Jeremy Goecks
7183eabb52
Removed unspecified build validators from Cufflinks/compare/diff tools as these cause trouble when running tools on custom genomes.
2011-06-06 09:08:59 -04:00
Kanwei Li
d28ca76db9
Remove error icon in front of red datasets, since red clearly denotes fail already
2011-06-03 17:00:20 -04:00
Greg Von Kuster
32dc995129
Clean up displaying content in the tool shed.
2011-06-03 16:46:14 -04:00
Kanwei Li
4237e09f34
tab -> spaces
2011-06-03 16:22:02 -04:00
Kanwei Li
395c0ddb61
Add dataset used for blastxml unit test
2011-06-03 16:09:01 -04:00
Kanwei Li
a8ff1a91b3
Grouping tool:
...
- Converted to use numpy, which is included with Galaxy, instead of rpy, which is not.
- Don't simply skip lines if a numeric parameter encounters non-numeric data, return descriptive error with line contents instead
- General refactoring
- Added new comprehensive test, disabled until test framework supports multiple repeat inputs
2011-06-03 16:08:26 -04:00
Greg Von Kuster
61c3ed305f
Move duplicate data type checker methods from sniff and upload into a new ~/datatypes/checkers.py.
2011-06-03 15:36:59 -04:00
Nate Coraor
005c1d352b
Prevent upload job creation from clobbering the input if linking data into Galaxy.
2011-06-03 15:18:31 -04:00
Nate Coraor
032aa7bdcf
SMTP Authentication support for all places where Galaxy sends mail. Use STARTTLS where available, too.
2011-06-03 11:25:02 -04:00
Daniel Blankenberg
d00372c8ca
Fixes for Implicit Datatype conversion and external display applications.
2011-06-03 10:16:20 -04:00
Kanwei Li
f2286c240a
BLAST: Fix sniffer for some dataset. Closes #567 . Set mimetype to application/xml. Closes #569
2011-06-02 17:36:38 -04:00
Nate Coraor
08204a78bf
merge backout
2011-06-02 16:38:34 -04:00
Nate Coraor
caee68afdc
Backed out changeset 2f84c42a548a. Unbreaks all checkboxes being checked by default, rebreaks default="true".
2011-06-02 16:38:19 -04:00
Greg Von Kuster
6186c9c81a
Delete community_datatypes_conf.xml.sample
2011-06-02 16:24:43 -04:00
Greg Von Kuster
cb8c0f4178
Add baseline support for translating special chars to html escape codes for correct html display. Fixes issue # 564.
2011-06-02 16:16:56 -04:00
Greg Von Kuster
5dde45d61b
Eliminate all suport for tool / tool suite archives from the tool shed. Yikes!
2011-06-02 15:18:35 -04:00
Daniel Blankenberg
6d7d8493b6
Provide an error message when trying to directly view a directory in extra_files_path.
2011-06-02 14:18:34 -04:00
Nate Coraor
93d60df4ef
Fix the race condition of the upload tool's outputs not being created before the output size check occurs. Thanks Tao Liu.
2011-06-02 13:10:28 -04:00
Nate Coraor
da2475b3e0
'fields' is apparently reserved in MySQL 4, fix migration scripts that use it unaliased. Thanks John Eppley.
2011-06-02 12:11:53 -04:00
Daniel Blankenberg
90aeffb5e6
Import patch contributed by Jim Johnson that supports sub directories in extra_files_path for displaying and downloading.
...
"Numerous applications create html files with a directory hierarchy. I\'m including a patch support the display and download of datasets that include subdirs in their extra_files_path."
2011-06-02 11:46:49 -04:00
Nate Coraor
c229b70b4c
Another fix for uploading datasets to a library without a history.
2011-06-02 11:40:06 -04:00
Nate Coraor
91a484c259
Fix for library upload when there is no current history.
2011-06-02 11:06:08 -04:00
Nate Coraor
b91ca79851
Set a catchall content-type (application/octet-stream) on metadata file downloads so Safari doesn't consider them to be html.
2011-06-01 16:27:28 -04:00
Greg Von Kuster
7c5e57f774
Fix the ToolParamSanitizer unit test. Since mercurial imports locale.getpreferredencoding(), which is part of the Python stdlib, the behavior of python strings is re-sorted, so we have to sort them back...
