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/ >
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