Jeremy Goecks
ffc478709b
Fix bug that prevented workflows with runtime parameters from being exported.
2011-04-14 10:05:00 -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
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
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
521059477e
Enable GFF and GFF3 attributes to be written in GTF format.
2011-04-11 12:35:23 -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
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
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
09d2657696
Gracefully handle parsing errors in GFFReader and accurately compute raw size of GFF features.
2011-04-02 16:43:02 -04:00
Daniel Blankenberg
4432911038
Better handling of errors on rerun when grouping constructs have been added or removed.
2011-04-01 18:10:47 -04:00
Jeremy Goecks
30bb64bbca
Trackster visual analytics: enable datasets that cannot be indexed--and hence cannot be subseted--to be used as tool inputs.
2011-03-31 17:22:10 -04:00
Jeremy Goecks
3ec9a1c91f
Trackster visual analytics: add support for static select parameters.
2011-03-31 15:07:02 -04:00
Dannon Baker
5aaeabe8ad
mapping change: For data libraries of sufficient size, eager loading related to getting the root_folder of a library was causing huge delays. This should reduce the delay in viewing a library of ~500 items by about 90%.
2011-03-31 14:09:47 -04:00
Dannon Baker
c5dda01276
workflows api: patch from Tobias Wohlfrom <twohlfrom@illumina.com>
...
Fixed label output in workflow API in order to map the input datasets.
2011-03-31 11:27:49 -04:00
Daniel Blankenberg
ba71264790
Fix for wrapping input values for change_format and label tags when tool is using check_values="false". Fixes issue seen when e.g. using an output label in a data_source tool.
2011-03-31 10:16:40 -04:00
Jeremy Goecks
3a9351eda1
Send visual analytics output datasets to user's current history rather than input datasets' history. This enables users not logged in to use visual analytics in shared visualizations.
2011-03-30 17:20:10 -04:00
Jeremy Goecks
cf3dc6ac01
Trackster: add BED and GFF support to visual analytics framework, and enable GOPS intersect and subtract tools to work with visual analytics.
2011-03-30 11:44:08 -04:00
Daniel Blankenberg
9229e32e52
Minor fix for 5283:41a416e61021.
2011-03-30 10:40:09 -04:00
Dannon Baker
e49d224f1e
Removing a debug print from previous commit.
2011-03-30 10:38:45 -04:00
Daniel Blankenberg
3b5562fcfd
Minor fix for 5283:41a416e61021.
2011-03-30 10:34:21 -04:00
Dannon Baker
d628f1a843
Refactor set_peek to a single method in class Text. Should also fix bug introduced in 5236 that prevented setting of some metadata.
2011-03-30 07:14:20 -04:00
Jeremy Goecks
8031354029
Fix read id bug in Trackster BAM data provider.
2011-03-29 14:28:17 -04:00
Nate Coraor
37cc99a9c1
Use new_file_path as tempfile's tempdir, obviates the need for $TEMP in the environment.
2011-03-29 08:18:49 -04:00
Jeremy Goecks
202b513f57
Another pass on Trackster filtering. Filtering now supports (a) score columns in BED and GFF and (b) GTF attributes. Refactoring so that slider behavior for dynamic tools and filters are the same.
2011-03-28 15:27:14 -04:00
Jeremy Goecks
6bb3133d54
Implement a data manager for trackster. Convert DataCache into a DataManager and use jQuery Deferred objects to move data management from the tile level to the track level. Implications of these changes include (a) callbacks are no longer needed when drawing tiles; (a) data is fetched before a tile is drawn; and (c) tile drawing is completely tracked so that actions can be taken after a track has been drawn.
2011-03-24 15:05:28 -04:00
Daniel Blankenberg
8bdda93ffc
Add more verbose error reporting to FASTQ Groomer tool.
2011-03-24 11:45:50 -04:00
Daniel Blankenberg
2ebf1448b8
Allow users to import copies of their own workflows.
