Jeremy Goecks
f514b9471e
Create and use ReferenceTrackDataManager to fetch ReferenceTrack data.
2011-04-14 14:34:39 -04:00
Jeremy Goecks
23efa70ebe
Trackster: (a) fix bug in acee660871cd that prevented line tracks from displaying properly and (b) set track height in show_tile rather than draw_tile, which obviates the need for parent_element to be passed to draw_tile.
2011-04-14 14:29:32 -04:00
Jeremy Goecks
254018a930
Trackster: refactor so that summary_tree and Histogram modes use the same code.
2011-04-14 10:37:42 -04:00
Jeremy Goecks
ffc478709b
Fix bug that prevented workflows with runtime parameters from being exported.
2011-04-14 10:05:00 -04:00
Dannon Baker
859d15f7cc
Merge!
2011-04-14 09:02:20 -04:00
Martijn Vermaat
9964bd8673
Give input selection and filtering a minimum width (run tool form).
2011-04-14 14:23:28 +02:00
Ross Lazarus
ee6bd2cf46
Changes to allow all test outputs generated by twill to be saved to a folder pointed to by
...
an environment variable "GALAXY_TEST_SAVE" if defined before running functional tests
If the environment variable is empty, all tests procede as usual and test outputs are deleted
without saving
2011-04-14 08:09:48 -04:00
Martijn Vermaat
71e298cdcb
Adds filtering to input selection on run workflow page.
2011-04-14 12:14:30 +02:00
Dannon Baker
2c81457e57
Merge.
2011-04-13 19:14:21 -04:00
Martijn Vermaat
100db97731
Typo.
2011-04-14 01:13:10 +02:00
Dannon Baker
254876a817
Merge.
2011-04-13 19:07:22 -04:00
Dannon Baker
1f59ddfa7d
Merge.
2011-04-13 19:05:45 -04:00
Martijn Vermaat
a8285d6160
Run a workflow on a selection of multiple inputs, one invocation for each.
...
- Makes input selections in the run workflow form support multiple
selection.
- If multiple inputs are selected, a workflow invocation is executed for
each selected input.
- Only of of the workflow inputs can have a multiple selection.
2011-04-14 01:04:40 +02:00
Jeremy Goecks
bfbe47327a
Add Tile objects to trackster to support better tracking of Tile data properties; use SummaryTreeTile objects to ensure that feature track coverage histograms are drawn with the same max. Some refactoring of TiledTrack.draw() done as well for simplicity. Finally, fixed typos and GFF display bugs.
2011-04-13 18:09:07 -04:00
Dannon Baker
ef2b1b9e7b
Faded document stack icon.
2011-04-13 16:46:36 -04:00
Dannon Baker
dd80436895
Bugfix for workflow run not reloading history, icon for document stack.
2011-04-13 16:35:08 -04:00
Greg Von Kuster
b70b4a1261
Streamline the process of importing library datasets into histories:
...
1) Allow imports from the admin view instead of just the Data Libraries view.
2) Add a new 1-click option when acting on multiple selected library datasets to import them into the current history.
3) when importing selected library datasets into selected histories, make the current history selected by default.
4) Add the ability to import the current library dataset into a selected history when viewing the library dataset info page.
2011-04-13 16:05:34 -04:00
Greg Von Kuster
9102fc3472
1. Add support for manual file transfer from external services to a Galaxy data library using scp. This is currently enabled via the enable_beta_job_managers flag. This should not currently be used because it hits the db significantly to determine if dererred jobs are queued for running. The plan is to use messaging for this, but that approach is not yet implemented. Rabbit mq is still being used to enable manual file transfer to Galaxy data libraries when the enable_beta_job_managers flag is not set.
...
2. Clean up the code that renders the jquery file browser plugin - things work much cleaner now. One remaining item is handing the issue where rsh / ssh keys are not set. Also clean up a lot of code related to manual file transfers in the requests_admin controller.
3. In addition to the new ManualDataTransferPlugin, add the Pacific Biosciences SMRTPortalPlugin that automatically transfers files produced by SMRT Portal to a Galaxy data library.
4. Add the external service type config for Pac Bio SMRT Portal version 1.1.0.
2011-04-13 13:52:05 -04:00
Kanwei Li
e2b633fd16
trackster: Don't load huge reference tracks now that we pre-load data, preventing hang
2011-04-12 23:41:06 -04:00
Kanwei Li
962f7d06ba
Fix some scramble problems
2011-04-12 22:08:09 -04:00
Jeremy Goecks
762a0becfa
Make changes in ddea56886275 compatible with python 2.4
2011-04-12 17:26:06 -04:00
Jeremy Goecks
c967bfa36d
Trackster: add histogram mode to feature tracks so that user can generate coverage histogram at any level of data. Refactor overlap computation out of modules for now since it's a general purpose method used in multiple modules.
