Hi Nate,

The last option you gave worked like a charm! Thank you for your assistance!

Warm regards,
Sonali Amonkar

-----Original Message-----
From: Nate Coraor [mailto:n...@bx.psu.edu] 
Sent: Thursday, January 27, 2011 7:21 PM
To: Sonali Amonkar
Cc: Galaxy Dev
Subject: Re: Error with setuptools version in Galaxy installation on Cluster

Hi Sonali,

Since this is a local installation question, I have moved the discussion to 
galaxy-dev.  Further responses are inline below.

Sonali Amonkar wrote:
> Hi,
> 
> First of all I would like to appreciate the clean and neat documentation 
> written for the Galaxy setup for Cluster.
> 
> I am attempting to install Galaxy on Penguin cluster with Torque PBS manager.
> While following the steps I came across an error as below:
> 
> ======================================================================
> ======================================================================
> =============== [user@server pbs_python]$ /galaxy/Python-2.4.6/python 
> scramble.py
> 
> ----------------------------------------------------------------------
> ----- This script requires setuptools version 0.6c12 to run (even to 
> display help).  I will attempt to download it for you (from 
> http://pypi.python.org/packages/2.4/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/2.4/s/setuptools/setuptools-0.6c12-py2
> .4.egg
> 
> and place it in this directory before rerunning this script.)
> ----------------------------------------------------------------------
> ----- Downloading 
> http://pypi.python.org/packages/2.4/s/setuptools/setuptools-0.6c12-py2
> .4.egg
> Traceback (most recent call last):
>   File "scramble.py", line 14, in ?
>     from scramble_lib import *
>   File "../../../lib/scramble_lib.py", line 150, in ?
>     use_setuptools( download_delay=8, to_dir=os.path.dirname( __file__ ) )
>   File 
> "/galaxy/galaxy-dist/scripts/scramble/build/py2.4-linux-x86_64-ucs2/pbs_python/ez_setup.py",
>  line 92, in use_setuptools
>     return do_download()
>   File 
> "/galaxy/galaxy-dist/scripts/scramble/build/py2.4-linux-x86_64-ucs2/pbs_python/ez_setup.py",
>  line 70, in do_download
>     egg = download_setuptools(version, download_base, to_dir, download_delay)
>   File 
> "/galaxy/galaxy-dist/scripts/scramble/build/py2.4-linux-x86_64-ucs2/pbs_python/ez_setup.py",
>  line 131, in download_setuptools
>     src = urllib2.urlopen(url)
>   File "/galaxy/Python-2.4.6/Lib/urllib2.py", line 130, in urlopen
>     return _opener.open(url, data)
>   File "/galaxy/Python-2.4.6/Lib/urllib2.py", line 364, in open
>     response = meth(req, response)
>   File "/galaxy/Python-2.4.6/Lib/urllib2.py", line 471, in http_response
>     response = self.parent.error(
>   File "/galaxy/Python-2.4.6/Lib/urllib2.py", line 402, in error
>     return self._call_chain(*args)
>   File "/galaxy/Python-2.4.6/Lib/urllib2.py", line 337, in _call_chain
>     result = func(*args)
>   File "/galaxy/Python-2.4.6/Lib/urllib2.py", line 480, in http_error_default
>     raise HTTPError(req.get_full_url(), code, msg, hdrs, fp)
> urllib2.HTTPError: HTTP Error 404: Not Found 
> ======================================================================
> ======================================================================
> ===============
> 
> 
> The scramble script here is trying to download an egg which does not exist at 
> the location (try opening the link it is trying to download in a browser - 
> you'll get 404, then see the parent directory - 
> http://pypi.python.org/packages/2.4/s/setuptools/ you'll see last version 
> available i.e. 0.6c11).
> 

Hi Sonali,

0.6c12 is still in development and I'm not sure where this is coming from.  The 
version of ez_setup.py in:

  /galaxy/galaxy-dist/scripts/scramble/lib/

references 0.6c11, and this file is copied to the build directory in:

  galaxy-dist/scripts/scramble/build/py2.4-linux-x86_64-ucs2/pbs_python/

What's the value of DEFAULT_VERSION in:

  
/galaxy/galaxy-dist/scripts/scramble/build/py2.4-linux-x86_64-ucs2/pbs_python/ez_setup.py

?

