Nate Coraor
95f951c337
The Galaxy-side job runner for execution via LWR, a light weight cluster setup written by John Chilton. For more information on implementing the cluster, see: https://bitbucket.org/jmchilton/lwr/
2011-02-11 15:32:13 -05:00
Nate Coraor
52916de087
Handle bugs encountered when fetching an egg during a version conflict and a sys.path item has been removed.
2011-02-11 15:01:04 -05:00
Nate Coraor
f5b125f311
Fix a minor bug which mad it completely impossible to run a job.
2011-02-11 14:17:22 -05:00
Nate Coraor
8198db3a8c
Make loading of job runners dynamic. Changes to lib/galaxy/config.py and lib/galaxy/jobs/__init__.py are no longer required. Existing runners which are not part of the Galaxy source will need to define the class name to instantiate in the __all__ list in the runner. See the included runners for an example.
2011-02-11 13:12:27 -05:00
Guruprasad Anada
02ee54b502
Updated path to sputnik binary in 'Extract orthologous microsatellites for multiple (>2) species alignments' tool
2011-02-11 09:27:10 -05:00
Jeremy Goecks
9293947608
Fix searching functionality and labels in published item grids.
2011-02-11 08:42:05 -05:00
Kanwei Li
b2c9c9322b
trackster: Properly return NO_DATA for LineTrack datasets, fix error when no data is available
2011-02-11 00:53:49 -05:00
Kanwei Li
07d79fcee3
trackster: Remove content-div margin and border-top
2011-02-10 17:43:39 -05:00
Jeremy Goecks
23a8b191a7
Extend extract_genomic_dna tool to support GFF/GTF features and custom genomes. For GFF/GTF files, tool provides option to return sequence data for each feature's intervals, which are split across lines in GFF/GTF files. Tool also now accepts sequence data from a history item, enabling the extraction of data from custom genomes. New functional tests added to cover new functionality.
2011-02-10 17:19:40 -05:00
Nate Coraor
f404736472
Another bugfix for egg conflicts, don't add items to the pkg_resources working set unless the item's not already in there.
2011-02-10 15:53:06 -05:00
Greg Von Kuster
a17f2c0b25
Migration script to add a subindex column to the run table.
2011-02-10 15:29:08 -05:00
Dannon Baker
031b0fca6e
workflows: jquery1.5 fix, quotations.
2011-02-10 13:58:48 -05:00
Nate Coraor
9c466e3b2d
Fix for pysam egg conditional, which would always fail, and actually check always_conditional eggs in the crate's all_eggs method. Fixes downloading of eggs for offline systems.
2011-02-10 12:13:55 -05:00
Guruprasad Anada
924ea2443b
Better handling of complex interrupted microsatellites in 'Extract orthologous microsatellites for multiple species alignments' tool.
2011-02-10 10:33:08 -05:00
Nate Coraor
acee93b7ad
Fix for MySQL index lengths in migration script 62. Thanks Leandro Hermida.
2011-02-09 16:49:43 -05:00
Nate Coraor
0c292a7d65
A fix for DRMs which can apparently cause a drmaa.InternalException in cases where the job is finished normally. If there are other conditions which raise this exception, failures may go undetected. The drmaa runner is not in active use by the development team, so please report problems with this change.
2011-02-09 16:46:30 -05:00
Nate Coraor
fae1d65d61
More comprehensive conflict resolution for eggs that are dependencies of other eggs, and eggs which conflict with system versions.
2011-02-09 16:31:43 -05:00
Nate Coraor
92de52f6e0
Fixes for scrambling python-daemon and pysam.
2011-02-09 16:29:50 -05:00
Greg Von Kuster
a7d33721d0
Optimize the printed output of the 0074... migration script.
2011-02-09 16:18:56 -05:00
Daniel Blankenberg
8cd2a39cc7
Add metabolicMine datasource tool.
2011-02-09 15:42:42 -05:00
Greg Von Kuster
b0b5df4e93
Add a purged column to the LibraryDataset table - a LibraryDataset is marked purged when all associated LibraryDatasetDatasetAssociations are marked deleted. Fix the cleanup_datasets.py script to more correclty handle the lifecycle of LibraryDatasets.
