Jeremy Goecks
adebc727df
Trackster: add a simple framework for determining when data subsetting should/can be done and use framework for better data subsetting in FeatureTracks.
2012-02-20 13:04:34 -05:00
Jeremy Goecks
fe1ddad19f
Trackster: move 'more rows' icon from tile level to track level and fix bug in displaying visualization name. Pack scripts.
2012-02-20 11:58:13 -05:00
Nate Coraor
410fcf87df
Make the job queue thread block on job recovery to avoid a race condition with jobs in the 'new' state. This should fix jobs showing up as 'ok' and then upon a later history reload showing up as 'error'.
2012-02-17 11:27:29 -05:00
Daniel Blankenberg
aa5eb3c4a4
Add tool-data/shared/rviewer/rviewer_build_sites.txt.sample to run.sh sample list.
2012-02-17 10:04:28 -05:00
Daniel Blankenberg
11fd8d08e4
Add RViewer external display application.
2012-02-17 10:00:42 -05:00
Jeremy Goecks
0416175a87
Bug fixes for creating and saving visualizations.
2012-02-17 09:50:02 -05:00
Jeremy Goecks
d6c22052ec
Trackster bug fixes.
2012-02-16 23:02:14 -05:00
Jeremy Goecks
79618a06bc
Fix initialization of tags and annotations in history datasets.
2012-02-16 14:05:03 -05:00
Jeremy Goecks
acb44176bc
Pack trackster scripts.
2012-02-15 11:20:25 -05:00
Jeremy Goecks
06da58a4bf
Trackster: save and restore tool state.
2012-02-14 15:34:18 -05:00
Jeremy Goecks
b2ca2855b9
Better error message when bias correction/sequence data cannot be used in Cufflinks/compare/merge/diff.
2012-02-14 12:27:47 -05:00
Greg Von Kuster
0a8e16c390
Encode application name and link name when sending as request params to display application.
2012-02-14 11:58:51 -05:00
Jeremy Goecks
9721927be4
Trackster: for flexibility, use dictionaries in all object constructors. Fixed bugs associated with saving/restoring visualizations.
2012-02-13 11:08:50 -05:00
Greg Von Kuster
76310510fc
Do not allow conflicting datatypes included in a tool shed repository currently being installed to override datattypes already in the datatypes registry. Also, a bit of cleanup in handling datatypes included in repositories being activated / installed / deactivated / uninstalled. A bit more cleanup is still necessary.
2012-02-10 16:33:19 -05:00
Greg Von Kuster
af72f2e36c
Fixes for handling proprietary datatypes included in installed tool shed repositories - import proprietary class modules within the registry.
2012-02-10 14:52:41 -05:00
Nate Coraor
14afde8c24
merge
2012-02-10 13:19:41 -05:00
Nate Coraor
52a49208af
closed branch dynamic_options_memory_fix
2012-02-10 13:19:06 -05:00
Jeremy Goecks
f44bf96d3c
Merged in jmchilton/umn-galaxy-central/dynamic_options_memory_fix (pull request #36 )
2012-02-10 11:26:18 -05:00
Jeremy Goecks
047c3b126f
Trackster: save and restore group/multi-track filters.
2012-02-10 11:13:55 -05:00
Jeremy Goecks
f8f5aabb4d
Merge
2012-02-10 09:52:14 -05:00
Jeremy Goecks
a3d8b1240d
Trackster: filter bug fix and abstract filter display control.
2012-02-10 09:52:01 -05:00
Jeremy Goecks
18c24dade3
Tophat wrapper modifications: (a) remove parameter junctions_filter and (b) change default value of max_multihits to 20.
2012-02-10 09:23:33 -05:00
Ross Lazarus
b4d4cf0f14
Updates to FastQC wrapper
...
1) improvement suggested by bwlang to pass the history file name in as the file name to fastqc so it appears in the outputs instead of the previously unhelpful internal galaxy filename
2) lack of html output from fastqc or return of non-zero error code now triggers job failure - outputs may still be there but at least it goes red.
2012-02-10 10:40:00 +11:00
Jeremy Goecks
b7c8477722
Trackster: save and restore single track filters.
2012-02-09 15:32:38 -05:00
Nate Coraor
c8f4c93799
Make set_user_disk_usage.py object store-aware.
2012-02-09 13:26:14 -05:00
Greg Von Kuster
ab648e32d2
Handle multiple relationships in the tool lineage chain at the time of repository installation.
2012-02-09 11:43:03 -05:00
Jeremy Goecks
5cafc0b7d3
Remove maximum value for Tophat parameter initial_read_mismatches.
2012-02-08 22:56:50 -05:00
Greg Von Kuster
d647177616
When handling datatype conflicts always override previously loaded datatypes with the datatype currently being loaded. Use the same behavior for sniffers.
