xml 
Delete r and rpy deps
 2016-07-12 13:28:42 +02:00
Gildas Le Corguillé e862067332 Update gsummary.xml 2016-07-07 16:41:06 +02:00
Gildas Le Corguillé f7cbefc1f3 Update gsummary.xml 
rpy seems not available within the Conda packages. 
So I add rpy2 in the requirements.

It works for me! I ❤️ Conda
 2016-07-07 12:02:51 +02:00
Timur Shtatland dba8d0bb0a Python3: tools/stats/aggregate_scores_in_intervals.py 2016-06-25 17:07:59 -04:00
Dannon Baker 618c644d2b Fix two errors in sff_extract.py detected by flake8 -- either of these code paths would have thrown an exception and failed prior to this. 2016-06-16 16:10:36 -04:00
Nicola Soranzo cc336f61c0 Make some files compatible with Python3 
Also enlarge the set of files tested with flake8 under Python3
 2016-06-03 19:24:46 +01:00
Martin Cech d72eee3d4a wrap bare str raises with generic Exception() 
as Pyton 2.7 does not support bare str
 2016-05-26 13:14:22 -04:00
Nicola Soranzo 1652e0ceed Add EDAM topics to tools and expose in API 2016-05-24 12:17:39 +01:00
Marius van den Beek c3ecd1eb72 Annotate tools with edam_operations 
to demonstrate usage of edam_operations in tool xml.
 2016-05-19 17:27:04 +02:00
Nicola Soranzo 6ba6f798ec Fix more E203 flake8 errors 2016-05-17 23:53:16 +01:00
Nicola Soranzo 8a43b2b492 Python 3: use "as" instead of comma in except clause 2016-05-17 23:53:16 +01:00
Nicola Soranzo ed4132d9c0 Python3: Use open() instead of file() 2016-05-17 23:53:16 +01:00
Nicola Soranzo bf5568d86a Quote some parameters in Trim tool command 
Make the tool more robust, see issue #2245.
Also:
- use format_source instead of deprecated format='input';
- explicitly call python in command instead of using the depredated interpreter attribute;
- use CDATA in command.
 2016-04-25 19:48:06 +01:00
Dannon Baker 97110e2655 Merge branch 'release_16.04' into dev 2016-04-20 11:54:22 -04:00
Dannon Baker e5290e1964 Merge pull request #2149 from martenson/fix-biomart 
[16.04] fix/replace biomart data source
 2016-04-20 10:26:57 -04:00
Nicola Soranzo 58f510fda9 Merge branch 'release_16.04' into dev 2016-04-15 09:47:45 +01:00
Dannon Baker 1e7edf0bd7 no parens 2016-04-14 16:59:25 -04:00
Dannon Baker 7bed69ba17 Specify Ensembl biomart server in descriptions. 2016-04-14 16:56:47 -04:00
Daniel Blankenberg 34900f87f5 Fix grouping tool broken in 7347d75a4a / fd85979a86, and enhance performance when removing lines. 2016-04-14 12:00:11 -04:00
John Chilton 997b53f3ae Implement option to prevent FTP uploads from being deleted on import. 
- Simply set `ftp_upload_purge` to `False` in galaxy.ini to enable this.
 - xref http://dev.list.galaxyproject.org/Data-removal-after-ftp-import-td4667111.html
 - slight xref http://dev.list.galaxyproject.org/Uploading-files-to-galaxy-from-a-folder-td4664614.html
 2016-04-14 11:34:21 -04:00
Martin Cech c49e7803fa fix biomart url 2016-04-13 11:12:15 -04:00
Nicola Soranzo 501a10c3f1 Do not import dumps and loads from galaxy.util.json . 2016-03-02 19:04:24 +00:00
Nicola Soranzo 39da6c3278 Fix the remaining 2180 flake8 errors in tools/ . 2016-02-10 18:46:03 +00:00
Nicola Soranzo 8703f3bd9e Remove unused files. 2016-02-10 17:35:31 +00:00
Nicola Soranzo 2ddf6eed63 Remove broken and hidden fix_errors tool. 2016-02-10 17:35:25 +00:00
Martin Cech db1bb2f191 Merge pull request #1556 from jmchilton/datatype_imports 
Code design and legacy cleanup of datatypes and metadata.
 2016-02-09 12:44:59 -05:00
pavanvidem e468c9882f Update david identifier types 
David identifier types seem to be changed. Some of them are no more available on david web server.
 2016-02-08 17:26:34 +01:00
John Chilton 448aee9f00 Fix for multi-byte char problem in PR #1556... 
... caught by @nsoranzo of course.
 2016-02-08 13:48:43 +00:00
guerler 193c5293d9 Remove invalid validator from upload.xml 2016-01-26 14:49:35 -05:00
John Chilton 499357e508 Remove unneeded galaxy.model import in upload.py... 
... and document the ability to remove from other data sources.
 2016-01-21 14:31:42 +00:00
John Chilton 1f4b329032 Refactor galaxy.tools.exception_handling... 
... so datatype module doesn't need to import something from galaxy.tools - which causes a bunch of more things to be imported because galaxy.tools at the top-level has so many imports.
 2016-01-21 14:31:41 +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