>
> Could you make sure $PYTHONPATH is unset before starting?  There are
>> monkeypatches in lib/galaxy/__init__.py that are supposed to add the -ucsX
>> to the platform string that are apparently not being applied here.
>>
>> Yes, I already checked PYTHONPATH was not set.  I ran the scramble twice
> and on the second time it succeeded, so I continued on. Everything seems to
> be okay.
>


In regards to this, I had to re-install galaxy trying to track down why
logging in isn't working.  I got the bright idea to install galaxy in
galaxy-dist-1, galaxy-dist-2, etc to track what changes I"m making when
something breaks and using the symbolic link galaxy-dist -> the appropriate
instance.  I'm at the point of scrambling pbs_python again and I can
reproduce this problem:

[galaxy@bic galaxy-dist]$ LIBTORQUE_DIR=/usr/lib64 python
scripts/scramble.py -e pbs_python
fetch_one(): Trying to fetch:
  http://eggs.g2.bx.psu.edu/pbs_python/pbs_python-4.1.0.tar.gz
fetch_one(): Fetched to:

/home/galaxy/galaxy-dist-4/scripts/scramble/archives/pbs_python-4.1.0.tar.gz
unpack_source(): Unpacked to:

/home/galaxy/galaxy-dist-4/scripts/scramble/build/py2.6-linux-x86_64-ucs2/pbs_python
copy_build_script(): Using build script
/home/galaxy/galaxy-dist-4/scripts/scramble/scripts/pbs_python.py
run_scramble_script(): Beginning build
run_scramble_script(): Executing in
/home/galaxy/galaxy-dist-4/scripts/scramble/build/py2.6-linux-x86_64-ucs2/pbs_python:
  /share/apps/Python-2.6.7/bin/python scramble.py

---------------------------------------------------------------------------
This script requires setuptools version 0.6c11 to run (even to display
help).  I will attempt to download it for you (from
http://pypi.python.org/packages/2.6/s/setuptools/), but
you may need to enable firewall access for this script first.
I will start the download in 8 seconds.