2011-04-12 14:40:59 -04:00
Kanwei Li
7a03b066e7
update jquery to 1.5.2, pack scripts
2011-04-12 12:10:48 -04:00
Jeremy Goecks
2b31c9737a
Fix bugs introduced in 03c02d86d011.
2011-04-12 09:35:36 -04:00
Jeremy Goecks
8a44d4f5e5
Trackster: refactor track filters out of TiledTracks and into a FiltersManager object.
2011-04-11 14:17:35 -04:00
Jeremy Goecks
521059477e
Enable GFF and GFF3 attributes to be written in GTF format.
2011-04-11 12:35:23 -04:00
Greg Von Kuster
be5da0c0ef
Fix for rating a tool in the tool shed.
2011-04-11 10:37:14 -04:00
Jeremy Goecks
1a371da9ae
Add tool 'Filter GTF by attribute values list.' Tool filters a GTF based on a list of attribute values; this tool is especially useful as a downstream analysis tool for filtering GTF files based on Cuffdiff outputs. Functional tests are included as well.
2011-04-11 09:39:55 -04:00
Jeremy Goecks
9199fcab12
Trackster: fix (a) bug that was not setting appropriate CSS class for track content divs and (b) padding issues with different track states. Also increase bottom border to better delineate tracks.
2011-04-08 17:07:08 -04:00
James Taylor
edfb5baca9
trackster: remove condition that sets mode to squish when less than four features in tile. mode selection must not change across tiles at the same level.
2011-04-08 16:43:45 -04:00
James Taylor
c42268680a
trackster: Painter class defining common interface for all painters
2011-04-08 14:14:58 -04:00
Kelly Vincent
72c21e0067
Removed unnecessary size check on BAM file produce in view step of sam-to-bam
2011-04-08 12:06:28 -04:00
Nate Coraor
7125edcc0a
Use cluster_files_directory for SGE/DRMAA instead of the hardcoded database/pbs/. Fixes issue #512 (thanks, Anonymous).
2011-04-08 09:45:38 -04:00
Nate Coraor
8f042a795b
Use JobWrapper.get_job() since it's there.
2011-04-08 09:37:33 -04:00
Jeremy Goecks
3171c8b024
Fix hyperlinks in Cuffcompare and Cuffdiff documentation.
2011-04-07 16:28:56 -04:00
Daniel Blankenberg
daf645f53a
Additional fix for typo propagated from manual_builds, which was updated in 5350:cd2aff5b117c.
2011-04-07 08:39:07 -04:00
Kelly Vincent
8d6ec35964
Added BWA for SOLiD to tool_conf.xml.main
2011-04-06 16:28:33 -04:00
Nate Coraor
0e33ca6acc
Disable eagerloading of a job's datasets. This results in more queries but does away with a join that was returning a far bigger result than it should've.
2011-04-06 12:44:58 -04:00
Kanwei Li
0bc3b0aff0
Delete unused BLAST tests
2011-04-06 12:40:20 -04:00
Kanwei Li
af3f4a2ff9
More BLAST tests
2011-04-06 12:38:00 -04:00
Kelly Vincent
d969f29c01
Corrected typo in manual build name
2011-04-06 10:16:30 -04:00
Jeremy Goecks
60ac2204e8
Trackster: ensure that reads are drawn in squish and pack modes even when view area is large by setting a minimum width of 1px.
2011-04-05 17:59:43 -04:00
Jeremy Goecks
dc36e0beed
Merge.
2011-04-05 14:16:26 -04:00
Jeremy Goecks
125dc5896f
Merge.
2011-04-05 14:14:32 -04:00
Ross Lazarus
d6945af461
reverted unintended changes to tool_conf.xml.main
2011-04-05 14:14:08 -04:00
Jeremy Goecks
5f5f659402
Trackster: mode is not reduced if in auto mode.
2011-04-05 14:12:39 -04:00
Ross Lazarus
70c8eccee0
change to weblogo test jpg comparison and code cleanups to rgCaCo
2011-04-05 14:07:10 -04:00
Ross Lazarus
a22e453676
merge
2011-04-05 13:57:14 -04:00
Nate Coraor
4d4f1763d8
Added clustalw and weblogo tools to Main tool_conf. Thanks Ross.
2011-04-05 12:08:42 -04:00
Jeremy Goecks
6416659211
Refactor and enhance trackster visual analytics: (a) move all visual analytics code into Tool class for encapsulation; (b) put tool outputs in appropriate history when user is rerunning his own tool; (c) enable users not logged in to run tools; (d) use tool HTML to display inputs rather than sliders.
2011-04-05 11:51:48 -04:00
Jeremy Goecks