2011-02-09 15:42:09 -05:00
Kanwei Li
dcc0d780bc
trackster: Recalc slots no matter what level it's on since it's fast enough
2011-02-09 13:24:35 -05:00
Kelly Vincent
edc75c49cb
Added bwa_index_color.loc to buildbot setup config
2011-02-09 13:11:28 -05:00
Kelly Vincent
7004393599
Adding several genomes to the manual builds list
2011-02-09 12:36:40 -05:00
Kanwei Li
b5f72b0afe
Make left and right panels openable to 1000px, up from 400px
2011-02-08 18:07:27 -05:00
Kanwei Li
d56e7e4191
trackster:
...
- Fix packing overlap issue due to font calculation being different in dummy context vs drawing context
- Refactor incremental_slots for simplicity/readability
- Properly add padding to text label for "pack"-view feature tracks
2011-02-08 17:45:03 -05:00
Jeremy Goecks
bf8648675f
Fix bug in changeset 36c27bfbb7a8; remove debugging statement.
2011-02-08 16:48:41 -05:00
Jeremy Goecks
a41e40ce60
Trackster: standardization and better handling of track heights. This fixes overly large spacing for zoomed-out interval_index tracks and does away with the no_detail parameter, which is not sufficient for setting track height. Also fixed bug in
...
BAM display label spacing.
2011-02-08 15:21:19 -05:00
Ramkrishna Chakrabarty
68182e3909
fix for transfer dataset bug caused due to un-sanitized sample names
2011-02-08 13:43:39 -05:00
Dannon Baker
aaa32d1d45
Merge.
2011-02-08 13:36:38 -05:00
Kanwei Li
dde2845880
Fix python 2.4 incompat
2011-02-08 13:36:15 -05:00
Dannon Baker
b40c7e5b40
workflows: Fixed jquery 1.5 errors related to workflow saving and flagging of outputs. Repack.
2011-02-08 13:36:12 -05:00
Nate Coraor
876ad428eb
Fix missing python_daemon egg on python2.4 problem.
2011-02-08 12:14:20 -05:00
Kanwei Li
4ed00252db
trackster: fix farb color picker playing badly with tipsy
2011-02-07 18:11:44 -05:00
Kanwei Li
31a66567ec
trackster: move summary count text darker and aligned at the top for better visibility in most cases, and only draw if there is some padding so that numbers don't bunch up
2011-02-07 16:59:12 -05:00
Jeremy Goecks
ea5d68bb76
Partially addressing packing bugs that cause features to be drawn overlapping. Pack scripts.
2011-02-07 15:22:23 -05:00
James Taylor
2af69d58b4
merge
2011-02-07 11:38:34 -05:00
Jeremy Goecks
fa0d2bea2c
Trackster: refactor interval index drawing. Modified interval index squish mode to display blocks and treat intervals as half-open. Also use constants to standardize the drawing height of different modes across tracks.
2011-02-07 09:23:57 -05:00
James Taylor
7ad70716af
trackster: use new jquery defereds to ensure draw happens after predraw_init in line tracks, eliminates failure to draw before scrolling
2011-02-06 14:44:14 -05:00
James Taylor
17352f3de5
jquery updated to 1.5, fixed minor bugs in use of jStore and some dom manipulation in workflows (both problems in our code, not backward incompatibility). Please help test.
2011-02-06 14:42:11 -05:00
James Taylor
b2863ca4af
trackster: tiny tweaks
2011-02-06 11:29:04 -05:00
James Taylor
e80a525fe9
trackster: color picker shows on click, not hover, and below the input element
2011-02-06 10:27:53 -05:00
James Taylor
ca61aa3a54
trackster: packed scripts
2011-02-06 02:21:10 -05:00
James Taylor
1dbbf1818e
trackster: color picker for color track config params
2011-02-06 02:20:31 -05:00
James Taylor
c3af1a8990
trackster: save line track height properly
2011-02-06 00:41:03 -05:00
James Taylor
8e2b990331
trackster: refactor track configuration to be data/configuration driven -- easier to extend
2011-02-06 00:39:09 -05:00
James Taylor
d3ecba9e6f
trackster: Move some CSS rules into trackster.css, fix CSS problem with label tracks
2011-02-05 16:04:30 -05:00
James Taylor
7b7b8a4ebd
Automated merge with https://bitbucket.org/galaxy/galaxy-central
2011-02-05 15:38:11 -05:00
James Taylor
8085f39738
Fix problem with adding filters when no data is returned, eliminates one of the problems drawing feature track tiles
2011-02-05 15:37:56 -05:00
Kanwei Li
02e154a8e7
trackster: Reference track should not have the new loading background and min-height
2011-02-04 21:13:36 -05:00
Nate Coraor