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Commit Graph
2372 Commits
Author SHA1 Message Date
guerler 7a6961e30d Undo dataset renaming 2017-05-01 11:57:07 -04:00
Nicola Soranzo d1974a42e5 Use detect_errors="exit_code" in Trim tool 
Prevent job failures due to spurious messages on stderr from the cluster
scheduler.
 2017-04-04 18:47:55 +01:00
Nate Coraor f645259dd0 Only keep the last path element when naming files uploaded via the URL 
paste method
 2017-02-27 10:59:21 -05:00
Nicola Soranzo 03a807e374 Lint some tools 2017-01-23 21:11:43 +00:00
John Chilton 45bf7ad8c4 Make requirement tags in bar_chart.xml functional with default dependency resolver. 
I'm not sure if we need to update the version since previously these tags were purely for documentation and had no functional purpose.

xref this comment https://github.com/galaxyproject/galaxy/pull/3444#issuecomment-273909855 from @bgruening
 2017-01-19 17:05:53 -05:00
John Chilton 52e4b6e89e Remove seemingly unused file sort_gtf.py. 
Added in df28aec040 - not used in that commit.
 2016-12-23 10:21:15 -05:00
John Chilton 58a3a5b71b Fix linting of gff_filter_by_attribute. 
Broken during security patching - Travis tests are failing now against dev.
 2016-12-16 10:10:44 -05:00
Nate Coraor 74923463cf Merge branch 'release_16.10' into dev 2016-12-15 13:08:22 -05:00
Nate Coraor 42cda96928 Merge branch 'release_16.07' into release_16.10 2016-12-15 13:07:39 -05:00
Nate Coraor 22fda449f9 Merge branch 'release_16.04' into release_16.07 2016-12-15 13:05:22 -05:00
Nate Coraor 4cf70aea79 Merge branch 'release_16.01' into release_16.04 2016-12-15 13:04:29 -05:00
Nate Coraor 4c07734f57 Merge branch 'release_15.10' into release_16.01 2016-12-15 12:55:39 -05:00
Nate Coraor 95daf69b37 Merge branch 'release_15.07' into release_15.10 2016-12-15 12:49:39 -05:00
Nate Coraor 790e60af60 Merge branch 'release_15.05' into release_15.07 2016-12-15 12:46:17 -05:00
Nate Coraor 7c443eda56 Merge branch 'release_15.03' into release_15.05 2016-12-15 12:38:28 -05:00
Nate Coraor da7afb4e22 Merge branch 'release_15.01' into release_15.03 2016-12-15 12:37:10 -05:00
Nate Coraor 9ee3d01c30 Merge branch 'release_14.10' into release_15.01 2016-12-15 12:36:21 -05:00
Nate Coraor c1e3087ca3 Fix an ACE vulnerability with gff filter tools. Thanks to David Wyde for 
the disclosure.
 2016-12-15 12:34:18 -05:00
Nicola Soranzo 3d57c22b63 Fix I201 errors from flake8-import-order 
Also fix Python3 compatibility.
Remove unused method
galaxy.tools.parameters.sanitize.ToolParameterSanitizer.restore_param() .
 2016-11-23 18:31:04 +00:00
Nicola Soranzo 1d17a29c79 Fixes for pycodestyle 2.2.0 2016-11-15 16:56:50 +00:00
Nicola Soranzo d26f46423e Merge pull request #3042 from dannon/image_detection_fixes 
Image detection fixes
 2016-10-14 10:27:17 +01:00
Dannon Baker 0062eacfdf Merge pull request #3044 from blankenberg/gff-filter-tool-fix 
Fix GFF attribute filtering tool broken in #2983
 2016-10-13 14:40:03 -04:00
Daniel Blankenberg 32bc17cdaa Whitespace fix 2016-10-13 11:08:18 -04:00
Daniel Blankenberg 5d294ea7d3 Fix GFF attribute filtering tool broken in #2983 2016-10-13 10:54:41 -04:00
Daniel Blankenberg ba07956117 Fix tabular filtering tool broken in #2983 2016-10-13 10:40:40 -04:00
Dannon Baker cb6e25278c Refactoring, because it was bugging me. 2016-10-13 10:25:18 -04:00
Dannon Baker bb44288968 Failthrough to using imghdr when PIL does not detect an image correctly. 
Some misc cleanup, avoiding use of system functions as variable names,
etc.
 2016-10-13 09:55:01 -04:00
Nicola Soranzo 11b4f3a60c Fix import order and Python3 compatibility for tools/ 
xref #1715
 2016-09-29 19:26:22 +01:00
John Chilton d06e2a672b XSD discovered tool problems. 2016-09-08 11:40:01 -04:00
Dannon Baker c9ac723174 Revert genomespace tool changes related to FILENAME_VALID_CHARS 2016-08-11 11:01:20 -04:00
Dannon Baker f87b08efa0 Consolidate usage of 'valid_chars' in the application. 2016-08-05 13:57:40 -04:00
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 ac902304ae 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. 2016-06-21 11:05:09 -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 a27e86786a wrap bare str raises with generic Exception() 
as Pyton 2.7 does not support bare str
 2016-05-26 16:45:31 -04:00
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