Question: Error With Setuptools Version In Galaxy Installation On Cluster
0
Sonali Amonkar • 150 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:
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[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/setuptool
s-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
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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.
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[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
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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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