bddbe4a68b
Update the description of Aggregate datapoints based on the changes of the output.
2007-04-06 13:45:03 +00:00
18b25d241f
Corrected behavior of upload tool under 2 conditions: 1) if user clicks execute button with no posted data or URL and 2) if user uploads an empty file.
2007-04-05 19:57:58 +00:00
6ea6c7bad1
Fix some tiny bugs in the xml file of tool Aggregate datapoints.
2007-04-05 19:34:28 +00:00
3b0852ee01
Add a tool to select maf blocks by number.
2007-04-05 18:26:44 +00:00
baacb7c67c
Enhanced security measures for condition entered as free text - should make tool more useful and reduce job errors.
2007-04-05 18:24:47 +00:00
fe136cdefa
Add tool to compute maf alignment coverage.
2007-04-05 17:57:16 +00:00
ab8bef0acc
change cf_maf_limit_to_species.dat
2007-04-05 15:39:59 +00:00
6d7d82cd93
Add a tool to allow filtering by MAF block size.
2007-04-05 14:55:05 +00:00
f8cd6433d2
Clean up comment.
2007-04-04 15:57:44 +00:00
5f1b12b56e
Add neighbor joining tree building via HYPHY.
2007-04-04 15:44:37 +00:00
a84ee14b5d
Add descriptions to tool EMBOSS:needle.
2007-04-02 19:05:30 +00:00
8f18223204
Add description for tool EMBOSS:isochore. More EMBOSS tools descriptions will be added soon.
2007-04-02 13:41:03 +00:00
9686682536
Modified get_flanks.py: Changed the approach for generating output.
2007-03-30 14:21:34 +00:00
ee8f20d2fe
New eggs
2007-03-29 20:23:46 +00:00
7ffa7b2fbd
Two more options to cluster. I believe cluster will need another pass soon to make it more efficient. I think there is a need for random-access-by-linenumber using some kind of table as reading the entire file into memory is a bad idea. That combined with an LRUcache could be useful for other tools (although not cluster).
2007-03-29 20:09:34 +00:00
d9ac464b9b
Unsequenced genome for April 2007
2007-03-29 02:27:47 +00:00
e2f1cc1abb
remove useless data
2007-03-28 14:03:57 +00:00
c2c485ad48
Changes made in get_flanks tool and the revised .py, .xml, test data and tool_conf.xml.sample files are being committed.
2007-03-27 17:12:58 +00:00
091d6fc023
remove load_test
2007-03-27 16:12:27 +00:00
f42b4c6742
Re-added the safety measures.
2007-03-27 13:56:16 +00:00
5cfc24d89e
Cleaned up the behavior of the filter tool and eliminated restrictions on filtering on words in the data. Should eliminate most job errors.
2007-03-27 13:18:33 +00:00
d79c18864b
comment out the tests which use ucsc_proxy
2007-03-23 19:32:54 +00:00
be2b8d74aa
add data for sc_3E test
2007-03-23 19:30:30 +00:00
e34fff8ff8
Added a corner-case fix for auto-detect file formats. Updated info displayed to user on upload and filter tools and added more valid words to filter tool.
2007-03-23 17:46:06 +00:00
c6dcb4e7dd
change/add some data for testing
2007-03-23 15:30:07 +00:00
b352e0f9a8
make changes to some tools for run_functional_tests
2007-03-23 14:24:36 +00:00
03130a65bb
Enhance build name grouping. Species are sorted alphabetically by name, but within a species
...
are sorted in decending db revision order.
2007-03-22 19:56:16 +00:00
59ad2219ac
Add ability to purge deleted datasets. Purged datasets have their file
...
contents deleted from disk and is done using the admin interface.
Database changes required:
alter table dataset add purged boolean;
update dataset set purged = False where purged is null;
2007-03-22 16:33:35 +00:00
c2dcfc064a
Add the ability to set which ucsc genome browsers to use when viewing user tracks. Option is configurable in universe_wsgi.ini.
2007-03-22 14:56:31 +00:00
e93efd0951
Override the default setting for dataset.metadata.strandCol for BED files that do not contain a strand column. This will result in changing the format of the file from BED to Interval. Also removed an extra if statement.
2007-03-22 14:49:39 +00:00
ad8719b852
Fix ucsc test browser.
2007-03-21 19:59:58 +00:00
8a207dcd87
Update UCSC direct connection to use main ucsc site. Add direct test
...
connection.
2007-03-21 19:52:01 +00:00
b6c07724fe
Reverting changes back to 1479 per Greg.
2007-03-21 15:06:34 +00:00
5edf1f941f
Updating Kaks data in test-data
2007-03-21 14:47:48 +00:00
3462a49ae4
Updated tool_conf.xml.sample: Renamed Graph data tab as Plot/Display data and included Display in UCSC, GMAJ and LAJ tools under it.
2007-03-20 21:56:32 +00:00
bf1a7e38cc
Updated tool_conf.xml.sample with a link to the new tool Display in UCSC under Get Data tab.
2007-03-20 20:14:56 +00:00
3345e2b3a0
Added new tool: Display in UCSC.
2007-03-20 19:39:29 +00:00
1dac83237e
Latest version from Cathy.
2007-03-20 18:41:29 +00:00
0f214504cf
Uploading empty files will now result in an error.
2007-03-20 15:37:11 +00:00
2b05ca975f
Fixed a bug in sniff.py and added a new unit test case to cover it. Added the hpvar data source tool to tool_conf.xml.sample. Slightly enhanced the filter and compute tools.
2007-03-19 19:55:57 +00:00
dde3ee7e3a
Tiny change in welcome
2007-03-16 19:40:50 +00:00
53b4c661af
Added an option for rounding to the Compute tool.
2007-03-16 18:36:24 +00:00
9a4e8dc19c
Integrated Belinda's hbvar data source. The functional test fails, but Jianbin will look at it.
2007-03-16 15:22:28 +00:00
f5fcf39ff0
Two new config vars to pull datasets from a server other than the
...
application server. When updating a cluster instance, the following
two new config vars must be set:
pbs_dataset_server = name-of-dataset-server
pbs_dataset_path = /path/to/datasets/on/dataset-server
2007-03-16 06:30:39 +00:00
15c38e5238
Welcome change
2007-03-16 03:47:35 +00:00
c7f6284136
Remove extraneous comment
2007-03-15 20:35:48 +00:00
cc4d6934bd
Random Intervals update.
2007-03-15 20:31:09 +00:00
cfc0d154bb
Print python path on startup (inside the interpreter)
2007-03-15 15:28:20 +00:00
9ea77e9719
Comment out some more validation stuff, modify active_datasets relation to
...
take advantage of partial index.
2007-03-15 15:19:06 +00:00
56b0e93910
Reversing Ian's change to output format of gops from revision 1457
2007-03-15 13:54:59 +00:00
Yi Zhang