Jeremy Goecks
30bb64bbca
Trackster visual analytics: enable datasets that cannot be indexed--and hence cannot be subseted--to be used as tool inputs.
2011-03-31 17:22:10 -04:00
Jeremy Goecks
3ec9a1c91f
Trackster visual analytics: add support for static select parameters.
2011-03-31 15:07:02 -04:00
Dannon Baker
5aaeabe8ad
mapping change: For data libraries of sufficient size, eager loading related to getting the root_folder of a library was causing huge delays. This should reduce the delay in viewing a library of ~500 items by about 90%.
2011-03-31 14:09:47 -04:00
Dannon Baker
c5dda01276
workflows api: patch from Tobias Wohlfrom <twohlfrom@illumina.com>
...
Fixed label output in workflow API in order to map the input datasets.
2011-03-31 11:27:49 -04:00
Daniel Blankenberg
ba71264790
Fix for wrapping input values for change_format and label tags when tool is using check_values="false". Fixes issue seen when e.g. using an output label in a data_source tool.
2011-03-31 10:16:40 -04:00
Jeremy Goecks
3a9351eda1
Send visual analytics output datasets to user's current history rather than input datasets' history. This enables users not logged in to use visual analytics in shared visualizations.
2011-03-30 17:20:10 -04:00
Jeremy Goecks
cf3dc6ac01
Trackster: add BED and GFF support to visual analytics framework, and enable GOPS intersect and subtract tools to work with visual analytics.
2011-03-30 11:44:08 -04:00
Daniel Blankenberg
9229e32e52
Minor fix for 5283:41a416e61021.
2011-03-30 10:40:09 -04:00
Dannon Baker
e49d224f1e
Removing a debug print from previous commit.
2011-03-30 10:38:45 -04:00
Daniel Blankenberg
3b5562fcfd
Minor fix for 5283:41a416e61021.
2011-03-30 10:34:21 -04:00
Dannon Baker
d628f1a843
Refactor set_peek to a single method in class Text. Should also fix bug introduced in 5236 that prevented setting of some metadata.
2011-03-30 07:14:20 -04:00
Jeremy Goecks
b752173b99
Trackster: simplify use of jQuery deferreds for getting data.
2011-03-29 16:27:35 -04:00
Jeremy Goecks
8031354029
Fix read id bug in Trackster BAM data provider.
2011-03-29 14:28:17 -04:00
Kelly Vincent
d3d26a7149
Modified add_manual_builds script so that it will include the build in parentheses after the name even if there are no chromosome lengths listed (previously would not because of line break after name); also added a couple of new manual builds
2011-03-29 13:59:07 -04:00
Jeremy Goecks
08a15195c4
Trackster: use gap to correctly position read connector in Pack mode. Also some code cleanup and commenting.
2011-03-29 13:43:24 -04:00
Nate Coraor
37cc99a9c1
Use new_file_path as tempfile's tempdir, obviates the need for $TEMP in the environment.
2011-03-29 08:18:49 -04:00
Jeremy Goecks
202b513f57
Another pass on Trackster filtering. Filtering now supports (a) score columns in BED and GFF and (b) GTF attributes. Refactoring so that slider behavior for dynamic tools and filters are the same.
2011-03-28 15:27:14 -04:00
Ross Lazarus
e48fa9d537
Remove bogus makeGFF from rgutils
2011-03-25 13:26:40 -04:00
Ross Lazarus
597a3d006f
Remove bogus makeGFF from rgutils
2011-03-25 13:21:13 -04:00
Ross Lazarus
0c5a868636
Revised rgenetics tools to remove post job hooks
2011-03-25 13:12:21 -04:00
Jeremy Goecks
f138afb629
Add selected attribute to default value for Tophat coverage search.
2011-03-24 20:29:40 -04:00
Kanwei Li
f99b11b73f
UI Tweaks and fixes:
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- View details icon no longer tooltip; it now links to a page
- Restore folder icon to data libraries
- Make popupmenu link boxes smaller so that link clickthroughs don't activate popup as easily
- Make popupmenu initial position lower after click
2011-03-24 18:26:29 -04:00
Jeremy Goecks
4e4ca2d542
Change default value for Tophat coverage search to true.
2011-03-24 17:36:06 -04:00
Jeremy Goecks
42084999ac
Trackster: put show_insertions and show_differences in track config and fix show_differences, which was broken in previous trackster commit.
2011-03-24 17:12:16 -04:00
Jeremy Goecks
6bb3133d54
Implement a data manager for trackster. Convert DataCache into a DataManager and use jQuery Deferred objects to move data management from the tile level to the track level. Implications of these changes include (a) callbacks are no longer needed when drawing tiles; (a) data is fetched before a tile is drawn; and (c) tile drawing is completely tracked so that actions can be taken after a track has been drawn.
