Greg Von Kuster
c68066fac2
Apply the improvements for generation of tool shed URLs to the repository controller.
2012-08-28 11:49:43 -04:00
Dave Bouvier
112d13e066
Improved generation of tool shed URLs
2012-08-28 11:32:17 -04:00
Greg Von Kuster
f047aa99e8
Add the ability to browse writable repositories in a tool shed.
2012-08-28 11:01:07 -04:00
Jeremy Goecks
e9c26d05d3
Fixes for phyloviz parser and a4c7aeb61c7b.
2012-08-28 09:05:31 -04:00
Jeremy Goecks
ce86cf2715
Comment out phyloviz XML parser until native Python XML parsing is used.
2012-08-27 15:44:01 -04:00
Jeremy Goecks
d2a96e66bd
Merged in Tomithy/galaxy-central-phyloviz-2 (pull request #65 )
2012-08-27 14:08:55 -04:00
Dave Bouvier
cb0614f0fa
Fixed truncation of downloaded fasta files.
2012-08-27 12:52:43 -04:00
Tomithy Too
516d727229
re-integrated phyloviz to a new fork of galaxy-central with a tat of minor touch up; save and edit now works
2012-08-26 18:22:23 +08:00
Jeremy Goecks
37c07fa1eb
Enable function to be used for generating a grid operation link; use this functionality to generate link for viewing/editing visualization.
2012-08-24 18:15:29 -04:00
Dave Bouvier
334983c4df
Added script to update NCBI builds list, replaced Broad data source with direct URL, cleaned up help text.
2012-08-23 16:36:58 -04:00
Dannon Baker
61059cc61d
Merged in jmchilton/galaxy-central-roles-api-fixes (pull request #62 )
2012-08-23 09:34:43 -04:00
Jeremy Goecks
f6ece851d3
Fix for handling missing quality values in VCF data provider + some whitespace. Thanks to Jim Johnson for fix.
2012-08-23 09:04:08 -04:00
John Chilton
508649e409
Include created history url in json rendered by histories API on successful history creation. Dannon verified this is the desired behvaior in the comments on issue 802 in bitbucket.
2012-08-22 17:05:53 -05:00
John Chilton
f9b2eb2438
Create method in libraries API should return the created library not an array containing only the created library. This was confirmed by dannon in the comments on issue 802.
2012-08-22 16:57:04 -05:00
Dannon Baker
0b2e939d4d
Remove blast tools and test data from the distribution, update tool_conf.xml.sample to reflect this.
2012-08-22 16:12:59 -04:00
Jeremy Goecks
60887b8a42
Add data placeholders so that BED files without all optional fields can be dynamically filtered.
2012-08-22 14:42:05 -04:00
Daniel Blankenberg
bb15315fed
Refactor GBrowse external display application. Update WormBase with latest builds and to be able to use reference sites.
2012-08-22 12:35:23 -04:00
Daniel Blankenberg
6c9d104f05
Better handling of invalid dynamic external display application links.
2012-08-22 11:40:55 -04:00
Enis Afgan
0b70fbb653
Rename an ObjectStore method not to be AWS-specific
2012-08-22 16:24:52 +10:00
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
John Chilton
f7ad41d4e6
Fix library permissions API which has been broken since security API
...
changes in 8731db1b2bfb (June 2011).
2012-08-21 23:05:05 -05:00
John Chilton
59ba42fffd
Roles API bug fixes.
2012-08-21 21:05:53 -05:00
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
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
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
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
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
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
Greg Von Kuster