Enis Afgan
87241f4c62
Merge
2012-08-22 16:13:51 +10:00
Enis Afgan
7b391611a6
Multipart upload to OpenStack Swift does not work with boto so don't use it
2012-08-22 16:12:46 +10:00
Jeremy Goecks
2a4012e03d
Final JS reorg to rename and move files so that all files follow standard conventions.
2012-08-21 17:08:35 -04:00
Jeremy Goecks
66d1892364
More JS file reorganization: (a) move IE and rgenetics into their own directories; (b) move additional external libraries to libs.
2012-08-21 16:54:19 -04:00
Daniel Blankenberg
85c985db82
Remove blastxml from datatypes_conf.xml.sample.
2012-08-21 16:05:55 -04:00
Jeremy Goecks
44d37d7eee
Move most jQuery files into own libs directory.
2012-08-21 15:52:50 -04:00
Jeremy Goecks
a3d8452df5
JavaScript cleanup: (a) create backbone lib in scripts/lib and use for backbone libraries; (b) clean up history.js; (c) pack scripts.
2012-08-21 14:27:18 -04:00
Dannon Baker
8faf5cc089
Rewrap text in blast tool migration script.
2012-08-21 10:57:52 -04:00
Dannon Baker
dc659b6262
Merge.
2012-08-21 10:52:33 -04:00
Carl Eberhard
5046dac563
fix to gff_to_fli.py to avoid breaking unittests
2012-08-20 13:50:12 -04:00
Jeremy Goecks
8eea8de39a
Make 'add dataset to trackster' dialog compatiable with new modal behavior.
2012-08-20 10:27:44 -04:00
Jeremy Goecks
009bd6fed6
Fix URL generation bug when dictifying tools.
2012-08-20 09:57:25 -04:00
Jeremy Goecks
871f72c956
Trackster: for explicit coverage histogram mode in Feature Tracks, use coverage indices rather than computing on client side.
2012-08-19 15:42:11 -04:00
Jeremy Goecks
5ab62c8746
Streamline creation of stats for BBI tracks data provider.
2012-08-18 18:00:31 -04:00
Jeremy Goecks
860bb2673c
Converters enhancements: (a) ignore track lines in wiggle to bigwig converter and add clip option and (b) enable visualization of bedgraph datasets via a bedgraph to bigwig converter.
2012-08-17 17:49:41 -04:00
Scott McManus
dbc2c27a82
Minor tweak to exit code handling
2012-08-17 15:15:48 -04:00
Carl Eberhard
3360fe3072
new data for bwa_wrapper/bwa_color_wrapper functional tests
2012-08-17 14:39:32 -04:00
Dannon Baker
97e69fbbdf
Fix chunk-serving logic for tabular files.
2012-08-17 13:55:37 -04:00
Dannon Baker
3d5fd7b5e2
Migrate NCBI Blast+ (and blastxml) to the toolshed.
2012-08-17 11:35:31 -04:00
Jeremy Goecks
9fabf5dfbe
Add feature/attribute name indexing framework to converters. Provide full text indexing for GFF attributes.
2012-08-16 16:32:00 -04:00
Dave Bouvier
48ad38ff3c
Improved error handling for failed indexing jobs.
2012-08-16 15:43:02 -04:00
John Chilton
65179d6c0b
Dynamic job runner bug fixes.
2012-08-16 10:58:01 -05:00
Enis Afgan
78e2d4f919
Merge
2012-08-16 09:57:05 +10:00
Enis Afgan
9a47e09e21
Handle AWS-specific config options for backward compatibility
2012-08-16 09:50:00 +10:00
Jeremy Goecks
54b1f8097a
Cleanup for previous commit, 565476ce4f03, mainly to further comment and simplify code and avoid going to index multiple times.
2012-08-15 18:09:48 -04:00
Jeremy Goecks
5dda060e33
Rewrite sampling code for BBI data provider to handle (a) boundary cases during base-level resolution and (b) remainder of region not sampled during first pass.
2012-08-15 17:49:39 -04:00
Greg Von Kuster
c0898c6882
Improve error message handling when setting metadata on tool shed repositories. Display the repository owner in the table grid when displaying invalid tools in the tool shed.
2012-08-15 14:50:38 -04:00
Greg Von Kuster
cdd15be456
Fix for setting tooll dependency metadata where at least one tool in the repository does not include a <requirements> tag set.
