Daniel Blankenberg
2bb78ef755
Improve ajax deleting refreshing of dataset contents.
2008-10-06 11:48:35 -04:00
Guruprasad Anada
15c4a863c2
Updating "regional variation' section in tool_conf.xml.main.
2008-10-06 09:40:47 -04:00
Guruprasad Anada
e78f34fb49
Modified help message for indel rate tool.
2008-10-06 09:33:52 -04:00
Daniel Blankenberg
846dfe6bda
Add axaj async undelete ability.
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Fix redisplay of dataset when asynchronously deleted under history view showing deleted datasets.
2008-10-03 16:06:01 -04:00
Daniel Blankenberg
9969d1515f
Add the ability to undelete deleted datasets from a history.
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A new selection under History Options allows users to select a history view containing deleted (and undeletable) datasets.
Known Issues:
1. When adding a new dataset to a history (tool execution), the history is always refreshed to show only non-deleted datasets.
2. When doing an ajax delete of a dataset while viewing deleted datasets, the newly deleted dataset is still removed from the current view of the history (instead of appearing with the deleted message), a refresh will bring it back.
2008-10-02 16:37:32 -04:00
Greg Von Kuster
ca364f7ed2
Reverting to rev 1459.
2008-10-02 15:51:17 -04:00
Greg Von Kuster
e01b8e5527
Remove a debug statement from root controller...
2008-10-02 13:18:50 -04:00
Greg Von Kuster
91620b3218
Fix all root controller methods so that history_dataset_association.id is not confused with history_dataset_association.dataset_id.
2008-10-02 12:45:03 -04:00
Greg Von Kuster
64c4c808f5
Fix for root/display() - history_dataset_association.dataset_id no longer confused with history_dataset_association.id.
2008-10-01 12:43:59 -04:00
Greg Von Kuster
53a4390863
Fix for histogram tool when input dataset is empty.
2008-10-01 10:17:58 -04:00
Wen-Yu Chung
d7b7c0795f
add error msg for shrimp_wrapper when memory error and zero hits.
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convert last column of megablast output to float.
2008-09-30 16:40:42 -04:00
Daniel Blankenberg
61ca17eade
Add a change_format tag to output datasets in tools. This allows for dynamic switching of output datatype based upon input values.
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Several tools have been updated to take advantage of this, eliminating their need for code_files.
2008-09-30 16:17:12 -04:00
Guruprasad Anada
550da8f952
Modified the way biomart tool runs: output generation will be completed before exec_afer_process hook is called.
2008-09-30 15:30:57 -04:00
Greg Von Kuster
48066e035d
Fix for disk usage report in the webapps system controller.
2008-09-29 10:37:54 -04:00
Daniel Blankenberg
929c68106d
Update to implicit converter discovery. Will now allow the use of converters that create datatypes that are a subclass of what is needed by the tool.
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i.e. If tool input requires 'interval', and a datatype has a BED converter available but no interval converter, the BED converter can now be used.
2008-09-26 14:22:37 -04:00
Daniel Blankenberg
0794f1315f
Fix for interval to bed converter.
2008-09-26 09:10:04 -04:00
Daniel Blankenberg
ba81daedf7
Enhance the way dataset.set_meta() behaves, by adding a flag 'overwrite', which when False will only overwrite metadata values that are not previously set or are not accessable for user modification.
2008-09-25 15:03:05 -04:00
Nate Coraor
fbe9d4e4e5
Update check_galaxy for new twill.
2008-09-25 10:19:56 -04:00
Guruprasad Anada
0f1130e84a
Adding tools to fetch microsatellites and estimate their mutabilities.
2008-09-24 18:20:39 -04:00
Greg Von Kuster
61ef35c0f3
Eliminate enable_beta_features ( and the concept of 'beta' from the controllers ).
2008-09-24 15:05:38 -04:00
Daniel Blankenberg
6ad31f73bc
Some metadata updates.
2008-09-24 13:52:01 -04:00
Greg Von Kuster
7aace9ccaa
Convert metadata unicode strings to ascii ( previous code doesn't seem to do anything, am I missing something? ). Add no_value metadata attribute to columns and column_types metadata. Fix for column_maker and filter tools.
2008-09-24 11:14:44 -04:00
Guruprasad Anada
9d3fd1eede
Modified INDEL tools under Regional variation section.
2008-09-22 12:02:35 -04:00
Greg Von Kuster
b4890c1bbb
Integrate with intermine ( data source ) and epigraph ( data destination ). Receiving data from epigraph coming soon. Data is sent to epigraph using a combination of DATA_URL and REDIRECT_URL tool params. This tool creates jobs, but does not queue them for execution.
2008-09-22 10:36:34 -04:00
Guruprasad Anada
e2f4f46a75
Adding tools to compute Substitution rates.
2008-09-21 17:36:28 -04:00
Guruprasad Anada
cb74e79f21
Adding a new set of toolss to perform multiple linear regression analysis.
2008-09-20 18:14:24 -04:00
Wen-Yu Chung
bd4022e5e7
Merge with b2a9827178e28d93e2a978f64033a556a72b4c51
2008-09-19 12:34:51 -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.
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Update datatype/fastqsolexa so the number of sequences is correct.
2008-09-19 12:02:13 -04:00
Daniel Blankenberg
25fd3e140f
Add a wrapper for metadata inside of DatasetFilenameWrapper to allow proper string substitution in
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commandline and templates.
2008-09-18 16:48:29 -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
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
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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.
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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
Daniel Blankenberg
9eb8caca6f
Small update for maf stats tool.
2008-09-16 13:25:42 -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
Anton Nekrutenko
74d5327978
Lastz with additional short read changes
2008-09-12 15:14:20 -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
d1d09a4c2b
Upgrade bx-python to r448.
2008-09-11 12:22:32 -04:00
James Taylor
5293399bcc
Allow complete logging configuration to be specified in the ini file,
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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
Daniel Blankenberg