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