Yan Luo wrote:
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
steps (a, b, and c)? If it is, I will try immediately.
... 188.8.131.52, 184.108.40.206
Connecting to bitbucket.org|220.127.116.11|: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
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
(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.
Looking forward to hearing from you.
On Fri, Feb 11, 2011 at 8:45 AM, Nate Coraor <nate(a)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'
> > changed all them as "kangtu/admin", there is only one user right now
> > use postgresql db).
> Okay, this should be fine.
> > 2. My colleague told me that he upgraded "numpy" to new version
> > it the problem? how can we fix it? I checked online, someone said we need
> > 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/
> > Looking forward to hearing from you.
> > Thanks,
> > Yan
> > On Thu, Feb 10, 2011 at 10:26 PM, Nate Coraor <nate(a)bx.psu.edu> wrote:
> > > Yan Luo wrote:
> > > > Dear Nate,
> > > >
> > > > Please find the following errors, it is the newest, and our restart
> > > > stopped. I hope we can get the solution from you as soon as
> > >
> > > 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
> > >
> > >