> If we try to download the last version of setuptools 0.6c11 and rename it to 
> the latest version (desperate attempt to make it work), that doesn't work 
> either.
> 
> ======================================================================
> ======================================================================
> =============== [user@server pbs_python]$ mv 
> setuptools-0.6c11-py2.4.egg setuptools-0.6c12-py2.4.egg
> 
> [user@server pbs_python]$ /galaxy/Python-2.4.6/python scramble.py 
> checking for pbs-config... /usr/lib64/../bin/pbs-config Found torque 
> version: 2.4.0-snap.200812091621 checking for python... 
> /galaxy/Python-2.4.6/python checking for python version... 2.4 
> checking for python platform... linux2 checking for python script 
> directory... ${prefix}/lib/python2.4/site-packages
> checking for python extension module directory... 
> ${exec_prefix}/lib/python2.4/site-packages
> configure: creating ./config.status
> config.status: creating Makefile
> config.status: creating setup.py
> scramble(): Patching setup.py
> Traceback (most recent call last):
>   File "scramble.py", line 49, in ?
>     execfile( "setup.py", globals(), locals() )
>   File "setup.py", line 32, in ?
>     build_version = int(tmp[2])
> ValueError: invalid literal for int(): 0-snap
> 
> ======================================================================
> ======================================================================
> ===============

This is a problem with your TORQUE version and pbs_python's assumptions about 
its version numbering.  pbs_python expects it to be all-numeric whereas yours 
is a development snapshot with a non-integer value in the revision portion of 
the version (2.4.0-snap.200812091621).
                                     ^^^^^^^^^^^^^^^^^^^

There are a few ways to proceed.  One would be to upgrade your TORQUE client to 
a release version.  Another would be to try the drmaa job runner instead of 
pbs, since TORQUE provides a DRMAA C library, although I don't believe anyone 
has used it with TORQUE yet.

The last would be to modify pbs_python's build process.  Start by changing 
directories to:

  /galaxy/galaxy-dist/scripts/scramble/build/py2.4-linux-x86_64-ucs2/pbs_python

Edit setup.py and comment all of the following:

#VERSION = "2.4.0-snap.200812091621"
#tmp = VERSION.split('.')

#major_version = int(tmp[0])
#minor_version = int(tmp[1])
#build_version = int(tmp[2])

#if major_version  >= 2 and minor_version >= 4 and build_version >= 7:
#    os.symlink('pbs_wrap_2.4.c', 'pbs_wrap.c')
#    os.symlink('pbs_2.4.py', 'pbs.py')
#    TORQUE_VERSION='TORQUE_2_4'
#else:

And then force the old version by un-indenting or doing something silly
like:

if True:
    os.symlink('pbs_wrap_2.1.c', 'pbs_wrap.c')
    os.symlink('pbs_2.1.py', 'pbs.py')
    TORQUE_VERSION='TORQUE_OLD'

However, running scramble.py again will overwrite your changes, so you will 
also need to modify scramble.py (in the same directory, not the main 
scramble.py in /galaxy/galaxy-dist/scripts) and comment out:

#run( 'sh configure --with-pbsdir=%s' % os.environ['LIBTORQUE_DIR'], 
os.getcwd(), 'Running pbs_python configure script' )

Once this is done you should be able to run the *LOCAL* scramble.py in the 
build directory:

  $ /galaxy/Python-2.4.6/python ./scramble.py

If this succeeds, the egg will be built and placed in the dist/ subdirectory.  
The egg can then be copied to:

  /galaxy/galaxy-dist/eggs/

Please let us know how this goes.

--nate

> 
> Do let me know if anyone else has faced this issue of the scramble script 
> trying to download a wrong version? Greatly appreciate your time.
> 
> Warm Regards,
> Sonali Amonkar
> 
> 
> 
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