galaxy

admin

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.

2011-04-13 13:52:05 -04:00

common

Workflow/History targets for individual samples.

2011-01-17 14:58:02 -05:00

dataset

Copy datasets feature:

2011-02-22 17:14:16 -05:00

external_services

Bug fix for diplaying menu item for manully selecting sample datasets for transfer.

2011-01-21 11:55:06 -05:00

genetrack

Added the missing "invalid.html" for GeneTrack.

2009-01-29 11:11:15 -05:00

history

Use jStorage (http://www.jstorage.info/) instead of jStore. Tested to be working on IE7 and IE8, where the latter was failing. Fixes links not showing up in history pane to expand histories.

2011-02-18 15:06:34 -05:00

library

trackster:

2011-04-14 20:25:54 -04:00

mobile

Abstract the code supporting data library templates so templates can be used in sample tracking as well. These templates now provide support for handling information about sample runs. A RequestType can have a single association to a Run, with the run details template made available to all samples. A Sample can have many associations to Runs.

2010-12-09 14:52:27 -05:00

page

Fix typo in 5093:1dfad17e81a8 that broke page editor.

2011-03-17 17:39:16 -04:00

requests

Extending sample search to include search using form fields. Resolved #489

2011-03-09 15:33:04 -05:00

root

Enable tags and annotations to work for new datasets in history. Fixes #550

2011-05-24 02:20:35 +02:00

tracks

When adding tracks to Trackster, add them in the order that they appear in the dataset listing.

2011-05-22 23:54:01 +02:00

user

Set and allow modification of the public username if use_remote_user = True

2011-04-28 11:33:07 -04:00

visualization

Trackster bug fixes when (a) running tools in a shared visualization and (b) when drawing a track created by a tool.

2011-05-19 14:29:58 -04:00

webapps

First pass of the next-gen Galaxy tool shed. See it demonsrated and discussed at the 2011 Gallaxy Community Conference in Lunteren on May 24,25,26.

2011-05-20 16:04:30 -04:00

workflow

Fix a few XSS issues in workflow/history

2011-05-25 11:31:26 +02:00

base_panels.mako

jquery.drag with touch support, trackster now works (well) on the ipad

2011-03-17 19:48:07 -04:00

base.mako

Add 'metas()' %def to base.mako, to allow subclassing templates to declare additional <meta/> tags.

2010-03-12 12:03:25 -05:00

community_rating.mako

Add CommunityRatingColumn to grid infrastructure and add 'Community Rating' columns to published item grids. Community ratings are computed on demand for now, but this may need to change in the future.

2010-09-08 11:43:25 -04:00

display_base.mako

Use jStorage (http://www.jstorage.info/) instead of jStore. Tested to be working on IE7 and IE8, where the latter was failing. Fixes links not showing up in history pane to expand histories.

2011-02-18 15:06:34 -05:00

display_common.mako

First pass of the new sequencer_type & sequencer framework

2010-12-20 10:50:50 -05:00

embed_base.mako

Fixes to item embedding in pages. In particular, fixed the editor color changes that were occurring when moving the cursor through embedded items.

2010-03-16 12:00:10 -04:00

export_base.mako

Make it easier to move workflows directly from one Galaxy instance to another. Workflow download/export page now provides URL that can be used to directly import a workflow from one instance to another.

2010-11-29 14:16:49 -06:00

form.mako

Add history import and export functionality to Galaxy. Options for exporting the current history to a file or importing a history from a file are now listed in the history options menu. Also modified the form builder to support file inputs.

2010-06-03 12:17:34 -04:00

grid_base_async.mako

Improve display of page numbers on grids so that not all page numbers are always shown. Add parameter 'num_page_links' to grid framework so that grid can control how many page links are shown.

2011-01-10 15:14:16 -05:00

grid_base.mako

trackster: Small UI tweaks

2011-04-18 17:02:32 -04:00

grid_common.mako

Modest improvements in grid search UI: (a) size of search box increases to show help text (column label); (b) help text is highlighted rather than hidden when user clicks on search box; (c) standard and advanced search divs are toggled correctly when moving between searches.

2011-01-28 13:12:02 -05:00

ind_share_base.mako

Enhancements and fixes for sharing framework: (a) sharing/publishing webpages can now be displayed in frames; (b) sharing webpages can display messages; (c) workflow sharing highlights correct tab; (d) history sharing for individual users now uses sharing framework; (e) item sharing with individual users now uses common template.

2010-08-16 17:05:59 -04:00

message.mako

Fix form.mako and message.mako to use the correct webapp version of base_panels.mako.

2010-05-28 09:51:57 -04:00

no_access.mako

You can now require that users log in to use Galaxy. The sample config is way different but it's only because I cleaned it up a bit. The only new options are require_login/allow_user_creation.

2008-11-20 15:14:47 -05:00

panels.mako

Decouple the masthead from base_panels.mako.

2010-03-31 13:11:05 -04:00

sharing_base.mako

Make published items set the "Shared Data" tab as the active tab

2010-10-07 15:33:54 -04:00

show_params.mako

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

tagging_common.mako

Clone annotation and tags when cloning workflows.

2011-05-18 16:48:02 -04:00

tool_executed.mako

Typos 'succesfully' -> 'successfully' fixed in tool_executed.mako

2010-09-15 17:11:10 -04:00

tool_form.mako

Refactor javascript in tool_form.mako; fix indentation for repeat groups

2011-02-22 18:49:57 -05:00