2011-03-24 15:05:28 -04:00
Richard Burhans
f67ab3c70c
fixed calculation of codon starts
2011-03-24 15:03:12 -04:00
Nate Coraor
05ba81a93d
Update the check_galaxy script for the recent changes to the User controller
2011-03-24 14:33:05 -04:00
Jeremy Goecks
2f64fc02a4
Trackster: small fix for read drawing and added note about larger issue.
2011-03-24 13:52:04 -04:00
Daniel Blankenberg
8bdda93ffc
Add more verbose error reporting to FASTQ Groomer tool.
2011-03-24 11:45:50 -04:00
Ross Lazarus
dc4b62c740
still having a problem with getting clustalw2 to print sequence indices - test does not cover so passes
2011-03-23 19:32:32 -04:00
Ross Lazarus
579cefd5f9
python wrapper for clustalw tool
2011-03-23 19:14:14 -04:00
Daniel Blankenberg
2ebf1448b8
Allow users to import copies of their own workflows.
2011-03-23 18:06:04 -04:00
Ross Lazarus
600d2f4275
test data updated for clustalw test
2011-03-23 17:20:47 -04:00
Ross Lazarus
76b86b9762
Fixes to clustalw tool - need a python wrapper to take care of Clustalw's bad habit of writing to an output path determined from the input path - naughty..Also added the dendrogram to the log output so test output sample updated; version bumped
2011-03-23 17:18:29 -04:00
Nate Coraor
d765f607c4
Slight output difference on the buildbot for weblogo, hopefully the difference is static.
2011-03-23 16:42:14 -04:00
Greg Von Kuster
cc624b2f5a
Fix unit tests by renaming ~/datatypes/test/3.bam to be 3unsorted.bam.
2011-03-23 14:55:27 -04:00
Daniel Blankenberg
6d4f4ac309
Remove 'data.file_name = data.file_name' from Rgenetics code files.
2011-03-23 12:41:39 -04:00
Greg Von Kuster
8ba7de4c8b
Improved checking to determine if a bam file is sorted. If the version of samtools being used is 0.1.13 or newer, determination of bam sorting is now much more robust. Add a new functional test to the test_library_features script that tests uploading a library_dataset (where the file is an unsorted bam file) using a combination of 'upload_paths' and 'link_to_files'. Rename the test-data file previously named 3.bam to now be named 3unsorted.bam to clarify that it is an unsorted bam file.
2011-03-23 12:18:57 -04:00
Ross Lazarus
43ed5f1953
fixed typo that broke weblogo test
2011-03-23 11:46:10 -04:00
Ross Lazarus
3a908497d5
Added subsequence and colour options to weblogo3 sequence logo generator; tweaks to clustalw tool help
2011-03-23 11:20:23 -04:00
Nate Coraor
1fdfacc977
Set the ftype of SRMA test outputs so the BAMs are compared as SAMs
2011-03-23 10:59:26 -04:00
Daniel Blankenberg
d95c6b2e52
Add IGV as an external display application. Contributed by Tobias Wohlfrom.
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Provides two links for IGV:
1) web - to view with Java web start IGV if the user has no IGV installed
2) local - to view in the user's running IGV instance (requires remote port enabled in IGV)
2011-03-23 09:57:06 -04:00
Daniel Blankenberg
7ab9f182dc
Add SGD Yeast genome Gbrowse display site.
2011-03-23 09:03:13 -04:00
Daniel Blankenberg
b5131d44ce
Disable functional test for not being able to import your own history which was enabled in 5248:dc9efb540f61.
2011-03-23 08:42:01 -04:00
Daniel Blankenberg
58963cc97d
Remove link target from intermine datasource tools.
2011-03-22 20:29:32 -04:00
Daniel Blankenberg
7d7b881226
Allow importing one's own history.
2011-03-22 19:43:32 -04:00
Kanwei Li
82dde6e37e
Refactor Grouping tool and fix bug where data after a blank value in the group_by column returns the wrong data.
2011-03-22 17:49:09 -04:00
Ross Lazarus
6646cfa80d
Adding two new tool wrappers and tests - clustalw ( http://www.clustal.org ) for multiple alignments and a sequence motif generator based on weblogo3 ( http://weblogo.berkeley.edu ) which works on fasta files such as alignments from clustalw
2011-03-22 14:08:32 -04:00
Richard Burhans
93911caa4f
fixed comment bug and added additional error messages for SIFT tool
2011-03-22 13:45:31 -04:00
Greg Von Kuster
3c906860c2
Fix for bug introduced in change set 5243:45b772580403.
2011-03-22 10:50:27 -04:00
Jeremy Goecks