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
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
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
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
Ross Lazarus
c600bed50c
grr - more vanity attribution removed
2011-05-17 13:14:15 -04:00
Ross Lazarus
5096aec964
cleaned up picard tool names - own section so (picard) was redundant
2011-05-17 13:04:35 -04:00
Ross Lazarus
e0545fcd8f
separated ngs picard tools and removed fastqc wrapper lgpl annotation
2011-05-17 12:52:24 -04:00
Ross Lazarus
e5a2a48285
branch merge with Kelly's fixes
2011-05-17 12:14:32 -04:00
Daniel Blankenberg
1dfdc42fe6
Update tool help for some MAF tools.
2011-05-17 12:07:25 -04:00
Kelly Vincent
778088bba9
Modified Tophat wrapper so dbkey will be properly set both for built-in and history references
2011-05-17 12:05:07 -04:00
Ross Lazarus
0aa96d8f0f
branch merge
2011-05-17 11:39:52 -04:00
Jeremy Goecks
2b7025f11d
Enable Cufflinks to work when setting metadata externally.
2011-05-17 11:21:26 -04:00
Ross Lazarus
2e286b5c2d
amerkinized spelin' and removed copyright notices on some picard tool forms
2011-05-17 10:29:06 -04:00
Kelly Vincent
7401ae6439
Numerous updates to Picard tools: Cleaned up and standardized wrapper's Python code, removing redundant variables and using the same ones in different segment of code when possible; Changed sam/bam outputs to be bam by default and use change_format if user requests sam and removed redundant output parameters; Got tests passing for AddOrReplaceReadGroups; Relaxed the matching constraints for output for BamIndexStats and InsertSize wrappers Standardized on the parameter output-format rather than newformat to indicate sam preference over bam
2011-05-17 01:57:04 -04:00
Kanwei Li
5caf51ddaa
trackster: Refactor LineTrack overflow, fix it to work better for Line and Filled modes
2011-05-16 17:08:06 -04:00
Ross Lazarus
6dcd6433e3
removed python2.4 from rgfakePed.py
2011-05-16 10:03:47 -04:00
Ross Lazarus
fa23935ae5
repairs to rgfakePed tool for generating null genotype data - since removing the _code.py trick of renaming composite file components means all of the parts (eg map and ped) acquire the default name of RgeneticsData, that's what the tool has to create - rather than sensibly named components based on the title - since only way to fix this wart is to reintroduce a bigger wart using the post execution hook, decided to just go with that default base_name to make things more sustanable in the long term
2011-05-16 09:12:19 -04:00
Ross Lazarus
7859f56954
reverting reorder test outputs - PhiX reference used to generate them seems different from that on the buildbot
2011-05-13 21:24:03 -04:00
Ross Lazarus
d5fbb00c33
picard wrapper typo fixed
2011-05-13 20:46:38 -04:00
Greg Von Kuster