e013dc254e
Make BED default datatype for UCSC direct connection.
2007-03-01 15:53:03 +00:00
bdb37ba8ce
Another change to ops to hopefully kill the never-ending strand problem. This makes anything that isn't a +/- into a +.
2007-02-28 21:59:38 +00:00
f4f9e1d7b2
Preliminary data validation comit, much more to come. There will be a new datatype for errors which will hold pickled exceptions and repr them for display. In addition, errors should probably be a reserved or somehow special child dataset, so that there can be only one. Finally, implementing a tool or interface to fix errors needs to be done (and is why the exceptions must be pickled). Also, only the validation for intervals is done, as the parsers in bx for mafs, fasta, axt's, etc do not have any kind of validation built.
2007-02-28 21:46:54 +00:00
412b9a9677
Add UCSC Table Browser direct connection tool.
2007-02-28 20:46:06 +00:00
0dfd869918
Enhanced column_maker.py to gracefully handle invalid data in input file and to display more meaningful info to user.
2007-02-28 16:10:31 +00:00
7ab5369033
Corrected the way these tools read input datasets to keep them from entering infinite loops if the dataset is empty.
2007-02-27 16:32:05 +00:00
8c09569e13
Unsequenced genome for March form Dulles airport
2007-02-27 02:34:21 +00:00
0191564e9b
Added another example since I noticed several jobs where the user was confused about the "==" requirement.
2007-02-26 20:43:31 +00:00
97e5cb8f9d
Enhanced event logging for session activity reports.
2007-02-26 19:03:37 +00:00
e830b83b9f
Removing import psyco_full from tools that throw warning (already imported).
...
Also, I noticed that the 2 aggregate score tools had the same tool id, and are live on the test server, so i fixed the tool ids.
2007-02-23 14:33:03 +00:00
5a8135f56c
Minor correction to the message for the location of the first invalid line in a dataset, if there is in fact one.
2007-02-21 21:44:22 +00:00
7285237f5b
Hack for database monitoring job queue to wait until after forking to start
...
monitor thread.
2007-02-21 20:16:35 +00:00
67e1bb8846
Enhanced the Filter tool to handle invalid data and to display more useful, informative messages to the user.
2007-02-21 18:41:58 +00:00
573e8cd8a2
Parameter sanitizer can now be turned off by individual tools. Refresh behavior after tool execution can now be defined in
...
the tool xml file.
To Do: Allow individual parameters to have sanitation control.
2007-02-21 18:01:07 +00:00
9903924f97
Name change: Gene BED to Exon BED changed to Gene BED to Exon/Intron BED
2007-02-19 21:14:03 +00:00
84912a92fa
Filename test_kaks.py changed to kaks_yn00.py
2007-02-19 19:34:26 +00:00
be8f660cd3
yn00 binary added
2007-02-19 19:21:38 +00:00
ac747b8d6f
Modified tool: Gene BED to Exon BED
2007-02-19 16:59:51 +00:00
0ac0ec4086
"new tool: gene bed to intron bed- test output filr"
2007-02-19 16:25:54 +00:00
112f94c176
new tool: gene bed to intron bed
2007-02-19 16:22:28 +00:00
fb3b9255f5
yn00 binary added: kaks tool
2007-02-16 21:37:34 +00:00
b37f332a35
new toold kaks added
2007-02-16 21:28:21 +00:00
092c23f41b
Made run.sh Bourne-friendly and added path fix for cluster nodes.
2007-02-16 21:21:24 +00:00
bfe9c45db9
Modify maf_to_bed to use database/tmp for its temp directory for additional output files.
2007-02-15 20:09:33 +00:00
e554fb4d79
added get_flanks plus two additional tools for a David Gilmore: srg2wig and aggTrack. These two are for demo only and should not go to main
2007-02-15 15:11:08 +00:00
f6274675db
Close connections after setting up the application (just is case the WSGI
...
server wants to fork, otherwise processes then try to share connections,
yikes!!!)
