Guruprasad Anada
3520ce3aec
Updating security from central
2008-09-24 18:22:55 -04:00
Guruprasad Anada
0f1130e84a
Adding tools to fetch microsatellites and estimate their mutabilities.
2008-09-24 18:20:39 -04:00
Nate Coraor
bc7dc21cdb
Fixed conflicts in templates.
2008-09-24 16:12:13 -04:00
Nate Coraor
9bda606dbc
Resolve conflicts in model/__init__.py from central.
2008-09-24 16:02:52 -04:00
Greg Von Kuster
7578582de6
my message
2008-09-24 15:09:24 -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
5e1d467c12
Merging heads
2008-09-24 13:54:25 -04:00
Daniel Blankenberg
6ad31f73bc
Some metadata updates.
2008-09-24 13:52:01 -04:00
Greg Von Kuster
d08d43cc2c
my message
2008-09-24 11:17:21 -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
Greg Von Kuster
97dad70d8e
Fix for building redirect URL.
2008-09-24 09:11:40 -04:00
Greg Von Kuster
b7e69706a1
1) Add a new <security_check> tag to DataToolParameters to filter out datasets from inclusion in the select list that do not pass the check. The tag set looks something like <security_check group="public" action="access"/>.
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2) Fixed some bugs in how we associate datasets with groups and permissions, specifically when a user logs in after creating a history with datasets while not authenticated.
3) Added a new active_histories mapper to User.
4) The DataToolParameter's dataset_collecter is now sent history.active_datasets rather than history.datasets.
2008-09-23 17:23:29 -04:00
Guruprasad Anada
47ca063006
Commiting changeset to security
2008-09-22 14:22:12 -04:00
Guruprasad Anada
9d3fd1eede
Modified INDEL tools under Regional variation section.
2008-09-22 12:02:35 -04:00
Greg Von Kuster
44bc594079
my message
2008-09-22 10:39:47 -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
Nate Coraor
830f545f1c
James, please review. Is the use of save_or_update okay?
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Corrected another 0.4 backref assignment bug that Anton found in workflow.
2008-09-19 16:29:55 -04:00
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 ©_access_from was being modified to
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'©_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.
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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
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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
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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
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
Guruprasad Anada