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 <n...@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 <n...@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
> :~/Downloads/galaxy-dist/galaxy_env/bin$
> > > >
> > > > 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 <luoma...@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 <n...@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
> permission
> > > 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
> 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
> > > > >>
> > > > >
> > > > >
> > >
>
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