Hi Tomithy,

Thanks, this worked for me too!

Just to be clear for interested devs:

If I run galaxy-dist on my mac it asks me to build a whole series of
eggs by hand using scripts/scramble.py, and if I follow these
instructions, galaxy runs. A bit tedious but trivial to do.

If I run galaxy-central on my mac the same thing happens for a few
dependencies, but then it gets stuck at the error I posted originally.
If I run `pip install fabric` as Tomithy suggests then I get the same
results as running galaxy-dist, ie galaxy works after using
scramble.py a few times.

If I run galaxy-central (or presumably galaxy-dist) on ubuntu it
doesn't complain about any of the dependencies, doesn't get stuck, and
doesn't ask me to build any eggs by hand.

So I'm now wondering if, for code editing, I should use the ubuntu
environment I've set up even though the code is working natively on
the mac, just to avoid future complications.

Cheers,
Clare

On 19 August 2012 21:36, Tomithy Too <tomithy....@gmail.com> wrote:
> Hi Clare,
>
> I ran into the same problem as well when I upgraded my galaxy-central
> version. I am running Mac Os10.6.8
>
> What I did to get use the command $ pip install fabric
>
> It manually fetches the latest version of fabric from pip
> (http://www.pip-installer.org/en/latest/index.html) which is a package
> manager from python, also its dependencies: ssh and pycrypto, which are the
> components causing the problem. I think it might be due to an erroneous
> version of the egg hosted on galaxy.
>
> Works fine after that for me.
>
> Cheers
> Tomithy
>
>
>
> On Wed, Aug 15, 2012 at 10:55 AM, Clare Sloggett <s...@unimelb.edu.au>
> wrote:
>>
>> Hi Scott,
>>
>> Thanks very much for this!
>>
>> virtualenv is ok I think:
>> clare$ echo $PATH
>> /Users/clare/galaxy/galaxy_central_env/bin: .....
>>
>> which is where I set up my environment.
>>
>> I'm not using anything in particular outside Enthought, that I can
>> think of. Enthought packages up a whole lot of things including scipy.
>>
>> The strange thing is that galaxy-dist runs but galaxy-central doesn't.
>> So, I was hoping it would actually be a temporary bug in the egg
>> distribution, but it sounds like the problem really is my environment.
>> I don't understand how Enthought can be causing problems that
>> virtualenv can't work around, but I've never really understood how
>> python is structured in OSX! So I think it's probably worth me going
>> through the effort of setting up a working environment in an ubuntu VM
>> rather than running it on my Mac - I don't want to be asking you to
>> pull code changes from an environment that's unusual.
>>
>> I'm setting it up in VirtualBox ubuntu now (which has python 2.7.1).
>> So far I've pulled the code into the vm and run it, without
>> virtualenv, and it gives none of the errors I see on the Mac. My plan
>> is to both share the drive containing galaxy-central and share the
>> network so that I can do both the editing and the browsing on my host
>> machine, but if there are better ways advice is welcome!
>>
>> Thanks,
>> Clare
>>
>>
>>
>> On 2 August 2012 07:26, Scott McManus <scottmcma...@gatech.edu> wrote:
>> >
>> > I haven't been able to reproduce this yet with the instructions you
>> > gave, but I'm not using the same environment. Can you give me an idea
>> > of what tools you're using outside of SciPy/NumPy/Enthought stuff?
>> >
>> > There is the possibility that the virtualenv.py script isn't being
>> > sourced correctly. We can check if it's actually using the correct
>> > environment by calling "echo $PATH" and checking that the path is
>> > pointing to the virtual environment. For example, I installed
>> > virtualenv stuff under /home/smcmanus/clare/galaxy_env/bin, and
>> > I got:
>> > (galaxy_env)$ echo $PATH
>> > /home/smcmanus/clare/galaxy_env/bin:/usr/local/bin:<other stuff deleted>
>> >
>> > -Scott
>> >
>> > ----- Original Message -----
>> >> Hi all,
>> >>
>> >> I'm trying to run galaxy-central on my laptop in order to play around
>> >> with some changes, and I'm having trouble getting it to run. I can
