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
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
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
Nate Coraor
d12a9ec367
Merged in jmchilton/galaxy-central-lwr-enhancement-1 (pull request #57 )
2012-08-10 14:35:44 -04:00
Jeremy Goecks
0881708333
Explicitly specify encodings for tool help templates to avoid unicode/ascii confusion.
2012-08-10 12:26:43 -04:00
Jeremy Goecks
2a1bbec58f
Make from_work_dir attribute work when outputs_to_working_directory is True.
2012-08-10 09:58:59 -04:00
John Chilton
5b641e7068
Implement a mechanism to secure access to lwr. If enabled on the
...
server, a private token must be passed along with all
interactions. This token may be specified as part of the job runner
url as such:
wintool = lwr://https://token@host:8913/
This token will not protect the client against a rouge server that has
exploited say a DNS spoofing vulnerability. It is only meant as a
mechanism for the lwr to ensure the client is authorized. This feature
should be used in conjunction with SSL to prevent a "man-in-middle"
from intercepting this token.
2012-08-09 17:25:35 -05:00
Jeremy Goecks
d4a109eae4
Data providers: unified and comprehensive handling of differences between different chromosome naming schemes.
2012-08-09 17:32:47 -04:00
John Chilton
6f12ab3c7a
Merge.
2012-08-09 15:18:00 -05:00
John Chilton
9bcbabfaa9
JJ's initial work on extending the API to allow operations on groups.
2012-08-09 15:15:23 -05:00
Greg Von Kuster
ae2bdd323d
Fixes to recent changes that broke the ability to install a tool shed repository to a local Galaxy instance.
2012-08-09 11:37:47 -04:00
Greg Von Kuster
d9e131e2cb
Fix imports broken in 9f790bc90769 using patch from Bjorn Gruning.
2012-08-09 06:46:13 -04:00
Greg Von Kuster
918294e6e1
Fixes for setting versions for tools included in a repository in the tool shed.
2012-08-08 16:15:06 -04:00
Greg Von Kuster
f0652d4515
More fixes for setting metadata on repositories in the toool shed. Change set includes other miscellaneous fixes, including the elimination of some problematice historical code that managed temporary working directories which resulted in problematic race conditions.
2012-08-08 14:31:46 -04:00
Carl Eberhard
217690a63a
fix to mako import and some up-stack error reporting in tools
2012-08-08 12:30:25 -04:00
Dave Bouvier
1d017ffd1c
Improved generation and display of local genome/indexes table. Handle missing tool data table entries.
2012-08-08 10:37:27 -04:00
Jeremy Goecks
33cfa95096
Make workflows compatible with change made in 29680fa5c35e that makes tool help a template rather than static text. Bonus: images in tool help now display in workflow editor as well.
2012-08-08 08:39:39 -04:00
Greg Von Kuster
c88b418e03
Ensure repository metadata records are unique in the tool shed.
2012-08-07 14:42:28 -04:00
Greg Von Kuster
c83c560e29
Fixes for setting metadata on repositories in the tool shed.
2012-08-07 13:52:50 -04:00
Greg Von Kuster
1e3aff12b8
Fix mercurial command line handling for pushes from the command line that were broken in change set d19fbfefb676 for versions of mercurial older than 2.2.3. Pushes should now function correctly for those running mercurial older than version 2.2.3.
2012-08-07 13:43:36 -04:00
Jeremy Goecks
9a5679c37c
Use mako template in tool help so that dynamic image paths can be used. Fixes #141
2012-08-07 09:40:51 -04:00
Enis Afgan