James Taylor
ed76bdaff2
The correct file for pre-fork server.
2007-02-13 05:17:32 +00:00
James Taylor
bd0ff71748
rollback...
2007-02-13 05:17:18 +00:00
James Taylor
b1650cfe3a
Fairly simple pre-fork server (forks n processes each with m threads).
...
WORK IN PROGRESS!
2007-02-13 05:13:17 +00:00
Guruprasad Anada
583e91610d
new tool added: kaks
2007-02-12 22:03:06 +00:00
Guruprasad Anada
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
Daniel Blankenberg
0177cd59cc
Add tool to allow users to limit a MAF to a set of species.
2007-02-08 21:24:39 +00:00
Jianbin He
ee16d8a956
Revision info
2007-02-08 20:16:16 +00:00
Jianbin He
15f1c23175
load test
2007-02-08 20:12:40 +00:00
Daniel Blankenberg
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
Daniel Blankenberg
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
Anton Nekrutenko
391f3a6a53
Unsequenced genome of the month
2007-02-03 19:24:37 +00:00
Ian Schenck
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
Greg Von Kuster
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
Nate Coraor
e2157a1957
Reverted changes to sample ini made by David.
2007-01-24 20:48:37 +00:00
David C. King
ccb175927b
score aggregate tool for .wig files
2007-01-22 20:28:36 +00:00
Yi Zhang
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
Yi Zhang
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
Greg Von Kuster
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
Ian Schenck
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
Yi Zhang
afe64697df
old changes copied to trunk: descriptions of 'Edit Queries' tools
2007-01-17 19:00:33 +00:00
Yi Zhang
d418956bf9
old changes copied to trunk: description of tool 'Compute'
2007-01-17 18:55:46 +00:00
Daniel Blankenberg
624037d52c
Fix aggregate binned scores in intervals. This tool could definitly use more friendly error messages.
...
misc module provided a method for opening and guessing the type of a compressed file by
extention. Does not appear that the module was even used.
2007-01-16 17:36:00 +00:00
Daniel Blankenberg
8a4006f82f
Remove Windows (cygwin) support.
2007-01-16 17:17:23 +00:00
Daniel Blankenberg
547ecf0960
Removing arch and module directories. Removing old operations (and tests), since they require arch; updated tool_conf.xml.sample.
...
Removed non-arch specific cheetah egg, since compiled c code (once located in arch) is included in arch specific eggs. Removed a
tool called basicStats2, which used arch, but hasn't been in tool_conf.xml for some time.
2007-01-16 17:05:33 +00:00
Daniel Blankenberg
f39f4d4694
New version of LAJ.
...
From Cathy: I have posted an updated version of Laj, which exits with an error message if there is an integer overflow in building the
composite y-axis for the dotplot (overflows for individual sequences would already be caught by the parser). I ran it on your file, and
indeed that was the problem.
2007-01-12 19:15:23 +00:00
Daniel Blankenberg
fc40c7f3d6
Fix help link for all EMBOSS tools.
2007-01-11 16:47:46 +00:00
Daniel Blankenberg
5a4c943fda
Fix for Biomart test. Why are there two biomart tests?
2007-01-11 16:28:14 +00:00
Ian Schenck
2612a17f26
Proxy changes copied to trunk...is there an easier way to do this?
2007-01-10 17:28:58 +00:00
Nate Coraor
8c21ccf8af
Only stagein if the file exists on disk. Fixes LAJ on the cluster.
2007-01-10 16:37:56 +00:00
Daniel Blankenberg
e4f2de8e63
Fix for LAJ ('fake datasets') and admin interface. Datasets and histories are no longer deleted from the database, a flag is set instead.
2007-01-10 15:47:21 +00:00
Daniel Blankenberg
8554c031ed
Push Microbial datasource changes onto trunk.
2007-01-10 15:23:30 +00:00
Nate Coraor
8f8dd92373
Remove last references to /depot/data1/cache.
...
All binned scores moved to scofield:/cache, chrominfo.txt is copied
nightly from herbie via a cron job. This can go away when galaxyOps is
no longer in use.
2007-01-03 19:36:07 +00:00
Nate Coraor
148922285a
Need to pass LC_ALL as well... if anyone can think of any other env vars
...
that need to exist when a job is run, please let me know.
2006-12-21 21:14:24 +00:00
Daniel Blankenberg
97c1ac33f7
Some items that were not copied over to trunk.
2006-12-21 00:14:11 +00:00
Nate Coraor
2392b88f77
Stage in output datasets (empty files) as well as input datasets so
...
PBS will stage empty files back out (if the tool produces no output).
2006-12-20 22:03:48 +00:00
James Taylor
ca4a90d1c4
Hide deleted histories so everything looks like the previous version.
2006-12-20 21:58:51 +00:00
James Taylor
a11d9618cf
Whoa, accidently turned on sqlalchemy echoing.
2006-12-20 21:10:52 +00:00
James Taylor
5b4c0bee7b
Log first 32K of job stdout and stderr to job table.
2006-12-20 21:09:09 +00:00
Anton Nekrutenko
c879bae96f
TRUNK:More fixes for uniq and STDERR printout
2006-12-20 19:15:54 +00:00
Anton Nekrutenko
90fe4385d1
TRUNK:a Typo
2006-12-20 02:52:00 +00:00
Anton Nekrutenko
c16dc08e00
TRUNK:More cut changes
2006-12-20 02:44:02 +00:00
Anton Nekrutenko
b840959a1c
TRUNK:This trunk/brunch stuff is VERY confusing. Again: Fix for uniq (count). No more leading spaces
2006-12-20 01:53:04 +00:00
Anton Nekrutenko
37d815d298
Trunk:Fix for uniq (count). No more leading spaces
2006-12-20 01:26:58 +00:00
Anton Nekrutenko
cea78e73f7
Fix for uniq (count). No more leading spaces
2006-12-20 01:23:07 +00:00
James Taylor
7a3e6d9b96
Fixes for biomart in the trunk.
2006-12-19 19:38:42 +00:00
Anton Nekrutenko
5a226c32ea
Trunk: Forgot the pic. Got rid of the lock. Now a picture will be updated monthly
2006-12-19 02:08:59 +00:00
Anton Nekrutenko
1b3c3e6fe8
Trunk: Got rid of the lock. Now a picture will be updated monthly
2006-12-19 02:08:03 +00:00
Nate Coraor
5d3e026ffe
Allow for stagein/stageout rather than relying on nfs for pbs runs.
2006-12-18 23:44:09 +00:00
Anton Nekrutenko
73b53ba17c
for Trunk: Updated gops text; added links to screencasts; made join and compare smarter so they look up column numbers from datasets
2006-12-18 21:35:43 +00:00
Anton Nekrutenko
32106fd6d5
cut for trunk
2006-12-18 18:38:37 +00:00
James Taylor