Yan Luo wrote:
> Dear Nate,
> 
> Thanks for your quick response, my colleagues of a small group are waiting
> for using galaxy, so it is better if we can restart it asap.
> 
> 1. If I try to set up a virtualenv, do I need to recompile "bx-python"? I am
> not familiar with "Python", if we need to do it, could you please let me
> know how to do it step by step?

You will not need to recompile bx-python.

> 2. I checked your instruction you mentioned, will I follow the following
> steps (a, b, and c)? If it is, I will try immediately.
> -------------------------------------------
> (a) download:
> 
> nate@weyerbacher% wget
> http://bitbucket.org/ianb/virtualenv/raw/tip/virtualenv.py
> --11:18:05--  http://bitbucket.org/ianb/virtualenv/raw/tip/virtualenv.py
>            => `virtualenv.py'
> Resolving bitbucket.org... 184.73.244.143, 184.73.226.175
> Connecting to bitbucket.org|184.73.244.143|:80... connected.
> HTTP request sent, awaiting response... 200 OK
> Length: 68,601 (67K) [text/x-python]
> 
> 100%[====================================>] 68,601        --.--K/s
> 
> 11:18:05 (729.46 KB/s) - `virtualenv.py' saved [68601/68601]

You should be able to run this exactly as stated.

> 
> (b) run command as follows
> nate@weyerbacher% /usr/bin/python2.6 virtualenv.py --no-site-packages 
> galaxy_env
> New python executable in galaxy_env/bin/python2.6
> Also creating executable in galaxy_env/bin/python
> Installing setuptools...............done.

Your path to python might be different.  Since you have a suitable
python interpreter on your $PATH already you can just use:

% python virtualenv.py --no-site-packages galaxy_env

Note that the `galaxy_env` directory will be created in whatever
directory you are currently in, so you probably want to make sure this
location makes sense.  Perhaps run the command from
`/home/kangtu/data/tools`.

> (c)run the following 3 commands
> nate@weyerbacher% . ./galaxy_env/bin/activate
> nate@weyerbacher% cd galaxy_dist
> nate@weyerbacher% sh run.sh

This should be fine.

--nate

> 
> 
> ------------------------------------------
> 
> Looking forward to hearing from you.
> 
> Best Wishes,
> 
> Yan
> 
> 
> On Fri, Feb 11, 2011 at 8:45 AM, Nate Coraor <n...@bx.psu.edu> wrote:
> 
> > 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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