On Feb 1, 2012, at 9:45 AM, Lucilla Luzi wrote:
> Thank you Nate,
>
> maybe there is something that I'm still missing...
>
> When I type what you suggest, I get again an error message that is
>
> $ python scripts/fetch_eggs.py
> Traceback (most recent call last):
> File "scripts/fetch_eggs.py", line 30, in <module>
> c.resolve() # Only fetch eggs required by the config
> File
> "/Users/lluzi/My_programs/Galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py",
> line 345, in resolve
> egg.resolve()
> File
> "/Users/lluzi/My_programs/Galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py",
> line 195, in resolve
> return self.version_conflict( e.args[0], e.args[1] )
> File
> "/Users/lluzi/My_programs/Galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py",
> line 226, in version_conflict
> r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env,
> egg.fetch )
> File
> "/System/Library/Frameworks/Python.framework/Versions/2.6/Extras/lib/python/pkg_resources.py",
> line 518, in resolve
> raise DistributionNotFound(req) # XXX put more info here
> pkg_resources.DistributionNotFound: numpy==1.6.0
>
> Do I correctly understand your suggestion?
>
> Should I manually download all the eggs from your site? If yes, do I need of
> all of them?
> Any other idea to overcome the problem?
It looks like you have a conflicting version of numpy already installed on the
system and Galaxy's conflict resolution code isn't handling this situation.
You may be able to fetch all the eggs with:
% python -ES ./scripts/fetch_eggs.py
If this works and running Galaxy still fails, you may need to set up a
virtualenv as described here:
http://usegalaxy.org/production
Sorry for the inconvenience.
--nate
>
> Thanks again!
> Lu
>
>
>
>
> On 1/30/12 20:37 , Nate Coraor wrote:
>> On Jan 30, 2012, at 1:46 PM, Lucilla Luzi wrote:
>>
>>
>>> Thank you Nate for your reply!! :)
>>>
>>> This is what I got.
>>>
>>> $ python ./scripts/get_platforms.py
>>> macosx-10.6-universal-ucs2
>>>
>>> (just FYI, I run this command from the galaxy-dist folder that has a path
>>> like this one:
>>> /Users/me/My_programs/Galaxy/galaxy-dist/ )
>>>
>> Okay, you should definitely be able to download prebuilt eggs for this
>> platform. Have you tried running python ./scripts/fetch_eggs.py multiple
>> times?
>>
>>
>>> BTW; have you also noticed my message of 25th of January?)
>>>
>> Yes, thanks for the extra info.
>>
>> --nate
>>
>>
>>> Thank you a lot!!
>>> Lu
>>>
>>>
>>> On 1/30/12 18:40 , Nate Coraor wrote:
>>>
>>>> On Jan 24, 2012, at 4:16 PM, Lucilla Luzi wrote:
>>>>
>>>>
>>>>
>>>>> ERRATA CORRIGE: sorry :(
>>>>>
>>>>> $ echo $PATH
>>>>> /System/Library/Frameworks/Python.framework/Versions/2.6/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin
>>>>>
>>>>> -------- Original Message --------
>>>>> Subject: [galaxy-dev] Some eggs are out of date...Fetch failed (Mac
>>>>> OS X 10.6)
>>>>> Date: Tue, 24 Jan 2012 22:06:42 +0100
>>>>>
>>>>>
>>>>> Hi,
>>>>>
>>>>> I'm pretty new to Galaxy, at least to this side.
>>>>> I'm sorry to bother you with my issue, that, I read, was quite
>>>>> extensively discussed previously, but even if I think to have followed
>>>>> correctly the instruction and further suggestions, I'm still not able to
>>>>> overcome the problem.
>>>>>
>>>>> I'm trying to install a local instance of Galaxy on my MAC (OS X10.6.8)
>>>>> My Python version is 2.6.1 and I just installed Mercurial 2.0.2 for MacOS
>>>>> X 10.6.
>>>>>
>>>>> FYI
>>>>>
>>>>> $ python --version
>>>>> Python 2.6.1
>>>>>
>>>>> --->> wrong <<---see above
>>>>> $ echo $PATH
>>>>> /Users/myName/System/Library/Frameworks/Python.framework/Versions/2.6/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin
>>>>>
>>>>> When I try to run the run.sh I get the error attached below.
>>>>> Can you envisage a possible reason why I'm getting this error?
>>>>> Sorry for the naive admission, but from the error message
>>>>> I'm not even capable to understand which are the "missing eggs"...
>>>>>
>>>>> If I'd have ignored a previous post with the solution, I apologize in
>>>>> advance.
>>>>> Thank you a lot for your attention.
>>>>>
>>>>>
>>>> Hi Lu,
>>>>
>>>> Could you provide the output of the following?:
>>>>
>>>> % python ./scripts/get_platforms.py
>>>>
>>>> Thanks,
>>>> --nate
>>>>
>>>>
>>>>
>>>>
>>>>> Lu
>>>>>
>>>>> ------------------
>>>>> $ sh run.sh
>>>>> Some eggs are out of date, attempting to fetch...
>>>>> Traceback (most recent call last):
>>>>> File "./scripts/fetch_eggs.py", line 30, in <module>
>>>>> c.resolve() # Only fetch eggs required by the config
>>>>> File
>>>>> "/Users/myName/My_programs/Galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py",
>>>>> line 345, in resolve
>>>>> egg.resolve()
>>>>> File
>>>>> "/Users/myName/My_programs/Galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py",
>>>>> line 195, in resolve
>>>>> return self.version_conflict( e.args[0], e.args[1] )
>>>>> File
>>>>> "/Users/myName/My_programs/Galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py",
>>>>> line 226, in version_conflict
>>>>> r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ),
>>>>> env, egg.fetch )
>>>>> File
>>>>> "/System/Library/Frameworks/Python.framework/Versions/2.6/Extras/lib/python/pkg_resources.py",
>>>>> line 518, in resolve
>>>>> raise DistributionNotFound(req) # XXX put more info here
>>>>> pkg_resources.DistributionNotFound: numpy==1.6.0
>>>>> Fetch failed.
>>>>>
>>>>>
>>>>> ___________________________________________________________
>>>>> Please keep all replies on the list by using "reply all"
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>>>>> and other Galaxy lists, please use the interface at:
>>>>>
>>>>>
>>>>>
>>>>> http://lists.bx.psu.edu/
>>
>
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