2007-02-13 23:49:49 +00:00
48cdd842f7
Support for the job "queue" reading new jobs from the database rather than
...
from a Queue.
Enable this when running the server in a forking environment. The job queue
threads will live in the parent process, while jobs will be added to the
database by the child processes. Lovely!
2007-02-13 21:00:18 +00:00
5c494af61a
try the post-job hook so it doesn't kill the queue if it fails.
2007-02-13 17:54:43 +00:00
5a4182c243
1) A 'prefork threaded' mixin hacked together from existing flup components
...
2) An AJP server using that mixin (we could also do fastcgi or scgi, but AJP
is the best option).
2007-02-13 17:27:25 +00:00
02a60145bf
2007-02-13 17:01:13 +00:00
0ef3bdbba0
modified test_kaks tool
2007-02-13 16:21:07 +00:00
ed76bdaff2
The correct file for pre-fork server.
2007-02-13 05:17:32 +00:00
bd0ff71748
rollback...
2007-02-13 05:17:18 +00:00
b1650cfe3a
Fairly simple pre-fork server (forks n processes each with m threads).
...
WORK IN PROGRESS!
2007-02-13 05:13:17 +00:00
583e91610d
new tool added: kaks
2007-02-12 22:03:06 +00:00
63a3bebef9
Added new tool: kaks (computes the ratio of nonsynonymous substitutions to synonymous substitutions for all the sequence alignments in the input
...
file).
2007-02-12 21:38:36 +00:00
0177cd59cc
Add tool to allow users to limit a MAF to a set of species.
2007-02-08 21:24:39 +00:00
ee16d8a956
Revision info
2007-02-08 20:16:16 +00:00
15f1c23175
load test
2007-02-08 20:12:40 +00:00
45e5088540
Update LAJ to latest version.
...
As per Cathy:
This one deals with the integer overflow by presenting a dialog box for filtering the input data.
It was a little tricky trying to make the dialog's behavior as intuitive as possible under
different usage scenarios; it's still not ideal but hopefully it won't be too confusing.
Please give it a try and let me know if you find any problems.
2007-02-05 18:52:51 +00:00
52b56c76eb
Build lists are now alphabetized (by display name) in edit attributes and the upload tool. More
...
advanced grouping is not possible without additional outside information.
2007-02-05 18:50:07 +00:00
391f3a6a53
Unsequenced genome of the month
2007-02-03 19:24:37 +00:00
07be68b0ed
UCSC Table Browser diff test is now implemented. I seems hacky though because of hgsid, which is assigned by the browser. We'll try this for now and change later if necessary.
2007-01-26 19:42:40 +00:00
f2042bef5b
1. Cleaned up new code for galaxy sessions.
...
2. Added some new methods to clean up boilerplate.
3. Enhanced some of the logging messages.
4. Moved newly added columns to end of event and job tables (rather than middle).
2007-01-25 16:30:45 +00:00
e2157a1957
Reverted changes to sample ini made by David.
2007-01-24 20:48:37 +00:00
ccb175927b
score aggregate tool for .wig files
2007-01-22 20:28:36 +00:00
6d798fdfef
test data for the test scripts: test_3D_Edit_Modify.py and test_3E_Filter.py
2007-01-18 22:30:27 +00:00
df09b23a7f
Add two test scripts to trunk. test_3D_Edit_Modify.py is committed in the old branch. test_3E_Filter.py is the test script for screencast 'Filter, Sort, Join and Compare'.
2007-01-18 22:26:08 +00:00
f55ac74e09
These are the changes we've been discussing to incorporate
...
galaxy sessions (using cookies) for all histories, events
and jobs.
2007-01-18 22:10:18 +00:00
59f764fe84
This should catch parse errors, which are errors with bad lines in interval files, such as bad strands or generally malformed lines. The message is a little more human readable, and I expect to improve this.
2007-01-17 20:41:52 +00:00
Daniel Blankenberg