Yan Luo wrote:
> Dear Nate,
> 
> Why did you say we have 3 paths? We have a link from
> "/home/kangtu/Downloads/galaxy-dist"
> 
> lrwxrwxrwx  1 kangtu admin        36 2010-11-01 17:07 galaxy-dist ->
> /home/kangtu/data/tools/galaxy-dist/
> 
> from "/home/kangtu/data", we have other link as follows.
> 
> lrwxrwxrwx  1 kangtu kangtu   28 2010-10-04 10:25 data ->
> /mnt/gluster-vol/home/kangtu
> 
> 
> They worked well before, when we just restarted, it has such problem, I
> couldn't start. By the way,
> 
> 1. I have found some files as "root:root" under
> "/home/kangtu/Downloads/galaxy-dist" including its subfolders' files, so I
> changed all them  as "kangtu/admin", there is only one user right now (we
> use postgresql db).

Okay, this should be fine.

> 2. My colleague told me that he upgraded "numpy" to new version recently, is
> it the problem? how can we fix it? I checked online, someone said we need to
> recompile something (http://projects.scipy.org/numpy/ticket/1320).

You would need to recompile whatever depends on numpy, which in this
case is bx-python.  However, we provide our own version of numpy 1.3.
The reason that version is not being used is due to a bug in our
dependency management code which was just fixed.

There are two ways to solve this problem.  The first would be to set up
a virtualenv as suggested in my last email.

The second would be to pull our in-development code, but be aware that
this has undergone very little testing at this point.  You can pull the
most recent changes with:

  % hg pull -u http://bitbucket.org/galaxy/galaxy-central/

--nate

> 
> 
> Looking forward to hearing from you.
> 
> Thanks,
> 
> Yan
> 
> On Thu, Feb 10, 2011 at 10:26 PM, Nate Coraor <n...@bx.psu.edu> wrote:
> 
> > Yan Luo wrote:
> > > Dear Nate,
> > >
> > > Please find the following errors, it is the newest, and our restart is
> > > stopped. I hope we can get the solution from you as soon as possible.
> >
> > Hi Yan,
> >
> > Your last 4 messages included 3 different paths to Galaxy.  It seems as
> > though there are quite a few copies of Galaxy in use here.
> >
> > To ensure there are no permissions problems, please do the following,
> > all as the same non-root user:
> >
> > 1. Remove the ~/.python-eggs directory and all of its contents.
> > 2. Clone a new copy of Galaxy.
> > 3. Start Galaxy using `./run.sh`
> >
> > And report back any errors which persist.  If the numpy error below
> > remains, I suggest setting up a Python virtualenv as described on:
> >
> >  http://usegalaxy.org/production
> >
> > --nate
> >
> >
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