>
> 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:~/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 <
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 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
> > > >>
> > > >
> > > >
> >