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"?

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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