2011-03-23 18:06:04 -04:00
Greg Von Kuster
cc624b2f5a
Fix unit tests by renaming ~/datatypes/test/3.bam to be 3unsorted.bam.
2011-03-23 14:55:27 -04:00
Greg Von Kuster
8ba7de4c8b
Improved checking to determine if a bam file is sorted. If the version of samtools being used is 0.1.13 or newer, determination of bam sorting is now much more robust. Add a new functional test to the test_library_features script that tests uploading a library_dataset (where the file is an unsorted bam file) using a combination of 'upload_paths' and 'link_to_files'. Rename the test-data file previously named 3.bam to now be named 3unsorted.bam to clarify that it is an unsorted bam file.
2011-03-23 12:18:57 -04:00
Daniel Blankenberg
7ab9f182dc
Add SGD Yeast genome Gbrowse display site.
2011-03-23 09:03:13 -04:00
Daniel Blankenberg
7d7b881226
Allow importing one's own history.
2011-03-22 19:43:32 -04:00
Greg Von Kuster
3c906860c2
Fix for bug introduced in change set 5243:45b772580403.
2011-03-22 10:50:27 -04:00
Greg Von Kuster
e83efed183
Fixes in the user controller:
...
1. Eliminate some long-standing security issues
2. Encode all object ids - many were not being encoded
3. Eliminate all unnecessary methods
4. Rewite several poorly written methods
5. Fix several bugs related to USER_INFO form definitions
2011-03-22 10:33:42 -04:00
Dannon Baker
2221337345
Added row id print and pre/post value prints to the migration script addressing form value errors.
2011-03-21 11:08:32 -04:00
Kanwei Li
160c053145
set_peek should check for None, not false
2011-03-18 14:12:10 -04:00
Daniel Blankenberg
f234457135
Fix check for displaying old-style display applications when line count approximation is used. Additional cleaner link display for display applications which was started in 4886:f820c9d2c285.
2011-03-17 09:57:25 -04:00
Kanwei Li
c7046d2c90
Description text for viz metadata column
2011-03-16 18:36:27 -04:00
Kanwei Li
2c06d0246d
Improved custom builds UI. Better help text explaining len file format. Now split on last whitespace instead of tab only so that len info can be typed into the box directly.
2011-03-15 23:40:53 -04:00
Greg Von Kuster
32fa542fca
Allow Importing items from a history to replace a library dataset with a new version.
2011-03-15 14:43:06 -04:00
Greg Von Kuster
7640af8e06
Don't alter the contents of a file while uploading to a data library if using the filesystem_paths option. This partially resolves the issue where a supposedly sorted BAM file was being resorted upon upload to a data library when using this option. A better imlementation of determining whether a BAM file has been sorted (so that it does not get resorted) remains to be done.
2011-03-15 09:38:29 -04:00
Daniel Blankenberg
5fc793c8f2
Allow upload to function on https URLs.
2011-03-14 23:01:11 -04:00
Kanwei Li
6d8eb1015e
Include
2011-03-11 15:57:06 -05:00
Greg Von Kuster
df6f94b1d0
Per request from Peter Cock, turn the "Copy data into Galaxy?" check box into a select list that clarifies the behavior. The default is to copy files into Galaxy.
2011-03-11 14:56:11 -05:00
Kanwei Li
2b83ae36b9
trackster: Suppress cython warning message causing bam_to_summary_tree to fail. Fix for chroms without 'chr' in front not being displayed
2011-03-11 13:36:29 -05:00
Greg Von Kuster
c650958915
Apply a corrected version of the patch from Peter Cock that flips the  "Preserve directory structure?" setting when uploading library datasets from filesystem paths.
2011-03-11 10:01:54 -05:00
Jeremy Goecks
ebab920cca
Trackster: access to datasets is based on accessibility, not ownership.
2011-03-10 17:30:35 -05:00
Jeremy Goecks
0c2b732e8e
Make shared visualizations work again and pack trackster.js
2011-03-10 16:42:34 -05:00
Jeremy Goecks