2012-02-08 13:46:14 -05:00
Jeremy Goecks
2324294f7f
Fix bug in GFFDataProvider's data iterator.
2012-02-08 11:55:49 -05:00
Greg Von Kuster
1c94a93c81
Load proprietary datatypes from installed tool shed repositories before the datatypes in the Galaxy distribution are loaded. We do this because the distribution includes some extremely generic sniffers (eg text,xml) which will catch pretty much anything, making it impossible for proprietary sniffers to be used. Proprietary datatypes contained in installed repositories are loaded in order of oldest installation first, followed by next olderst installation, etc.
2012-02-08 11:30:58 -05:00
Nate Coraor
c43633c5cb
Pass the config file name to set_metadata.py rather than relying on a hardcoded value.
2012-02-08 11:12:10 -05:00
Greg Von Kuster
bfc3baf665
Fix for getting updates for an installed tool shed repository change set revision.
2012-02-08 09:11:19 -05:00
Jeremy Goecks
154b2704b3
Trackster: do not subset data with a message.
2012-02-07 17:29:31 -05:00
Jeremy Goecks
d9cf1aedc2
Trackster: bug fixes for 36d36384704b
2012-02-07 17:07:35 -05:00
Greg Von Kuster
7194acdd47
Fix for loading tools from an installed tool shed repository into the tool panel outside of any sections.
2012-02-07 16:20:48 -05:00
Greg Von Kuster
2f559757dc
When an installed tool shed repository that includes tools is being reinstalled, allow the admin to select a different section in the tool panel (than was originally selected when the repository was last installed) to contain the included tools.
2012-02-07 15:10:03 -05:00
Greg Von Kuster
81edcca688
Tool version grid cleanup.
2012-02-07 13:04:52 -05:00
John Chilton
d6fb79b4a2
One more fixed typo.
2012-02-07 10:50:22 -06:00
John Chilton
2365c309ff
Fix a typo made with last commit.
2012-02-07 10:38:00 -06:00
Jeremy Goecks
f923c686c5
Fix bug in GFFDataProvider iterator.
2012-02-07 11:35:48 -05:00
John Chilton
1d18fb6cd2
Patch dynamic_options.py to just read just the first megabyte of an
...
input dataset (if it is larger than that). Otherwise Galaxy will
attempt the read the entire file into memory, this can causes crashes
and freezeups without the user even selecting a bad input (for
instance, if a large FASTQ file is the top most history item and a txt
input is sought, Galaxy will freezeup as soon as the tool is clicked
because it will try to load the options for the top item immediately
by default).
Though the implementation is not as clean, I am restricting it to a
megabyte instead of a number of lines/options in case the top most history
item has no line breaks. I imagine in that case the same problem could
occur even if the input is restricted to a reasonable number of lines
(say 100).
2012-02-07 10:35:17 -06:00
Jeremy Goecks
1e1c0b1744
Trackster: small variable reference fix.
2012-02-07 11:30:45 -05:00
Greg Von Kuster
bc486d508e
Fix for loading proprietary datatype sniffers that are included in installed tool shed repositories.
2012-02-07 11:15:20 -05:00
Greg Von Kuster
9d4b107536
Fix for 39e03997f78f - change buffer to string so older postgres versions work.
2012-02-07 11:06:17 -05:00
Nate Coraor
d9e075a8bf
Use PG9 hex bytea fix to decode tool shed repository metadata in migration script 91.
2012-02-07 10:41:22 -05:00
Jeremy Goecks
65fd278440
Trackster: renable data subsetting for all non-LineTracks.
2012-02-07 10:17:44 -05:00
Dannon Baker
40efce029a
Multiple-run workflows: When run into separate new histories, naming is now based on the varied input dataset instead of the execution number, so "<workflowname> on <varied_input>".
2012-02-07 09:45:19 -05:00
Jeremy Goecks
d8e3aedade
Trackster: simple framework for notifying view of changes; use framework to indicate changes when (a) config values are changed and (b) items are reordered or grouped.
2012-02-07 09:41:59 -05:00
Greg Von Kuster
3668d757f1
Add a new grid to view the tool version lineage by tool id (parent/child ordered) for any tool that was ever used in the local Galaxy instance. Tool ids in this grid that are associated with tools currently loaded in the tool panel are highlighted in green and are click-able, displaying the tool. Eliminate the mappers for determining lineage, and use methods instead as the mappers were problematic.
2012-02-06 15:22:56 -05:00
Jeremy Goecks
bb028c5d15
Trackster: compute resolution in continous rather than discrete units; this enables precise control over tile size and number.
2012-02-06 14:58:54 -05:00
Jeremy Goecks