Nicola Soranzo
69cda48690
Remove remaining references to galaxy.eggs . flake8 some files in tools/ .
2015-10-26 19:29:13 +00:00
Daniel Blankenberg
5e3e287ce3
Update MAF to BED to use job working directory and built-in primary dataset collection.
2014-04-18 13:23:38 -04:00
Daniel Blankenberg
87938b9894
Fix MAF to BED tool. This tool should be rewritten to not use a code file, but instead use one of the standard ways to create additional outputs, similar to how maf_to_interval functions.
2009-11-30 15:33:45 -05:00
Greg Von Kuster
5657e61320
Misc tool cleanup: eliminated all references to python2.3 / python2.4, imported galaxy eggs in several missed tools. Commented Pattern Matching tool section from tool_conf.xml.sample since tool is not functional. Added job runner info for short read tools in universe_wsgi.ini.sample.
2008-04-25 13:04:55 +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
4dd1f044e1
Removed tool version directiories for some of the tools...the rest soon.
2008-03-03 16:14:06 +00:00
Greg Von Kuster
a2f475b55a
Added tool version directories for maf tool directory.
2008-02-22 18:35:01 +00:00
Daniel Blankenberg
49566ee14f
Forgot to import tempfile in maf_to_bed.py. Used when creating multiple
...
output BED files (not supported by testing framework).
2008-02-05 16:37:49 +00:00
Daniel Blankenberg
5b1552ffa8
Fix memory issues when dealing with MAF tools.
...
Add new bx-python eggs.
Reorganize all MAF tools into a unified directory, and update tool_conf.
Remember to update tool_conf.xml from one of the samples (tool_conf.xml.sample or tool_conf.xml.main).
2008-01-16 18:01:09 +00:00
Nicola Soranzo