2012-08-15 11:55:17 -04:00
Carl Eberhard
7ee4bce898
small fix to twilltestcase when GALAXY_TEST_SAVE fails
2012-08-15 11:13:13 -04:00
Nate Coraor
5752c297d9
Merged in jmchilton/galaxy-central-configuration-directory (pull request #44 )
2012-08-15 10:57:14 -04:00
Nate Coraor
a7f4a7534a
Merged in jmchilton/galaxy-central-preseeding (pull request #38 )
2012-08-15 10:54:50 -04:00
Greg Von Kuster
2393ef7b30
Eliminate the freebay specific functional test data from the distribution since it is now included in the freebayes repository in the tool shed.
2012-08-15 10:52:46 -04:00
John Chilton
79937a5398
Enable the lwr & dynamic job runners automatically. Neither require
...
any special libraries and deployers must assign tools to use them
before they have any affect on Galaxy (i.e. no subtle/implicit
behaviors), so I don't anticipate any down side to doing this. Also
clean up logic in lib/galaxy/jobs/handler.py a little to accommodate
this.
2012-08-14 23:38:24 -05:00
Scott McManus
95119845d9
Reworked some stdout/stderr parsing to make errors and warnings more apparent.
2012-08-14 18:58:58 -04:00
Greg Von Kuster
02794376ad
Fix for recently introduced bug that breaks installation of tool shed repositories into a local Galaxy instance if the repository includes tools that use the ToolDataTableManage. Also, move processing of sample files and other config files included in installed tool shed repositories to disk rather than memory.
2012-08-14 16:24:54 -04:00
Nate Coraor
a3c1064c8f
Reclaim ownership of job's working dir prior to reading stdout/stderr/ec files to avoid permissions problems.
2012-08-14 15:22:29 -04:00
Carl Eberhard
b2a5996a6c
tool-data change to fix bwa_wrapper.test_tool_000001; backbone history.js start
2012-08-14 13:15:48 -04:00
Jeremy Goecks
5c3fe00060
Include fusions output in Tophat2 wrapper.
2012-08-14 12:17:01 -04:00
Enis Afgan
47b63cbf91
Add the ability for Galaxy's ObjectStore to use OpenStack's SWIFT object store as the backend data storage
2012-08-14 10:04:25 +10:00
Greg Von Kuster
226c34b583
Enable reversing the list of tool version ids for tool included in tool shed repositories installed into a local Galaxy instance.
2012-08-13 16:41:47 -04:00
Greg Von Kuster
8847ebba5d
Fixes for setting metadata on tool shed repositories and specific add tool lineage information on the view tool metadata page in the tool shed as well as for tool shed repositories installed into a local Galaxy instance.
2012-08-13 14:54:07 -04:00
Dannon Baker
6513b2a59d
Merge pull request.
2012-08-13 13:22:51 -04:00
Dannon Baker
89afe027be
Whitespace cleanup.
2012-08-13 13:00:09 -04:00
Dannon Baker
e0d6ddc0e0
Fix convert_newlines and sep2tabs to return '0' lines in the event of an empty file, instead of blowing up.
2012-08-13 12:59:17 -04:00
Ross Lazarus
11349f28b5
Added unicode and raw flags to the re.sub string - not tested with unicode name yet..
2012-08-11 09:42:48 +10:00
Ross Lazarus
5238e15eb7
Unicode/raw for re.sub string in rgFastQC.py
2012-08-11 09:36:29 +10:00
Ross Lazarus
f2fa4636b6
Branch merge
2012-08-11 09:22:57 +10:00
Ross Lazarus
8bdddafc71
Add - and . to re.sub exclusion list for user supplied filename at Scott's suggestion and use _ as a substitute for
...
all other characters so
'cd \/; rm -rf'
becomes
'cd_____rm_-rf'
FastQC wrapper should now be reasonably hard to pervert but user filenames will be at least vaguely recognizable...
2012-08-11 09:21:45 +10:00
Nate Coraor
d12a9ec367
Merged in jmchilton/galaxy-central-lwr-enhancement-1 (pull request #57 )
2012-08-10 14:35:44 -04:00
Nate Coraor
31c7003d4d
Merged in jmchilton/umn-galaxy-central/add_requirement_tags_for_plink (pull request #35 )
2012-08-10 14:33:59 -04:00
Enis Afgan