Daniel Blankenberg
86f0862aa4
Move ucsc and gbrowse data from static to tool-data/shared.
...
Cron scripts on test and main will need to be updated when the server is.
GOPS complement tool and annotation profiler will now correctly use chromosome lengths files if available.
2008-06-03 18:53:26 +00:00
Greg Von Kuster
fab2f2dcca
Corrected the way we handle exceptions in the gops tools when building / using bitsets dictionaries. Added several new functional tests.
2008-05-23 20:43:20 +00:00
Greg Von Kuster
bf0a8cc462
Added another wrapper around bx to handle exceptions, all gops tools affected. Added 2 new tests to gops_intersect.
2008-05-07 14:07:23 +00:00
Nate Coraor
7560751dc8
Separate framework and tool environments.
...
Whether running locally or via PBS, $PATH should now be handled in your
user's environment.
This also fixes problems like PYTHONPATH on the new blast nodes being
wrong (because they are x86_64 and the frontends are i686).
Note that you can actually start Galaxy without having an eggs dir now.
2008-04-11 20:11:21 +00:00
Greg Von Kuster
135c9a0377
Removed the remainder of the tool version subdirectories.
2008-03-03 18:38:57 +00:00
Greg Von Kuster
99bc8db3fd
Added tool version directories to new_operations tools directory.
2008-02-22 19:23:18 +00:00
James Taylor
09db8088dd
Cleanup: removing the cookbook package. Bunch and odict move to galaxy.util, tools
...
that use doc_optparse should now get it from bx-python. In general tools should never
import things from inside Galaxy's lib directory.
2007-07-31 15:45:59 +00:00
Ian Schenck
ab162d938a
Operations now won't fail on bad data. It skips the lines and tells the user about it. There is a possibility of getting a traceback from python though, along with data in the file, which won't change the job state to ERROR. How is this accomplished? Oh yeah...closes out ticket 135.
2007-05-30 21:07:33 +00:00
Ian Schenck
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
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
James Taylor
f788a34fca
Moving james-wsgi branch to new trunk.
2006-11-15 16:28:21 +00:00
Daniel Blankenberg