>> >> run
>> >> galaxy-dist without problems and have been working with that (so its
>> >> eggs are all installed already), but now I want to create a pull
>> >> request so want to run galaxy-dist. I'm not trying to install any
>> >> extra tools or data, just the code.
>> >>
>> >> I'm running on OSX 10.7.4 and using virtualenv. I have Enthought
>> >> installed, and I assume I will be using its version of python by
>> >> default. The default python seems to be 2.7.3.
>> >>
>> >> I'm using the same virtualenv environment for galaxy-dist and
>> >> galaxy-central (though it doesn't seem to matter if I give
>> >> galaxy-central its own environment, I see the same error). So the
>> >> steps were:
>> >> - create a virtualenv environment and activate it
>> >> - get galaxy-dist and call run.sh - it asked me to build quite a lot
>> >> of dependencies myself, which was just a matter of running the
>> >> requested commands, and then it worked with no problems.
>> >> - shut down galaxy-dist, and in another directory, get galaxy-central
>> >> and call run.sh. I think it asked me to build a couple of
>> >> dependencies, but then it gives up with the following:
>> >>
>> >> (galaxy_env)Clares-MacBook-Pro:galaxy-central clare$ sh run.sh
>> >> --reload
>> >> Some eggs are out of date, attempting to fetch...
>> >> Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched
>> >> Warning: pycrypto (a dependent egg of Fabric) cannot be fetched
>> >> Warning: simplejson (a dependent egg of WebHelpers) cannot be fetched
>> >> Fetched http://eggs.g2.bx.psu.edu/ssh/ssh-1.7.14-py2.7.egg
>> >> One of Galaxy's managed eggs depends on something which is missing,
>> >> this is almost certainly a bug in the egg distribution.
>> >> Dependency "ssh" requires "pycrypto>=2.1,!=2.4"
>> >> 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/clare/galaxy/galaxy-central/lib/galaxy/eggs/__init__.py",
>> >> line 345, in resolve
>> >>     egg.resolve()
>> >>   File
>> >>   "/Users/clare/galaxy/galaxy-central/lib/galaxy/eggs/__init__.py",
>> >> line 168, in resolve
>> >>     dists = pkg_resources.working_set.resolve( (
>> >> self.distribution.as_requirement(), ), env, self.fetch )
>> >>   File
>> >>
>> >> "/Users/clare/galaxy/galaxy_env/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg/pkg_resources.py",
>> >> line 569, in resolve
>> >>     raise VersionConflict(dist,req) # XXX put more info here
>> >> pkg_resources.VersionConflict: (ssh 1.7.14
>> >> (/Users/clare/galaxy/galaxy-central/eggs/ssh-1.7.14-py2.7.egg),
>> >> Requirement.parse('pycrypto>=2.1,!=2.4'))
>> >> Fetch failed.
>> >>
>> >> Any idea what is causing this?
>> >>
>> >> Thanks,
>> >> Clare
>> >>
>> >> --
>> >>
>> >> Clare Sloggett
>> >> Research Fellow / Bioinformatician
>> >> Life Sciences Computation Centre
>> >> Victorian Life Sciences Computation Initiative
>> >> University of Melbourne, Parkville Campus
>> >> 187 Grattan Street, Carlton, Melbourne
>> >> Victoria 3010, Australia
>> >> Ph: 03 903 53357          M: 0414 854 759
>> >> ___________________________________________________________
>> >> 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/
>> >>
>> >
>> >
>>
>>
>>
>> --
>>
>> Clare Sloggett
>> Research Fellow / Bioinformatician
>> Life Sciences Computation Centre
>> Victorian Life Sciences Computation Initiative
>> University of Melbourne, Parkville Campus
>> 187 Grattan Street, Carlton, Melbourne
>> Victoria 3010, Australia
>> Ph: 03 903 53357          M: 0414 854 759
>> ___________________________________________________________
>> 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/
>
>



-- 

Clare Sloggett
Research Fellow / Bioinformatician
Life Sciences Computation Centre
Victorian Life Sciences Computation Initiative
University of Melbourne, Parkville Campus
187 Grattan Street, Carlton, Melbourne
Victoria 3010, Australia
Ph: 03 903 53357          M: 0414 854 759
___________________________________________________________
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/

Reply via email to