Kanwei Li
efe0cba6d8
trackster: Fix border and error not lining up at right place
2011-05-11 15:43:33 -04:00
Jeremy Goecks
01ec149d82
Add support for comment handling to gff_to_interval_index tool.
2011-05-11 15:38:57 -04:00
Kanwei Li
a706fc3796
Show details: now works even when tool is obsolete. Show inheritance chain where the dataset came from if it was copied from a history or library
2011-05-11 11:36:22 -04:00
Kanwei Li
5b5b243b9b
trackster: Greatly improve LineTrack performance as it was fetching an unoptimal amount of data, decreasing performance by orders of magnitude
2011-05-06 16:02:25 -04:00
Nate Coraor
fb99bf73f1
Standardize naming of reserved/predefined values in the param_dict. Old values are maintaned as well.
2011-05-06 11:49:02 -04:00
Jeremy Goecks
86826cc91d
Trackster: use GTF metadata to create dynamic filters.
2011-05-05 19:05:39 -04:00
Jeremy Goecks
1d03c82144
Enable GFF filter attributes tool to accept arbitrary conditions.
2011-05-05 16:51:56 -04:00
Jeremy Goecks
c7cfc3d67f
Add metadata for GTF attribute values.
2011-05-04 16:45:10 -04:00
Jeremy Goecks
faafc762bf
Trackster: enable a tool to be run on complete dataset or a visible region.
2011-05-04 10:20:54 -04:00
Jeremy Goecks
5e350f9208
Fix bugs in tracks/run_tool.
2011-05-02 15:14:53 -04:00
Jeremy Goecks
1e0b6bb5c3
Make gops intersect tool compatible with GFF features rather than GFF lines.
2011-05-02 13:59:49 -04:00
Daniel Blankenberg
5c7daee0f0
Only allow a user to rerun if they have access permissions on the dataset.
2011-04-29 16:51:51 -04:00
Greg Von Kuster
2749ab91b0
Apply patch from taoliu - ticket #529 - Missing controller when creating user with require_login & allow_user_creatio is on.
2011-04-29 15:32:04 -04:00
Nate Coraor
e7c5ff5c08
Minor fix for setting the username during user creation under use_remote_user = True. Converts the user portion of the user's email to lowercase and replaces invalid characters with '-' as per the public name format requirements.
2011-04-29 10:35:42 -04:00
Ross Lazarus
899de56e61
tweaks to fasta locations for tests for ASM and insertsize
2011-04-28 19:30:48 -04:00
Kanwei Li
f52f8fcada
trackster: Fix filters, restore name of IntervalIndex provider
2011-04-28 13:17:51 -04:00
Nate Coraor
41730ac15b
Set and allow modification of the public username if use_remote_user = True
2011-04-28 11:33:07 -04:00
Kanwei Li
2e3c767ec4
trackster: Restore interval_index as Gff indexer for now due to sorting issues
2011-04-27 19:08:31 -04:00
Kanwei Li
19e18e1899
trackster: Fix incorrect "end" calculation
2011-04-27 17:33:08 -04:00
Kanwei Li
43de1e17ce
Fix GTF for trackster
2011-04-27 15:41:25 -04:00
Daniel Blankenberg
f9c267f406
When label text for a static option in a SelectToolParameter is not provided, default to using the 'value'.
2011-04-26 11:25:54 -04:00
Kanwei Li
8e2f6f4c8f
trackster:
...
- Make GFF, Bed and Vcf use Tabix data provider instead of interval_index. PLEASE UPDATE with new entries in datatypes_conf.xml.sample
- Refactoring for data providers
2011-04-25 18:59:37 -04:00
Daniel Blankenberg
1f9abea3fe
Bug fix for 5454:2379785017d7
2011-04-25 17:21:21 -04:00
Daniel Blankenberg
129448a30c
Fix for dynamic options when referencing a DataToolParameter that has already been wrapped.
2011-04-25 14:41:54 -04:00
Kanwei Li
86d6c6f73b
trackster: new gff and vcf converters for tabix
2011-04-22 19:01:12 -04:00
Richard Burhans
47b2015610
added wsf datatype
2011-04-21 18:26:36 -04:00
Richard Burhans
d3b7aaeb6b
initial version of Webb's genome diversity tools
2011-04-21 17:22:27 -04:00
Daniel Blankenberg
694300ce97
Some reworking of data_source tools and the standard data_source.py script. Remove hard-coded special-case handling of UCSC Table Browser and GBrowse datasource tools; functionality remains, but is now a part of the individual tools' XML configuration files. Auto-detect is now available by providing data_type=auto parameters.
2011-04-21 13:12:10 -04:00
Kanwei Li
97a21ddb4f
trackster: use simple hash to calculate unique ID for tabix
2011-04-19 14:45:55 -04:00
Greg Von Kuster
938f4f490c
Improved exception handling in the tool shed.
2011-04-19 10:20:01 -04:00
Nate Coraor
7535161d6d
Make all tool tag related functionality conditional on 'enable_tool_tags = True' in the Galaxy configuration file.
2011-04-19 08:22:48 -04:00
Nate Coraor
467885c59d
Merge changes from the NBIC Galaxy Hackathon. Includes the addition of scripts which automatically generate the tool_conf.xml from tool configuration files. Tool configuration files also support optional syntax which specifies their placement in sections, as well as what tags the tool should be associated with. Also includes support for associating tags with tool IDs and filtering tools by tag in the tool menu.
2011-04-19 08:21:54 -04:00
Kanwei Li
b2ba5d422a
trackster:
...
- Use tabix (through pysam) as the indexer for feature formats. Bed support included in this commit
- Add bigBed format support (same interface as bigWig)
- Improve implicit converter error handling
2011-04-18 18:07:52 -04:00
Kanwei Li
6802b93c7c
trackster: Small UI tweaks
2011-04-18 17:02:32 -04:00
Kanwei Li
51acb08b30
trackster: Fix page switch links breaking in Add Tracks menu, restore Last Updated column
2011-04-18 14:35:14 -04:00
Greg Von Kuster
5fa67fa134
Fixes for external service file browser.
2011-04-15 16:37:56 -04:00
Jeremy Goecks
4b636226b9
Trackster visual analytics: set initial parameter values properly.
2011-04-15 09:42:55 -04:00
Kanwei Li
4797b23824
trackster:
...
- UI support for adding datasets from Data Libraries
- Cleaner, more consistent "Add Tracks" dialog that implements above
Sync .css changes with their corresponding .css.tmpl template
2011-04-14 20:25:54 -04:00
Greg Von Kuster
0d1f540e99
Fixes for transferring files from external services using the http protocol. Automatic file transfers from Pac Bio SMRT Portal are functional for version 1.1.0.
2011-04-14 16:42:12 -04:00
Jeremy Goecks
ffc478709b
Fix bug that prevented workflows with runtime parameters from being exported.
2011-04-14 10:05:00 -04:00
Freek de Bruijn
b237a87ef2
Alex and Freek: clear the tool tag associations in init_tools before adding these associations.
2011-04-14 14:20:48 +02:00
Nate Coraor
777043352e
Persist tool tag selections for logged-in users.
2011-04-14 13:54:46 +02:00
Nate Coraor
c12968d7da
Fix for searching tools, and then selecting tags. Also refactoring to remove duplicated javascript.
2011-04-14 12:44:25 +02:00
Nate Coraor
4515f0b8cd
More functionality for tool tags, still needs to be refactored to remove javascript duplicated from the tool search.
2011-04-14 10:53:22 +02:00
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
Nate Coraor
03908bc2f5
Unfinished preliminary support for tagging tools. Requires enable_tool_tags = True in universe_wsgi.ini.
2011-04-13 23:19:24 +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
Kanwei Li