Yan Luo wrote:
Why did you say we have 3 paths? We have a link from
lrwxrwxrwx 1 kangtu admin 36 2010-11-01 17:07 galaxy-dist ->
from "/home/kangtu/data", we have other link as follows.
lrwxrwxrwx 1 kangtu kangtu 28 2010-10-04 10:25 data ->
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/
Looking forward to hearing from you.
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 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: