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




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).


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




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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