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.auwrote:
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( (
