I'd say I'm an intermediate Linux user. I'm trying to get Galaxy setup on a new install of CentOS. Python 2.7 is installed. Following the instructions at https://wiki.galaxyproject.org/Admin/GetGalaxy .Things start initializing just fine when I run sh run.sh, but then I hit this error:
<snip>
Initializing tool-data/twobit.loc from twobit.loc.sample
Initializing static/welcome.html from welcome.html.sample
Some eggs are out of date, attempting to fetch...
Fetched http://eggs.galaxyproject.org/Mako/Mako-0.4.1-py2.7.egg
Fetched http://eggs.galaxyproject.org/Whoosh/Whoosh-0.3.18-py2.7.egg
Fetched http://eggs.galaxyproject.org/Parsley/Parsley-1.1-py2.7.egg
Fetched http://eggs.galaxyproject.org/Cheetah/Cheetah-2.2.2-py2.7-linux-x86_64-u cs4.egg
Fetched http://eggs.galaxyproject.org/sqlalchemy_migrate/sqlalchemy_migrate-0.7. 2-py2.7.egg
Fetched http://eggs.galaxyproject.org/NoseHTML/NoseHTML-0.4.1-py2.7.egg
Fetched http://eggs.galaxyproject.org/pexpect/pexpect-2.4-py2.7.egg
Fetched http://eggs.galaxyproject.org/PasteDeploy/PasteDeploy-1.5.0-py2.7.egg
Fetched http://eggs.galaxyproject.org/WebHelpers/WebHelpers-1.3-py2.7.egg
Traceback (most recent call last):
File "./scripts/fetch_eggs.py", line 46, in <module>
c.resolve() # Only fetch eggs required by the config
File "/home/stewarpa/galaxy-dist/lib/galaxy/eggs/__init__.py", line 347, in re solve
egg.resolve()
File "/home/stewarpa/galaxy-dist/lib/galaxy/eggs/__init__.py", line 197, in re solve
return self.version_conflict( e.args[0], e.args[1] )
File "/home/stewarpa/galaxy-dist/lib/galaxy/eggs/__init__.py", line 228, in ve rsion_conflict
r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, egg. fetch )
File "/usr/lib/python2.7/site-packages/pkg_resources.py", line 626, in resolve
raise DistributionNotFound(req)
pkg_resources.DistributionNotFound: Beaker==1.4
Fetch failed.
Traceback (most recent call last):
File "./scripts/paster.py", line 29, in <module>
pkg_resources.require( "Paste" )
File "/home/stewarpa/galaxy-dist/lib/galaxy/eggs/__init__.py", line 416, in re quire
raise EggNotFetchable( str( [ egg.name for egg in e.eggs ] ) )
galaxy.eggs.EggNotFetchable: ['Paste']
I Googled the problem, and it was suggested that someone having similar issues follow the instructions at https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer and try using a virtualenv which apparently gives you a clean slate to work on with Python. I did:
wget http://bitbucket.org/ianb/virtualenv/raw/tip/virtualenv.py
followed by
/usr/bin/python2.7 virtualenv.py --no-site-packages galaxy_env
and get the following:
New python executable in galaxy_env/bin/python2.7
Also creating executable in galaxy_env/bin/python
Installing setuptools.....................
Complete output from command /home/stewarpa/galaxy-dist/gal...on2.7 -c "#!pyth on
\"\"\"Bootstrap setuptoo...
" --always-copy -U setuptools:
Downloading http://pypi.python.org/packages/2.7/s/setuptools/setuptools-0.6c11 -py2.7.egg
Traceback (most recent call last):
File "<string>", line 278, in <module>
File "<string>", line 210, in main
File "<string>", line 158, in download_setuptools
File "/usr/lib64/python2.7/urllib2.py", line 127, in urlopen
return _opener.open(url, data, timeout)
File "/usr/lib64/python2.7/urllib2.py", line 404, in open
response = self._open(req, data)
File "/usr/lib64/python2.7/urllib2.py", line 422, in _open
'_open', req)
File "/usr/lib64/python2.7/urllib2.py", line 382, in _call_chain
result = func(*args)
File "/usr/lib64/python2.7/urllib2.py", line 1216, in http_open
return self.do_open(httplib.HTTPConnection, req)
File "/usr/lib64/python2.7/urllib2.py", line 1186, in do_open
raise URLError(err)
urllib2.URLError: <urlopen error [Errno -2] Name or service not known>
----------------------------------------
...Installing setuptools...done.
Traceback (most recent call last):
File "virtualenv.py", line 1649, in <module>
main()
File "virtualenv.py", line 558, in main
prompt=options.prompt)
File "virtualenv.py", line 654, in create_environment
install_setuptools(py_executable, unzip=unzip_setuptools)
File "virtualenv.py", line 384, in install_setuptools
_install_req(py_executable, unzip)
File "virtualenv.py", line 360, in _install_req
cwd=cwd)
File "virtualenv.py", line 624, in call_subprocess
% (cmd_desc, proc.returncode))
OSError: Command /home/stewarpa/galaxy-dist/gal...on2.7 -c "#!python
\"\"\"Bootstrap setuptoo...
" --always-copy -U setuptools failed with error code 1
I've got no idea what to do from here. Any help would be much appreciated.
Try deleting your eggs folder and then running the fetch directly (make sure to run it on Python 2.7)
I deleted all eggs in ./eggs/, ran
python ./scripts/fetch_eggs.pyand got the following:Traceback (most recent call last):File "./scripts/fetch_eggs.py", line 46, in <module>
c.resolve() # Only fetch eggs required by the config
File "/home/stewarpa/galaxy-dist/lib/galaxy/eggs/__init__.py", line 347, in resolve
egg.resolve()
File "/home/stewarpa/galaxy-dist/lib/galaxy/eggs/__init__.py", line 197, in resolve
return self.version_conflict( e.args[0], e.args[1] )
File "/home/stewarpa/galaxy-dist/lib/galaxy/eggs/__init__.py", line 228, in version_conflict
r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, egg.fetch )
File "/usr/lib/python2.7/site-packages/pkg_resources.py", line 626, in resolve
raise DistributionNotFound(req)
pkg_resources.DistributionNotFound: Mako==0.4.1
Mako was one of the eggs that I deleted that was in the folder if that's any help. Also, I seem to be getting a lot of timeouts when installing other things unrelated to galaxy with yum. Could connectivity be an issue?
Yep, as Bjoern states below it looks like it. It would be next area to explore.
It looks like it's a connection issue. I can keep rerunning
python ./scripts/fetch_eggs.pyand get a few extra eggs each time, but eventually it will timeout and error on me. I've been running this manually all day. Is there an easy way to manually download all of these at once using wget or other so I can just start the server? Thanks!