Yan Luo wrote:
Dear Nate,
Sorry for a lot of questions. To set up virtualenv, should I enter the root folder of "galaxy-dist" and run the commands for steps "a", "b" and "c"?
For step "b", I only need to run "python virtualenv.py --no-site-packages galaxy_env " from root folder of "galaxy-dist"(don't need to run "/usr/bin/python2.6 virtualenv.py --no-site-packages galaxy_env"), is it right?
Yes. You can just run:
% python virtualenv.py --no-site-packages galaxy_env
You mentioned I need to run command from "/home/kangtu/data/tools"
/home/kangtu/Downloads/Galaxy-dist --> /home/kangtu/data/tools/galaxy-dist/
Using `/home/kangtu/data/tools` was only a suggestion. You may create galaxy_env in whatever directory is most convenient for you.
By the way, I found a folder called "galaxy_env" from root folder of "galaxy-dist" form the both folder, they are same (date, time, and size ), can I run step "b" directly from "/home/kangtu/Downloads/Galaxy-dist"? drwxr-xr-x 5 kangtu admin 36864 2011-01-24 01:49 galaxy_env
It would appear that someone already set up a virtualenv, unless this directory is something else. I don't know the specifics of your system or who did what.
For step "c", is there a space in the beginning? I plan to run it from folder of "galaxy-dist"
". ./galaxy_env/bin/activate" or "../galaxy_env/bin/activate"
The space is intentional. The single '.' is analagous to 'source' in Bash but is compatible with other non-bash shells like Bourne and Dash (Debian). See the "SHELL BUILTIN COMMANDS" section of the bash(1) man page for an explanation.
You could simply try these commands out as I suggested and then report back if there are any problems.
--nate
Looking forward to hearing from you.
Best Wishes,
Yan
On Fri, Feb 11, 2011 at 9:00 AM, Yan Luo luomails@gmail.com 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.
- 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?
- 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]
(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.
(c)run the following 3 commands nate@weyerbacher% . ./galaxy_env/bin/activate nate@weyerbacher% cd galaxy_dist
nate@weyerbacher% sh run.sh
Looking forward to hearing from you.
Best Wishes,
Yan
On Fri, Feb 11, 2011 at 8:45 AM, Nate Coraor nate@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,
- 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/
--nate
Looking forward to hearing from you.
Thanks,
Yan
On Thu, Feb 10, 2011 at 10:26 PM, Nate Coraor nate@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:
- 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:
http://usegalaxy.org/production
--nate