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
Nate Coraor
b8fd7dbe2e
Add Picard and fastqc tools to Main
2011-05-19 10:07:53 -04:00
Jeremy Goecks
41446bb4b0
Merge.
2011-05-18 16:52:38 -04:00
Jeremy Goecks
c6797482af
Remove obsolete test values for Cufflinks and Cuffdiff tests.
2011-05-18 16:52:14 -04:00
Kelly Vincent
ac95877120
merge
2011-05-18 16:51:51 -04:00
Kelly Vincent
6308d93385
Further tweaks to Picard help text
2011-05-18 16:50:37 -04:00
Jeremy Goecks
8db5b83322
Clone annotation and tags when cloning workflows.
2011-05-18 16:48:02 -04:00
Peter Cock
720dea16dc
Fix for BLAST XML to tabular when both query and subject have XXX masking
2011-05-18 18:43:46 +01:00
Kanwei Li
68a514d789
Fix a few XSS issues in workflow/history
2011-05-25 11:31:26 +02:00
Kelly Vincent
804f9ab60a
Cleaned up help text across Picard tools (and FastQC) to standardize style as much as possible
2011-05-17 21:31:34 -04:00
Kanwei Li
d340c2ab22
Fix data.py typo. Fixes #543
2011-05-17 18:41:12 -04:00
Kanwei Li