Yan Luo wrote:
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,
- 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.
- 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 firstname.lastname@example.org wrote:
Yan Luo wrote:
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.
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:
- Remove the ~/.python-eggs directory and all of its contents.
- Clone a new copy of Galaxy.
- 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: