That worked, Nate!

Thank you very much.  I really appreciate your efforts.

Jeff

________________________________________
From: Nate Coraor [n...@bx.psu.edu]
Sent: Wednesday, September 07, 2011 10:33 AM
To: Whyte, Jeffrey
Subject: Re: [galaxy-dev] Galaxy egg fetching error? Mac OS X 10.7 (Lion)

Hi Jeff,

Could you try:

    % python ./scripts/fetch_eggs.py

>From the top-level galaxy-dist directory?  I have just placed eggs for
py2.7-macosx-10.6-intel-ucs2 on http://eggs.g2.bx.psu.edu/

--nate

Whyte, Jeffrey wrote:
> Thanks, Nate!  Much appreciated.
> Jeff
>
>
>
> On Sep 7, 2011, at 7:54 AM, Nate Coraor wrote:
>
> > Whyte, Jeffrey wrote:
> >> Nate,
> >>
> >> For some reason, ~/galaxy-dist wasn't in my PATH.  Here is the output when 
> >> the script is run from the ~/galaxy-dist directory:
> >>
> >> [~/galaxy-dist] myuserid 03:50 PM > python ./scripts/get_platforms.py
> >> macosx-10.6-intel-ucs2
> >> [~/galaxy-dist] myuserid 03:50 PM >
> >>
> >> Looks like it is set for Mac OS X 10.6 Snow Leopard instead of 10.7 Lion.  
> >> (?)
> >
> > This is normal since OS X has binary compatibility with older releases,
> > the Python distributors build for an older platform rather than each
> > individual platform.
> >
> > I see there's now an Intel-only build for 10.6+, I'll work on this ASAP.
> >
> >>
> >> Thanks,
> >> Jeff
> >>
> >>
> >> On Sep 6, 2011, at 10:18 AM, Nate Coraor wrote:
> >>
> >>> Whyte, Jeffrey wrote:
> >>>> Thanks for the information, Nate.
> >>>>
> >>>> I installed Python as you described, and the error I get now is pasted 
> >>>> below.  I appreciate your help.
> >>>>
> >>>> Jeff
> >>>>
> >>>> [~/galaxy-dist] myuserid 03:06 PM > ./run.sh
> >>>> Some eggs are out of date, attempting to fetch...
> >>>> Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched
> >>>> Warning: simplejson (a dependent egg of WebHelpers) cannot be fetched
> >>>> pysam 0.4.2 couldn't be downloaded automatically.  You can try
> >>>> building it by hand with:
> >>>> python scripts/scramble.py -e pysam
> >>>> Fetch failed.
> >>>> [~/galaxy-dist] myuserid 03:06 PM >
> >>>
> >>> Could you report back with the output of:
> >>>
> >>>   % python ./scripts/get_platforms.py
> >>>
> >>> ?
> >>>
> >>> Thanks,
> >>> --nate
> >>>
> >>>> ________________________________________
> >>>> From: Nate Coraor [n...@bx.psu.edu]
> >>>> Sent: Friday, September 02, 2011 1:16 PM
> >>>> To: Whyte, Jeffrey
> >>>> Cc: galaxy-dev@lists.bx.psu.edu
> >>>> Subject: Re: [galaxy-dev] Galaxy egg fetching error? Mac OS X 10.7 (Lion)
> >>>>
> >>>> Whyte, Jeffrey wrote:
> >>>>> Hi,
> >>>>>
> >>>>> I've been having trouble running a local instance of Galaxy on a Mac 
> >>>>> Pro after upgrading to OS X 10.7 (Lion).  My Python version is 2.7.1 
> >>>>> and Mercurial is 1.9.1 for MacOS X 10.7.  I don't have any MacPorts 
> >>>>> installed.
> >>>>>
> >>>>> The error I see after running the startup script is pasted at the end 
> >>>>> of this message.  Thanks in advance for any help or advice.
> >>>>> jjw
> >>>>
> >>>> Hi Jeffrey,
> >>>>
> >>>> We haven't yet gotten our dependencies up to speed on Lion.  Could you
> >>>> grab a copy of Python from python.org and use this?  It'll install under
> >>>> /Library/Frameworks/Python.framework, just add the correct bin/
> >>>> directory to the front of your $PATH and start Galaxy as normal.
> >>>>
> >>>> Sorry for the inconvenience,
> >>>> --nate
> >>>>
> >>>>>
> >>>>> -----
> >>>>>
> >>>>> [~/galaxy-dist] myuserid 10:11 AM > ./run.sh
> >>>>> Some eggs are out of date, attempting to fetch...
> >>>>> Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched
> >>>>> Warning: decorator (a dependent egg of sqlalchemy-migrate) cannot be 
> >>>>> fetched
> >>>>> Warning: simplejson (a dependent egg of WebHelpers) cannot be fetched
> >>>>> 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/myuserid/galaxy-dist/lib/galaxy/eggs/__init__.py", line 
> >>>>> 345, in resolve
> >>>>>  egg.resolve()
> >>>>> File "/Users/myuserid/galaxy-dist/lib/galaxy/eggs/__init__.py", line 
> >>>>> 195, in resolve
> >>>>>  return self.version_conflict( e.args[0], e.args[1] )
> >>>>> File "/Users/myuserid/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/2.7/Extras/lib/python/pkg_resources.py",
> >>>>>  line 565, in resolve
> >>>>>  raise DistributionNotFound(req)  # XXX put more info here
> >>>>> pkg_resources.DistributionNotFound: numpy==1.6.0
> >>>>> Fetch failed.
> >>>>> [~/galaxy-dist] myuserid 10:12 AM >
> >>>>>
> >>>>>
> >>>>>
> >>>>> ___________________________________________________________
> >>>>> Please keep all replies on the list by using "reply all"
> >>>>> in your mail client.  To manage your subscriptions to this
> >>>>> and other Galaxy lists, please use the interface at:
> >>>>>
> >>>>> http://lists.bx.psu.edu/
> >>>>
> >>
> >>
>
>

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