details: http://www.bx.psu.edu/hg/galaxy/rev/db7ee1dc19c4 changeset: 3462:db7ee1dc19c4 user: Nate Coraor <nate@bx.psu.edu> date: Tue Mar 02 11:52:16 2010 -0500 description: Scratch that, just upgrade pbs_python instead diffstat: eggs.ini | 2 +- lib/galaxy/eggs/scramble.py | 2 +- scripts/scramble/patches/pbs_python/setup.py | 64 ---------------------------- scripts/scramble/scripts/pbs_python.py | 3 - 4 files changed, 2 insertions(+), 69 deletions(-) diffs (105 lines): diff -r cb10a08016eb -r db7ee1dc19c4 eggs.ini --- a/eggs.ini Tue Mar 02 11:37:55 2010 -0500 +++ b/eggs.ini Tue Mar 02 11:52:16 2010 -0500 @@ -16,7 +16,7 @@ Cheetah = 2.2.2 DRMAA_python = 0.2 MySQL_python = 1.2.3c1 -pbs_python = 2.9.4 +pbs_python = 2.9.8 psycopg2 = 2.0.6 pycrypto = 2.0.1 pysam = 0.1.1 diff -r cb10a08016eb -r db7ee1dc19c4 lib/galaxy/eggs/scramble.py --- a/lib/galaxy/eggs/scramble.py Tue Mar 02 11:37:55 2010 -0500 +++ b/lib/galaxy/eggs/scramble.py Tue Mar 02 11:52:16 2010 -0500 @@ -56,7 +56,7 @@ self.run_scramble_script() new_egg = os.path.join( self.buildpath, 'dist', os.path.basename( self.distribution.location ) ) if not os.path.exists( new_egg ): - raise ScrambleFailure( self, "%s(): Egg build for %s did not appear to fail, but no egg found to copy from expected path:\n %s" % ( sys._getframe().f_code.co_name, self.name, egg_name ) ) + raise ScrambleFailure( self, "%s(): Egg build for %s did not appear to fail, but no egg found to copy from expected path:\n %s" % ( sys._getframe().f_code.co_name, self.name, new_egg ) ) shutil.copyfile( new_egg, self.distribution.location ) log.warning( "%s(): Copied egg to:" % sys._getframe().f_code.co_name ) log.warning( " %s" % self.distribution.location ) diff -r cb10a08016eb -r db7ee1dc19c4 scripts/scramble/patches/pbs_python/setup.py --- a/scripts/scramble/patches/pbs_python/setup.py Tue Mar 02 11:37:55 2010 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,64 +0,0 @@ -#!/usr/bin/env python -# -# $Id: setup.py 434 2005-11-04 15:02:07Z bas $ -# -# set ts=4 -# - -import sys -import os - -from distutils.core import setup, Extension - -# Try some usefule defaults if not set -# -PBS_LIB_DIR='/opt/local/lib' -NEW_BUILD_SYSTEM=1 - -if not PBS_LIB_DIR: - for dir in ['/usr/lib', '/usr/local/lib', '/opt/pbs/usr/lib', '/usr/lib/torque', '/opt/pbs/lib', '/opt/torque/lib' ]: - dummy_new = os.path.join(dir, 'libtorque.so') - dummy_old = os.path.join(dir, 'libpbs.a') - if os.path.exists(dummy_new): - PBS_LIB_DIR=dir - break - elif os.path.exists(dummy_old): - PBS_LIB_DIR=dir - NEW_BUILD_SYSTEM=0 - break - -if not PBS_LIB_DIR: - print 'Please specify where the PBS libraries are!!' - print 'edit setup.py and fill in the PBS_LIB_DIR variable' - sys.exit(1) - -# Test if we have all the libs: -# -if NEW_BUILD_SYSTEM: - LIBS = ['torque'] -else: - LIBS = ['log', 'net', 'pbs'] - for lib in LIBS: - library = 'lib%s.a' %(lib) - dummy = os.path.join(PBS_LIB_DIR, library) - if not os.path.exists(dummy): - print 'You need to install "%s" in %s' %(library, PBS_LIB_DIR) - sys.exit(1) - -setup ( name = 'pbs_python', - version = '2.9.4', - description = 'openpbs/torque python interface', - author = 'Bas van der Vlies', - author_email = 'basv@sara.nl', - url = 'http://www.sara.nl/index_eng.html', - - extra_path = 'pbs', - package_dir = { '' : 'src' }, - py_modules = [ 'pbs', 'PBSQuery' ], - - ext_modules = [ - Extension( '_pbs', ['src/pbs_wrap.c'], - library_dirs = [ PBS_LIB_DIR ], - libraries = LIBS) - ] -) diff -r cb10a08016eb -r db7ee1dc19c4 scripts/scramble/scripts/pbs_python.py --- a/scripts/scramble/scripts/pbs_python.py Tue Mar 02 11:37:55 2010 -0500 +++ b/scripts/scramble/scripts/pbs_python.py Tue Mar 02 11:52:16 2010 -0500 @@ -19,9 +19,6 @@ # the build process doesn't set an rpath for libtorque os.environ['LD_RUN_PATH'] = os.environ['LIBTORQUE_DIR'] -# patch setup.py -shutil.copy( os.path.join( patches, 'pbs_python', 'setup.py' ), 'setup.py' ) - # run the config script run( 'sh configure --with-pbsdir=%s' % os.environ['LIBTORQUE_DIR'], os.getcwd(), 'Running pbs_python configure script' )