Dave Bouvier
35bc12d769
Migrate tools from the distribution to the tool shed.
2014-07-28 11:58:52 -04:00
Dave Bouvier
448d9f55eb
Migrate 43 tools from the distribution to the tool shed.
2014-01-27 09:53:14 -05:00
Daniel Blankenberg
1e55e46201
Performance enhancements for Build custom track for UCSC genome browser tool.
2012-10-16 15:25:01 -04:00
Daniel Blankenberg
a6ecae74fd
Minor tool help updates.
2011-09-08 10:34:56 -04:00
Rob Hooft
ff227df117
fixed some configuration files
2011-04-13 21:02:06 +02:00
Daniel Blankenberg
37ae9ac29d
Create NGS peak calling section. Add MACS peak caller. Move GeneTrack to new section. Increment sam2interval tool version.
2010-02-05 16:06:27 -05:00
Daniel Blankenberg
5a0b072e56
Make the GeneTrack datatype binary, containing only the 'indexed' data needed by the GeneTrack server. Better creation of the URL for running the peak predictor tool. \nStill some cleanup/decoupling possible.
2010-02-03 16:33:25 -05:00
Daniel Blankenberg
973031f918
Fixes for GeneTrack. TODO: HDF indexes are handled in a fragile way: GeneTrack should accept an explicit filename for the index instead of using dataset_name.hdf.
2010-01-27 16:33:49 -05:00
Greg Von Kuster
8f6e8213a0
Fix most of the db flushes to be compatibel with sqlalchemy 05. Add the _monkeypatch_query_method() back into assignmapper due to a single object.get() method in the MetadataCollection class since Metadata has no current hook into mapping.context ( the sqlalchemy session ). There a 4 flushes in metadata,py and 20 flushes in model.__init__.py that still use the _monkeypatch_session_method in assignmapper due to the same issue, but all other flushes are fixed.
2009-11-11 15:59:41 -05:00
Nate Coraor
607d670872
Add Genetrack tools and display site
2009-11-06 14:22:44 -05:00
Kanwei Li
a947686b77
fix some typos for tools in folders N-Z
2009-09-25 02:06:03 -04:00
Greg Von Kuster
d0d7875192
Deprecated code corrections for supporting Python 2.6. Many of the Python 2.6 eggs are still throwing DeprecationWarning messages, so some things still won't work. Eggs for 2.6 need to be re-scrambled after corrections are made.
2009-08-14 15:37:31 -04:00
Ian Schenck
28016bd908
Using deprecated sha module in place of hashlib to keep compatibility with python2.4
2009-02-05 15:34:31 -05:00
Ian Schenck
937e568e19
Ironed out nasty exceptions thrown on invalid genetrack outputs. Still need a way to resolve the optional 2nd output (exported intervals), and ensure the user picks at least 1 coverage dataset or 1 feature dataset.
2009-01-27 17:10:30 -05:00
Ian Schenck
82d09f5824
Finally remerged changeset. Should be good now.
2009-01-21 16:48:54 -05:00
Nate Coraor
427bc02028
Backed out changeset 83a0c394a797
2009-01-21 16:03:59 -05:00
Ian Schenck
b8e76a8ca6
Made Genetrack load only if the dependencies import
2009-01-21 11:45:30 -05:00
Ian Schenck
6a0aa166aa
Initial GeneTrack commit. Most parts are in, but dependencies will still be a problem.
2009-01-19 17:45:28 -05:00
Daniel Blankenberg
18f4037ba2
Update GMAJ help.
2008-12-04 15:09:57 -05:00
Daniel Blankenberg
7e0479473c
Update GMAJ to latest beta.
2008-11-24 11:19:48 -05:00
Greg Von Kuster
5331dee076
Add functioal test baseline support for the repeat construct, more work needed ( e.g., multiple repeat elements, refresh_on_change when the input to be refreshed is within a repeat construct ). Added functional tests for some tools that use this construct.
2008-11-10 14:22:01 -05:00
Daniel Blankenberg
b9e242e4eb
Add a new metadata type of Metadata Files.
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These are now used to store the list of chromosomes for species as well as the index for MAF files.
MAF tools have been enhanced to make use of index files when available.
TODO: When datasets are purged from disk, these files should also be purged.
2008-10-22 13:49:22 -04:00
Daniel Blankenberg
beb7e3cf97
Update GMAJ tool interface.
2008-09-19 12:27:20 -04:00
Daniel Blankenberg
134e7ea7d6
Update GMAJ tool to allow the specifying of annotations in two styles.
2008-09-08 16:00:49 -04:00
Daniel Blankenberg
d112668c6a
Fix for GMAJ tool when species chromosomes are not specified. Error appears in paster.log as 'TypeError: iterable argument required'
2008-09-03 12:06:33 -04:00
Daniel Blankenberg
5073bfb57a
Add a metadata parameter to Alignment datatypes which stores chromosome information found in the alignment for each species.
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GMAJ tool no longer needs to have the chromosome specified for annotations.
2008-08-28 15:12:53 -04:00
Daniel Blankenberg
da3db3020a
Allow the user to optionally set a reference sequence in GMAJ.
