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
4170eba30e
Eager load validation errors.
2007-03-15 04:49:15 +00:00
da086cc522
Rolling back Cheetah upgrade.
2007-03-15 04:12:24 +00:00
238126a69a
Commented out Ian's validation call in upload.py.
2007-03-14 21:45:51 +00:00
878d893013
single dataset choice for aggregate options
2007-03-14 19:58:23 +00:00
224bd67cc0
On errors in history, renamed "more info" link to be "report this error" and on the error report form, changed heading from "Report this error" to "Report this error to Galaxy Team"
2007-03-14 19:17:00 +00:00
a92f234e86
Added id in hidden input for missing argument to report_error.
2007-03-14 15:46:16 +00:00
9fa822d603
Appeasing the build-list on scofield?
2007-03-13 21:45:49 +00:00
7ac51f24fc
All of the stuff in /cache has been moved to /depot/data2.
2007-03-13 21:27:39 +00:00
f3eab4c4ca
cleaned up tests and old script for aggregate(binned) scores
2007-03-13 21:20:31 +00:00
f8905abb2b
Fix: will now kindly tell the user if they have failed to actually select an input dataset.
2007-03-13 20:20:11 +00:00
Yi Zhang