Yan Luo wrote:
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
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/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
"galaxy-dist" form the both folder, they are same (date, time, and size ),
can I run step "b" directly from
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_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.
Looking forward to hearing from you.
On Fri, Feb 11, 2011 at 9:00 AM, Yan Luo <luomails(a)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
> 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
... 126.96.36.199, 188.8.131.52
> Connecting to bitbucket.org|184.108.40.206|: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,
> 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' files, so
>> > changed all them as "kangtu/admin", there is only one user right
>> > 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.
>> > Thanks,
>> > Yan
>> > On Thu, Feb 10, 2011 at 10:26 PM, Nate Coraor <nate(a)bx.psu.edu>
>> > > Yan Luo wrote:
>> > > > Dear Nate,
>> > > >
>> > > > Please find the following errors, it is the newest, and our
>> > > > 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
>> > > 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
>> > >
>> > >