2008-08-27 12:06:47 -04:00
Daniel Blankenberg
70b22fbc60
All datasets are now properly wrapped by DatasetFilenameWrapper. Certain cases had some datasets wrapped by InputValueWrapper.
2008-06-05 18:52:26 +00:00
Daniel Blankenberg
11a2c767c3
Rewrite of dynamic options for select lists. There are no more 'special cases' and new filters are much easier to incorporate, as neeeded.
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MAF tool interfaces now support the use of index species and all species existing in cached alignment sets.
Until main is updated and the old maf_location files can be overwritten, these symbolic links are required:
maf_index.loc -> /depot/data2/galaxy/maf_index_new.loc
maf_pairwise.loc -> /depot/data2/galaxy/maf_pairwise_new.loc
2008-05-29 17:38:46 +00:00
Daniel Blankenberg
fbcb5b6220
Typo in GMAJ no warn.
2008-05-27 15:32:53 +00:00
Daniel Blankenberg
6859f36c8c
Update nowarn Options for GMAJ tool.
2008-05-23 20:38:01 +00:00
Daniel Blankenberg
69116c95b1
Add additional nowarn parameter options to GMAJ.
2008-05-22 17:20:09 +00:00
Daniel Blankenberg
8c5787f21d
Fix Errors reported by Cathy regarding the GMAJ tool.
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With these notes:
User's can now specify the warnings that they which to report ('nowarns'). There are likely more options but they are unknown.
Using Firefox 1.5.0.12 on Ubuntu with no extensions/addons installed gives me no issues with loading the applet while Javascript is enabled or disabled (works for me).
2008-05-20 19:54:12 +00:00
Daniel Blankenberg
8dbd35176f
Small fixes for GMAJ.
2008-05-16 19:01:09 +00:00
Daniel Blankenberg
310911f861
Update GMAJ to the latest beta.
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GMAJ can now export MAF blocks back into the user's history.
The Interface for defining annotations has been updated.
2008-05-16 18:39:41 +00:00
Greg Von Kuster
43d2cb311d
Fix for optional DataToolParameters and fix for GMAJ tool imports.
2008-04-16 18:33:26 +00:00
Greg Von Kuster
af3b0669aa
Eliminated all Python2.4 references, added necessary assert statements to ensure minimum version of Python 2.4.
2008-03-28 15:24:50 +00:00
Daniel Blankenberg
8c075e0d70
Fix for Applet/JavaScript incompatibility in FireFox (tested under WindowXP, Firefox/2.0.0.12 [and IE 7]). Updated to use the 'object' tag, instead of deprecated 'applet'.
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It seems wrapping the object/applet in a div tag was the solution to preventing FireFox from crashing.
2008-03-19 18:52:40 +00:00
Greg Von Kuster
9879521d32
Fix for build_ucsc_custom_track, will no longer throw server error if history does not include valid input dataset, tool also now skips invalid lines instead of throwing exception.
2008-03-14 19:41:56 +00:00
Greg Von Kuster
135c9a0377
Removed the remainder of the tool version subdirectories.
2008-03-03 18:38:57 +00:00
Greg Von Kuster
9262212acd
Added tool version directories for validation and visualization tools directories.
2008-02-22 20:36:20 +00:00
Guruprasad Anada
5e4177b827
Modified "Build custom track" to work on Interval files without strand column.
2008-02-08 16:11:03 +00:00
Greg Von Kuster
75b84e0e4d
Eliminated Dataset.state.FAKE (requires db update), replacing it with Dataset.state.OK since fake datasets are removed, causing problems for workflow.
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Database update:
update dataset set state = 'ok' where state = 'fake'
2007-12-21 19:31:58 +00:00
James Taylor
2a39285bb3
Fix for building custom tracks from interval files.
2007-11-10 01:32:19 +00:00
Greg Von Kuster
db8eee7889
Changing all tools that use 'text' as file extension to now use 'txt'. We are eliminating the use of 'text' as a file extension within Galaxy and will now use only 'txt' for Text data types.
2007-09-27 12:24:27 +00:00
Greg Von Kuster
b22fecf1d3
Fix for invalid interval file sent to build_ucsc_custom_track.
2007-08-03 15:15:43 +00:00
Daniel Blankenberg
07a7dd60af
Update GMAJ to latest version. Also have help link to the local
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copy of the supplied help documents.
2007-07-30 19:22:24 +00:00
Daniel Blankenberg
a3390c3dc4
Update GMAJ to latest version. This now accepts BED as input for annotations.
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TODO: Allow annotations to be specified for all species in the file, not just the
'primary' organism (as specified by the dbkey). Metadata for sequences will need to be
fleshed out more first (i.e. store all species present in the file).
2007-07-25 20:39:16 +00:00
Guruprasad Anada
b16e569c0f
Updating help for extract_GFF_features, get_flanks, xy_plot and Build_ucsc_custom_track tools.
2007-07-16 15:27:26 +00:00
Jianbin He
a6d5eaa93f
rollback. sorry, removed the wrong files
2007-06-04 14:18:13 +00:00
Dave Bouvier