Dannon Baker
c733ce370b
Fix path insertion vs appending of <galaxy>/lib for all scripts.
2015-02-12 10:34:51 -05:00
Nate Coraor
29dda3e11a
Remove GeneTrack remnants.
2015-01-28 16:29:21 -05:00
Dave Bouvier
5bdb75aa82
Correct usage of "it's" versus "its".
2014-04-17 15:49:32 -04:00
Nate Coraor
126c02eb71
Experimental/alpha/in-development/incomplete object store plugin for iRODS. This plugin will probably set your iRODS instance on fire: do not use except in development/testing.
2013-08-28 16:20:19 -04:00
Nate Coraor
478470e8b0
Testing Python 2.7.
2011-06-08 23:50:07 -04:00
Nate Coraor
f60a292e91
Scramble script for bx-python on Solaris (needs some C99 defines).
2011-04-18 16:40:43 -04:00
Nate Coraor
92de52f6e0
Fixes for scrambling python-daemon and pysam.
2011-02-09 16:29:50 -05:00
Nate Coraor
6e1ed92e79
Minor fixes for scrambling and dist-scrambling
2010-08-17 09:29:38 -04:00
Nate Coraor
85c6a3193a
Upgrade pbs_python to 4.1.0 and use PBS exit_status (if keep_completed is set) so we can detect PBS failures. This is a reapplication of 3786:48432330228e, which was backed out in a subsequent revision due to crashes experienced in pbs_python 2.9.8.
2010-07-19 12:29:53 -04:00
Nate Coraor
8c872c16e7
Add numpy egg, update bx_python egg (now with 100% more numpy) and include code that allows scrambling to depend on other eggs existing and being importable.
2010-03-15 14:35:35 -04:00
Nate Coraor
b10c2324f5
Update psycopg2 to 2.0.13/postgresql 8.4.2
2010-03-09 14:13:05 -05:00
Nate Coraor
4a0c9b3175
I am having a bad day
2010-03-02 12:10:43 -05:00
Nate Coraor
1b8bcabd1e
pbs_python 2.9.8 doesn't work
2010-03-02 12:08:01 -05:00
Nate Coraor
9b912184d0
Scratch that, just upgrade pbs_python instead
2010-03-02 11:52:16 -05:00
Nate Coraor
a0bd85dbb3
Use the old method for fixing pbs_python's version
2010-03-02 11:37:55 -05:00
Nate Coraor
9a8c5f6711
psycopg2 scramble fix
2010-03-02 00:38:57 -05:00
Nate Coraor
006716f53a
Egg support overhaul, introduces a number of fixes to the ABI recognition, better build scripts, a rewrite of the eggs library and eliminition of the need for python -ES
2010-03-01 15:41:30 -05:00
Nate Coraor
bb6a16d1f4
Fix MySQL_python static egg on OS X
2010-02-19 14:34:25 -05:00
Nate Coraor
a3aaa1e780
Fix libdrmaa runtime link path on OS X
2009-12-09 10:15:15 -05:00
Nate Coraor
a3d62f4036
Explicitly check eggs and fetch when starting, instead of relying on automatic in-process fetching. Also contains a fix for pysqlite egg building
2009-11-16 14:42:09 -05:00
Nate Coraor
588ea5e038
Update PySQLite to latest version. This resolves bitbucket issue #101
2009-11-13 17:08:12 -05:00
Nate Coraor
1561cd8af8
Upgrade Paste/PasteDeploy/PasteScript. Paste can go no further without changing the way we stream templates and tarballs.
2009-11-12 13:12:12 -05:00
Nate Coraor
56032de2bd
Upgrade to Cheetah 2.2.2
2009-11-10 13:47:34 -05:00
Nate Coraor
29694cda88
Fix for GeneTrack egg
2009-11-06 14:23:21 -05:00
Nate Coraor
d0769e236a
Add the GeneTrack egg. Also includes some enhancements and cleanup of the eggs/fetch/scramble code.
2009-11-04 12:58:48 -05:00
Nate Coraor
8b0dcb7e4d
Fixes for native Leopard Python eggs
2009-04-22 14:43:54 -04:00
Nate Coraor
aafccaa367
Use LD_RUN_PATH when building pbs_python
2008-10-30 16:11:44 -04:00
Nate Coraor
32e98de2b7
Fix pbs_python to just use existing torque.
2008-10-29 17:20:54 -04:00
Nate Coraor
83daeb74bb
It doesn't make sense to even distribute DRMAA_python eggs. So instead
...
of downloading its own SGE and linking, scramble now just links to a
user-supplied SGE in $SGE_ROOT.
Added a seperate script to make it build right on sparc/x86 32/64
Solaris.
2008-05-30 20:18:03 +00:00
Nate Coraor
04127ff3d5
DRMAA build scripts, eggs.ini entry.
...
And a minor bugfix to eggs.require.
2008-04-16 20:53:27 +00:00
Nate Coraor
746fa583d0
Update pkg_resources to 0.6c8 to fix the cygwin non-executable dll
...
bug. Also, fix the setup script to create database/tmp and
database/files.
2008-04-14 19:25:35 +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
Nate Coraor
feff769b6f
Build script for Cheetah on Python 2.5.
2008-04-04 13:38:46 +00:00
Nate Coraor
83389f54eb
pbs_python egg changed from static to dynamic for the reasons explained
...
here:
http://g2.trac.bx.psu.edu/wiki/ClusteringGalaxy#Anoteonlibtorque
Also includes a rather ridiculous fix for compiling a fat dynamic
libtorque on OS X due to some autoconf/libtool weirdness.
2008-03-28 21:22:10 +00:00
Nate Coraor
5f189e45c3
The enormous eggs-out-of-svn commit. More details at:
...
http://g2.trac.bx.psu.edu/wiki/GalaxyEggs
2008-03-27 19:27:05 +00:00
Dannon Baker