Question: Error With Setuptools Version In Galaxy Installation On Cluster
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gravatar for Sonali Amonkar
6.1 years ago by
Sonali Amonkar150 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/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 ====================================================================== ====================================================================== =============== 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 DISCLAIMER ========== This e-mail may contain privileged and confidential information which is the property of Persistent Systems Ltd. It is intended only for the use of the individual or entity to which it is addressed. If you are not the intended recipient, you are not authorized to read, retain, copy, print, distribute or use this message. If you have received this communication in error, please notify the sender and delete all copies of this message. Persistent Systems Ltd. does not accept any liability for virus infected mails.
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