(Note: if this machine does not have network access, please obtain the file


http://pypi.python.org/packages/2.6/s/setuptools/setuptools-0.6c11-py2.6.egg

and place it in this directory before rerunning this script.)
---------------------------------------------------------------------------
Downloading
http://pypi.python.org/packages/2.6/s/setuptools/setuptools-0.6c11-py2.6.egg
checking for pbs-config... /usr/lib64/../bin/pbs-config
Found torque version: 2.5.9
checking for python... /share/apps/Python-2.6.7/bin/python
checking for python version... 2.6
checking for python platform... linux2
checking for python script directory...
${prefix}/lib/python2.6/site-packages
checking for python extension module directory...
${exec_prefix}/lib/python2.6/site-packages
configure: creating ./config.status
config.status: creating Makefile
config.status: creating setup.py
scramble(): Patching setup.py
running egg_info
creating src/pbs_python.egg-info
writing src/pbs_python.egg-info/PKG-INFO
writing top-level names to src/pbs_python.egg-info/top_level.txt
writing dependency_links to src/pbs_python.egg-info/dependency_links.txt
writing manifest file 'src/pbs_python.egg-info/SOURCES.txt'
reading manifest file 'src/pbs_python.egg-info/SOURCES.txt'
writing manifest file 'src/pbs_python.egg-info/SOURCES.txt'
running bdist_egg
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
creating build
creating build/lib.linux-x86_64-2.6
copying src/pbs.py -> build/lib.linux-x86_64-2.6
copying src/PBSQuery.py -> build/lib.linux-x86_64-2.6
running build_ext
building '_pbs' extension
creating build/temp.linux-x86_64-2.6
creating build/temp.linux-x86_64-2.6/src
gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall
-Wstrict-prototypes -fPIC -DTORQUE_2_4
-I/share/apps/Python-2.6.7/include/python2.6 -c src/pbs_wrap.c -o
build/temp.linux-x86_64-2.6/src/pbs_wrap.o
src/pbs_wrap.c:2622: warning: function declaration isn't a prototype
src/pbs_wrap.c:2630: warning: function declaration isn't a prototype
gcc -pthread -shared build/temp.linux-x86_64-2.6/src/pbs_wrap.o
-L/usr/lib64 -ltorque -o build/lib.linux-x86_64-2.6/_pbs.so
creating build/bdist.linux-x86_64
creating build/bdist.linux-x86_64/egg
copying build/lib.linux-x86_64-2.6/pbs.py -> build/bdist.linux-x86_64/egg
copying build/lib.linux-x86_64-2.6/PBSQuery.py ->
build/bdist.linux-x86_64/egg
copying build/lib.linux-x86_64-2.6/_pbs.so -> build/bdist.linux-x86_64/egg
byte-compiling build/bdist.linux-x86_64/egg/pbs.py to pbs.pyc
byte-compiling build/bdist.linux-x86_64/egg/PBSQuery.py to PBSQuery.pyc
creating stub loader for _pbs.so
byte-compiling build/bdist.linux-x86_64/egg/_pbs.py to _pbs.pyc
creating build/bdist.linux-x86_64/egg/EGG-INFO
copying src/pbs_python.egg-info/PKG-INFO ->
build/bdist.linux-x86_64/egg/EGG-INFO
copying src/pbs_python.egg-info/SOURCES.txt ->
build/bdist.linux-x86_64/egg/EGG-INFO
copying src/pbs_python.egg-info/dependency_links.txt ->
build/bdist.linux-x86_64/egg/EGG-INFO
copying src/pbs_python.egg-info/top_level.txt ->
build/bdist.linux-x86_64/egg/EGG-INFO
writing build/bdist.linux-x86_64/egg/EGG-INFO/native_libs.txt
zip_safe flag not set; analyzing archive contents...
creating dist
creating 'dist/pbs_python-4.1.0-py2.6-linux-x86_64.egg' and adding
'build/bdist.linux-x86_64/egg' to it
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
Traceback (most recent call last):
  File "scripts/scramble.py", line 50, in <module>
    egg.scramble()
  File "/home/galaxy/galaxy-dist-4/lib/galaxy/eggs/scramble.py", line 60,
in scramble
    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 ) )
galaxy.eggs.scramble.ScrambleFailure: scramble(): Egg build for pbs_python
did not appear to fail, but no egg found to copy from expected path:

/home/galaxy/galaxy-dist-4/scripts/scramble/build/py2.6-linux-x86_64-ucs2/pbs_python/dist/pbs_python-4.1.0-py2.6-linux-x86_64-ucs2.egg
[galaxy@bic galaxy-dist]$ echo $PYTHONPATH

[galaxy@bic galaxy-dist]$
[galaxy@bic galaxy-dist]$ LIBTORQUE_DIR=/usr/lib64 python
scripts/scramble.py -e pbs_python
fetch_one(): Using existing source, remove to download again:

/home/galaxy/galaxy-dist-4/scripts/scramble/archives/pbs_python-4.1.0.tar.gz
unpack_source(): Removing old build directory at:

/home/galaxy/galaxy-dist-4/scripts/scramble/build/py2.6-linux-x86_64-ucs2/pbs_python
unpack_source(): Unpacked to:

