Dear Nate, It is great, it started. Thanks you very much for your help, otherwise I will spend very long time to handle it. I will ctrl-c the process, activate, and './run.sh'. I hope it will still work and let you know. Best Wishes, Yan On Fri, Feb 11, 2011 at 10:43 AM, Nate Coraor <nate@bx.psu.edu> wrote:
Yan Luo wrote:
Dear Nate,
It is running, I am a little nervous, hope it is well. By the way, I forgot set it to the background. If it can start, should I kill the process again, start screen, and './run.sh'? Do I need any activate and "./run/sh"?
If you close the terminal in which Galaxy is running, Galaxy will stop. You can prevent this using screen as you have suggested, or the --daemon/--stop-daemon method I mentioned in an earlier email.
You will need to source `activate` before you run Galaxy if you start a new shell (for example, starting screen). You can see whether it's necessary by looking at the prompt. If your prompt looks like this:
kangtu@dscbc-compute:~$
Your virtualenv is not activated. As you can see from the output, once activated your shell prompt will look like:
(galaxy_env)kangtu@dscbc-compute:~$
--nate
Thanks for your help, I hope it is smooth.
Best Wishes,
Yan
On Fri, Feb 11, 2011 at 10:31 AM, Nate Coraor <nate@bx.psu.edu> wrote:
Yan Luo wrote:
Dear Nate,
When I run ". /home/kangtu/data/tools/galaxy-dist/galaxy_env/bin/activate" directly,
kangtu@dscbc-compute:~/Downloads/galaxy-dist/galaxy_env/bin$ . /home/kangtu/data/tools/galaxy-dist/galaxy_env/bin/activate (galaxy_env)kangtu@dscbc-compute
Can I cd the root folder of "galaxy-dist" and "./run.sh"? Or I must
install
"activate", run it, and then "./run.sh"
The syntax you used above:
% . /home/kangtu/data/tools/galaxy-dist/galaxy_env/bin/activate
Is correct. Executing `activate` directly as in your previous email is incorrect. activate is not an executable, it is a shell environment file which is meant to be sourced with the `.` command.
Since you have properly sourced `activate` as shown above, you can now execute `./run.sh`.
--nate
Best Wishes,
Yan
On Fri, Feb 11, 2011 at 10:19 AM, Yan Luo <luomails@gmail.com>
wrote:
Dear Nate,
I cd "/home/kangtu/Downloads/galaxy-dist/galaxy_env/bin" and run
activate
and get message:
kangtu@dscbc-compute:~/Downloads/galaxy-dist/galaxy_env/bin$ activate The program 'activate' is currently not installed. You can install it by typing: sudo apt-get install lilo
Should I first install it?
when I check the above folder, I do find the file 'activate'
kangtu@dscbc-compute:~/Downloads/galaxy-dist/galaxy_env/bin$ ls activate activate.fish easy_install pip python activate.csh activate_this.py easy_install-2.6 pip-2.6 kangtu@dscbc-compute:~/Downloads/galaxy-dist/galaxy_env/bin$
Could you please let me know if you have any suggestion?
Best WIshes,
Yan
On Fri, Feb 11, 2011 at 10:05 AM, Nate Coraor <nate@bx.psu.edu> wrote:
Yan Luo wrote: > Dear Nate, > > I just run the first step and must use sudo to "wget" and it is ok. > Otherwsie, I can't write (Cannot write to `virtualenv.py.1' (Success).)
I would strongly advise against using sudo for any part of this, since this is how permissions get screwed up. If you don't have
to
write to the directory in which you're downloading virtualenv.py and setting up the galaxy_env directory, choose another directory in which your regular unprivileged user can write.
virtualenv.py already exists where you are downloading it, since wget is trying to save the file as virtualenv.py.1. You do not need to download it again.
> ------------------- > > kangtu@dscbc-compute:~/Downloads/galaxy-dist$ sudo wget > http://bitbucket.org/ianb/virtualenv/raw/tip/virtualenv.py > [sudo] password for kangtu: > --2011-02-11 09:36:31-- > http://bitbucket.org/ianb/virtualenv/raw/tip/virtualenv.py > Resolving bitbucket.org... 207.223.240.182, 207.223.240.181 > Connecting to bitbucket.org|207.223.240.182|:80... connected. > HTTP request sent, awaiting response... 301 Moved Permanently > Location:
https://bitbucket.org/ianb/virtualenv/raw/tip/virtualenv.py[following]
> --2011-02-11 09:36:31-- > https://bitbucket.org/ianb/virtualenv/raw/tip/virtualenv.py > Connecting to bitbucket.org|207.223.240.182|:443... connected. > HTTP request sent, awaiting response... 200 OK > Length: unspecified [text/x-python] > Saving to: `virtualenv.py.1' > > [ <=> ] 75,592 --.-K/s in 0.04s > > 2011-02-11 09:36:31 (1.74 MB/s) - `virtualenv.py.1' saved [75592] > ------------------------------------------- > > When I checked the root folder of "galaxy-dist", and found: > > -rw-r--r-- 1 kangtu admin 75592 2011-01-27 02:38 virtualenv.py > -rw-r--r-- 1 root root 75592 2011-02-11 09:40 virtualenv.py.1 > -rw-r--r-- 1 kangtu admin 69811 2011-01-27 02:38 virtualenv.pyc > > Should I chang something for step b "python virtualenv.py --no-site-packages > galaxy_env"? > for example, "python virtualenv.py.1 --no-site-packages galaxy_env", or > rename "python virtualenv.py.1" as "python virtualenv.py".
Skip the download and setup steps. Someone already created a virtualenv. Use the existing one. I am unclear from your
:~/Downloads/galaxy-dist/galaxy_env/bin$ permission previous
emails whether the galaxy_env directory is at:
/home/kangtu/data/tools/galaxy_env
or:
/home/kangtu/data/tools/galaxy-dist/galaxy_env
Whichever it is, do the following:
% . /home/kangtu/data/tools/galaxy_env/bin/activate
or:
% . /home/kangtu/data/tools/galaxy-dist/galaxy_env/bin/activate
Then:
% cd ~/Downloads/galaxy-dist % ./run.sh
--nate
> > Best Wishes, > > Yan