Guruprasad Anada
b45b74f3ec
Fixes to get functional tests working.
2009-02-03 18:34:27 -05:00
Guruprasad Anada
1f62ffbb01
Adding modified hyphy functional test output files, which have changed as the new version of HYPHY is installed on Galaxy. Also changing version numbers for all the affected tools.
2009-01-27 16:17:22 -05:00
Greg Von Kuster
04e0834500
Revert 2715.
2008-06-04 13:02:15 +00:00
Greg Von Kuster
dedc7278a1
Requires config change, temporary files are now created in a configurable location - affects many tools.
2008-06-03 20:29:54 +00:00
Nate Coraor
f53cb1d7f1
Added tool dependencies to xml.
2008-04-25 19:40:16 +00:00
Nate Coraor
8e46b08fb9
Remove hardcoded HYPHY path. HYPHY should now be a directory under
...
tool-data (or in our case, a symlink to the real HYPHY dir).
2008-04-18 19:01:57 +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
af3b0669aa
Eliminated all Python2.4 references, added necessary assert statements to ensure minimum version of Python 2.4.
2008-03-28 15:24:50 +00:00
Greg Von Kuster
717c9d8107
Fixes for functional tests for several tools.
...
- Select list control options require a "value" attribute, not a "values" attribute.
- Corrected the test data for 2 tests that probably have never worked - Dan, please verify!
- Improved the information displayed ( in most cases ) if a test fails.
2008-03-26 19:07:15 +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
073d392616
Added tool version directories for hyphy tools, also added galaxy/tools/util directory to house utility code used acroos multiple tools.
2008-02-22 16:50:12 +00:00
Guruprasad Anada
a9cf68821e
Minor modifications to HYPHY dN/dS tool.
...
Ran functional test and added new test data.
2008-01-23 16:17:30 +00:00
Guruprasad Anada
1e1474fdde
Adding HYPHY tool to compute dN/dS ratio.
2007-07-11 20:05:20 +00:00
Daniel Blankenberg
f8b0ab3f88
Add pairwise maf extractor for converted AXTs, add
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interval_to_maf_merged, and a whole bunch of MAF updates.
2007-05-16 18:42:34 +00:00
Daniel Blankenberg
323041dba0
HYPHY nj tree builder now also makes species-only-labeled trees as well
...
as others.
2007-04-06 13:58:24 +00:00
Daniel Blankenberg
f8cd6433d2
Clean up comment.
2007-04-04 15:57:44 +00:00
Daniel Blankenberg
5f1b12b56e
Add neighbor joining tree building via HYPHY.
2007-04-04 15:44:37 +00:00
Daniel Blankenberg
429feed14d
Fix branch lengths test.
2007-03-13 19:43:38 +00:00
Daniel Blankenberg
005a444f9c
Add HYPHY branch lengths tool.
2007-03-13 18:23:08 +00:00
Guruprasad Anada