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.
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?
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]
(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,
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 <nate@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
is 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