/home/galaxy/galaxy-dist-4/scripts/scramble/build/py2.6-linux-x86_64-ucs2/pbs_python
copy_build_script(): Using build script
/home/galaxy/galaxy-dist-4/scripts/scramble/scripts/pbs_python.py
run_scramble_script(): Beginning build
run_scramble_script(): Executing in
/home/galaxy/galaxy-dist-4/scripts/scramble/build/py2.6-linux-x86_64-ucs2/pbs_python:
  /share/apps/Python-2.6.7/bin/python scramble.py
checking for pbs-config... /usr/lib64/../bin/pbs-config
Found torque version: 2.5.9
checking for python... /share/apps/Python-2.6.7/bin/python
checking for python version... 2.6
checking for python platform... linux2
checking for python script directory...
${prefix}/lib/python2.6/site-packages
checking for python extension module directory...
${exec_prefix}/lib/python2.6/site-packages
configure: creating ./config.status
config.status: creating Makefile
config.status: creating setup.py
scramble(): Patching setup.py
running egg_info
creating src/pbs_python.egg-info
writing src/pbs_python.egg-info/PKG-INFO
writing top-level names to src/pbs_python.egg-info/top_level.txt
writing dependency_links to src/pbs_python.egg-info/dependency_links.txt
writing manifest file 'src/pbs_python.egg-info/SOURCES.txt'
reading manifest file 'src/pbs_python.egg-info/SOURCES.txt'
writing manifest file 'src/pbs_python.egg-info/SOURCES.txt'
running bdist_egg
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
creating build
creating build/lib.linux-x86_64-2.6
copying src/pbs.py -> build/lib.linux-x86_64-2.6
copying src/PBSQuery.py -> build/lib.linux-x86_64-2.6
running build_ext
building '_pbs' extension
creating build/temp.linux-x86_64-2.6
creating build/temp.linux-x86_64-2.6/src
gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall
-Wstrict-prototypes -fPIC -DTORQUE_2_4
-I/share/apps/Python-2.6.7/include/python2.6 -c src/pbs_wrap.c -o
build/temp.linux-x86_64-2.6/src/pbs_wrap.o
src/pbs_wrap.c:2622: warning: function declaration isn't a prototype
src/pbs_wrap.c:2630: warning: function declaration isn't a prototype
gcc -pthread -shared build/temp.linux-x86_64-2.6/src/pbs_wrap.o
-L/usr/lib64 -ltorque -o build/lib.linux-x86_64-2.6/_pbs.so
creating build/bdist.linux-x86_64
creating build/bdist.linux-x86_64/egg
copying build/lib.linux-x86_64-2.6/pbs.py -> build/bdist.linux-x86_64/egg
copying build/lib.linux-x86_64-2.6/PBSQuery.py ->
build/bdist.linux-x86_64/egg
copying build/lib.linux-x86_64-2.6/_pbs.so -> build/bdist.linux-x86_64/egg
byte-compiling build/bdist.linux-x86_64/egg/pbs.py to pbs.pyc
byte-compiling build/bdist.linux-x86_64/egg/PBSQuery.py to PBSQuery.pyc
creating stub loader for _pbs.so
byte-compiling build/bdist.linux-x86_64/egg/_pbs.py to _pbs.pyc
creating build/bdist.linux-x86_64/egg/EGG-INFO
copying src/pbs_python.egg-info/PKG-INFO ->
build/bdist.linux-x86_64/egg/EGG-INFO
copying src/pbs_python.egg-info/SOURCES.txt ->
build/bdist.linux-x86_64/egg/EGG-INFO
copying src/pbs_python.egg-info/dependency_links.txt ->
build/bdist.linux-x86_64/egg/EGG-INFO
copying src/pbs_python.egg-info/top_level.txt ->
build/bdist.linux-x86_64/egg/EGG-INFO
writing build/bdist.linux-x86_64/egg/EGG-INFO/native_libs.txt
zip_safe flag not set; analyzing archive contents...
creating dist
creating 'dist/pbs_python-4.1.0-py2.6-linux-x86_64-ucs2.egg' and adding
'build/bdist.linux-x86_64/egg' to it
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
scramble(): Copied egg to:

/home/galaxy/galaxy-dist-4/eggs/pbs_python-4.1.0-py2.6-linux-x86_64-ucs2.egg


So, I do in fact need to scramble it twice to work...
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