2011-06-01 16:21:12 -04:00
Greg Von Kuster
95ffc3243f
Fixes for editing role name, descriptionn, and renaming groups. Resolves issue #539 .
2011-06-01 15:47:04 -04:00
Greg Von Kuster
72dfb35375
Several data library bug fixes:
...
- Determiining if an accessible dataset exists somewhere in the data library hierarchy now works all the time ( I believe ). It used to work most of the time, but under corner conditions, it would break.
- When importing dataset from a history into a data library, the dataset permissions are now correctly applied to the library dataset. The DATASET_MANAGE_PERMISSIONS permission is a spoecial case in that if it exists on the dataset, the LIBRARY_MANAGE permission must be applied to the library dataset.
- Fix for message display and db flushing when importing library dataset into a history.
- Do not render the folder pop-up menu option for selecting library dataset to import into histories if the folder does not contain any accessible library datasets.
2011-06-01 15:20:43 -04:00
Nate Coraor
51aeadf8e5
Fix the user create/login links in the FTP upload form
2011-06-01 15:12:12 -04:00
Daniel Blankenberg
05242912c7
Minor reformatting for 5609:f530dbdde1f5
2011-06-01 11:40:38 -04:00
Daniel Blankenberg
0a47db9aa4
Allow VCF parser to accept unknown values for QUAL field.
2011-06-01 11:29:07 -04:00
Greg Von Kuster
9dede7be76
Fix for importing library datasets into a new named history. Library datasets will no longer be imported into both the current history and the new named history ( only the latter ) in this scenario.
2011-05-31 12:03:52 -04:00
Jeremy Goecks
71cc5195d1
Fix bugs in reading and visualizing GFF3 datasets.
2011-05-28 01:07:06 +02:00
Richard Burhans
be928c2d7c
Updated help text for genome diversity tools
2011-05-27 09:22:27 -04:00
Kanwei Li
8c1ed15245
Fix brand not being clickable
2011-05-27 11:19:16 +02:00
Kanwei Li
a037747141
Velvet wrapper: fix typos, tabs -> spaces, spacing
2011-05-27 11:01:46 +02:00
Kanwei Li
34155271b3
[Peter Cock] Filtering tool: Only cast used columns. Fix valid lines and skipped info lines. [Kanwei] Add new testcases to test this behavior. Fixes #537 . Fixes #535
2011-05-27 10:47:17 +02:00
Richard Burhans
5432bb543f
updated help section for the genome diversity extract primers tool
2011-05-26 13:29:00 -04:00
Kanwei Li
d270433ccc
Remove debug
2011-05-26 08:27:52 -04:00
Kanwei Li
5f36576880
Fix user/create from direct URL access
2011-05-26 08:20:37 -04:00
Kanwei Li
3167d89bcc
Make branding not cover header links
2011-05-26 09:50:07 +02:00
Kanwei Li
aed56ce4c3
Fix lack of quotes
2011-05-25 17:12:21 +02:00
Kanwei Li
2037dc102d
Sanitize defaults
2011-05-25 16:39:43 +02:00
Nate Coraor
5dbf59c2fc
Fix the non-working default="true" for checkboxes, thanks Louise-Amélie Schmitt.
2011-05-24 05:33:07 -04:00
Jeremy Goecks
6e807d0f09
Enable tags and annotations to work for new datasets in history. Fixes #550
2011-05-24 02:20:35 +02:00
Jeremy Goecks
fe60a1ea8b
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
Greg Von Kuster
212433fe2c
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
Anton Nekrutenko
f808de6c90
Fixes to picard tool intefaces and help sections. Disabled java heap selection by the user (set to 4G default, which was changed in picard_wrapper.py).
2011-05-20 13:26:45 -04:00
Daniel Blankenberg
ef795f04e0
Fix typo (val to value).
2011-05-20 06:17:35 +01:00
Kelly Vincent
acb1fbc6f0
Added hg_g1k_v37 to manual builds
2011-05-19 15:38:12 -04:00
Jeremy Goecks
38479cf5c4
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
Jeremy Goecks
44beb62a25
Trackster: have child track inherit mode from parent track.
2011-05-19 13:47:52 -04:00
Jeremy Goecks