3:23 p.m.
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"
Best Wishes,
Yan
On Fri, Feb 11, 2011 at 10:19 AM, Yan Luo <luomails(a)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(a)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
>