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Author SHA1 Message Date
Anton Nekrutenko bf540d2628 Unseq genomes for oct 2008-09-19 16:28:11 -04:00
Daniel Blankenberg 1e5d2759f8 Change the way GMAJ peeks are generated. A non-escaped &copy_access_from was being modified to 
'©_access_from'.
 2008-09-19 15:37:36 -04:00
Wen-Yu Chung fd1a49f9fe Fix a bug in shrimp_wrapper and add a tool to split paired-end reads. 2008-09-19 12:42:26 -04:00
Wen-Yu Chung bd4022e5e7 Merge with b2a9827178e28d93e2a978f64033a556a72b4c51 2008-09-19 12:34:51 -04:00
Daniel Blankenberg a5422f8f81 merge heads 2008-09-19 12:29:46 -04:00
Daniel Blankenberg ba3d30eed5 merge heads 2008-09-19 12:29:34 -04:00
Daniel Blankenberg beb7e3cf97 Update GMAJ tool interface. 2008-09-19 12:27:20 -04:00
Wen-Yu Chung 07118387a1 Fix a bug in shrimp_wrapper and add a tool for splitting paired-end reads. 
Update datatype/fastqsolexa so the number of sequences is correct.
 2008-09-19 12:02:13 -04:00
Nate Coraor 0cfd2717f0 Need uselist=False for these backrefs in alchemy 0.4... are there others? 2008-09-19 10:29:37 -04:00
Daniel Blankenberg 03a82e1cb5 merging heads 2008-09-18 16:50:17 -04:00
Daniel Blankenberg 25fd3e140f Add a wrapper for metadata inside of DatasetFilenameWrapper to allow proper string substitution in 
commandline and templates.
 2008-09-18 16:48:29 -04:00
Daniel Blankenberg 9ddbf1a0c3 merging heads 2008-09-18 16:34:28 -04:00
Daniel Blankenberg 6d2e714820 merging heads 2008-09-18 16:02:48 -04:00
Wen-Yu Chung 5adbb0ef6f update shrimp_wrapper. 2008-09-18 15:41:23 -04:00
Daniel Blankenberg 0dff1b0662 Update to latest gmaj. 2008-09-18 15:24:51 -04:00
Greg Von Kuster 8e17384a79 Upgrade to SQLAlchemy 0.4.7 and correct conflicts in ~/model/__init__.py. 2008-09-18 15:18:12 -04:00
Guruprasad Anada e53c5a15a3 Updating security from central 2008-09-17 17:25:17 -04:00
Guruprasad Anada 6b68878aec Forgot to update tool_conf.sample with the new tool details. 2008-09-17 17:14:59 -04:00
Guruprasad Anada fd8458e86a New tool to format short read mapping data as a UCSC custom track,. 2008-09-17 16:42:08 -04:00
Nate Coraor d8c3162dab Quick 'n easy solution to the EMBOSS stage in/out problem: read the 
outputs from the "real" galaxy path instead of the temp stage path.
 2008-09-17 10:45:20 -04:00
Daniel Blankenberg 90e30a30ae The MetadataCollection object is now created only once per dataset object instance (and when datatype is changed), instead of each time dataset.metadata is called. 
The 'no_value' attribute for a metadata element's spec is returned when the metadata element's value is None.
 2008-09-16 15:23:23 -04:00
Daniel Blankenberg 924dcba729 Merge local heads 2008-09-16 14:26:14 -04:00
Daniel Blankenberg 218a631b81 Strip whitespace from columns in file for dataset_metadata_in_file validator. 2008-09-16 14:10:53 -04:00
Guruprasad Anada edf314ddc7 Rewrote "Compare two queries" tool in Python. 2008-09-16 14:09:16 -04:00
Nate Coraor 4e87b28149 Make the user aware of permissions issues when they share a history. 2008-09-16 13:53:07 -04:00
Daniel Blankenberg 9eb8caca6f Small update for maf stats tool. 2008-09-16 13:25:42 -04:00
Wen-Yu Chung e7c4d75b34 add SHRiMP mapper for short read tools 2008-09-15 15:18:28 -04:00
Wen-Yu Chung bca6ad57e1 add SHRiMP mapper for short reads analysis. 2008-09-15 15:04:41 -04:00
Anton Nekrutenko f8915c416f Forgot two test datasets 2008-09-14 14:58:50 -04:00
Daniel Blankenberg 940432f0e8 Update MAF stitcher to be more efficient. Requires bx-pyhon rev>=449. 2008-09-12 15:50:20 -04:00
Anton Nekrutenko aac7409449 Typos 2008-09-12 15:35:50 -04:00
Nate Coraor ffd0be5a3a Merged from central. 2008-09-12 15:16:38 -04:00
Anton Nekrutenko 74d5327978 Lastz with additional short read changes 2008-09-12 15:14:20 -04:00
Nate Coraor f2f7550188 A couple bugfixes and a multi-update for datasets in the admin-side browser. 2008-09-12 14:54:06 -04:00
Nate Coraor e99e6164e2 Fix link colors in admin. 2008-09-12 11:00:47 -04:00
James Taylor b828d319ae Prevent workflow editor form loading in IE6 and print a message 2008-09-12 07:13:09 -04:00
Nate Coraor 35d9707056 Merge from central. 2008-09-11 13:17:04 -04:00
Nate Coraor d1d09a4c2b Upgrade bx-python to r448. 2008-09-11 12:22:32 -04:00
Nate Coraor b1caa7431a Admin side of the new file browser. It's late, I've been working all night, 
and I'm not sure what my name is... so there are probably bugs.  Please play
with this stuff and try to break it.

This commit also includes permissions editing that actually (finally!) lets you
create new group->dataset associations after the dataset already exists.
Currently the only entry point is from the Library, but the "display a group's
datasets" page can now be extended to contain useful information about
associated datasets (like whose history a dataset is part of and what folder a
dataset is in) to make it actually, like, useful and stuff.
 2008-09-10 23:22:06 -04:00
James Taylor 9030c528b0 imported patch workflow-index-bug 2008-09-10 11:21:57 -04:00
Nate Coraor 4edc6d6626 Spiffy new library browser interface. Also, dim datasets in your 
history on which you don't have permissions.
 2008-09-10 10:10:13 -04:00
James Taylor 5293399bcc Allow complete logging configuration to be specified in the ini file, 
in which case this is used instead of the "log_level" and "log_format"
keys under the app configuration. PasteScript actually handles this, so
we just do nothing related to logging config if the ini file contains a
"[loggers]" section. For example, you could add this to the end of your
universe_wsgi.ini to include SQLAlchemy debugging and include the thread
name with every log message.

# Logger overrides

[loggers]
keys = root, sqlalchemy.engine, sqlalchemy.orm.unitofwork, paste.httpserver.ThreadPool

[logger_root]
level = DEBUG
handlers = console

[logger_sqlalchemy.engine]
level = INFO
handlers = console
qualname = sqlalchemy.engine

[logger_sqlalchemy.orm.unitofwork]
level = DEBUG
handlers = console
qualname = sqlalchemy.orm.unitofwork

[logger_paste.httpserver.ThreadPool]
level = INFO
handlers = console
qualname = paste.httpserver.ThreadPool

[handlers]
keys = console

[handler_console]
class = StreamHandler
args = (sys.stderr,)
level = NOTSET
formatter = generic

[formatters]
keys = generic

[formatter_generic]
format = %(threadName)s %(name)s    %(levelname)s   %(asctime)s %(message)s
 2008-09-10 09:58:29 -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
Guruprasad Anada e0bf31431c Fix for grouping.py: New line character appended when grouping by the last column will now be trimmed. 2008-09-08 14:54:40 -04:00
Guruprasad Anada 9887101d60 Fix for scatterplot.py: Handling an uncaught exception. 2008-09-08 14:36:37 -04:00
James Taylor 8266801ea0 Fix for admin interface functional test. 2008-09-08 14:27:56 -04:00
James Taylor bd1a4e01cc More cleanup for admin UI. 2008-09-08 13:41:55 -04:00
Daniel Blankenberg 8bdd875488 my message 2008-09-08 11:21:29 -04:00
Daniel Blankenberg 2495dc5166 The interval to BED converter will now use the name field specified via metadata, if available. 2008-09-08 11:15:58 -04:00
James Taylor a212c44899 Update packed version of workflow editor script (fix z-index problem again?) 2008-09-08 09:47:37 -04:00