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?
On Fri, Feb 11, 2011 at 10:05 AM, Nate Coraor email@example.com wrote:
Yan Luo wrote:
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... 18.104.22.168, 22.214.171.124 Connecting to bitbucket.org|126.96.36.199|:80... connected. HTTP request sent, awaiting response... 301 Moved Permanently Location:
--2011-02-11 09:36:31-- https://bitbucket.org/ianb/virtualenv/raw/tip/virtualenv.py Connecting to bitbucket.org|188.8.131.52|:443... connected. HTTP request sent, awaiting response... 200 OK Length: unspecified [text/x-python] Saving to: `virtualenv.py.1'
[ <=> ] 75,592 --.-K/s in
2011-02-11 09:36:31 (1.74 MB/s) - `virtualenv.py.1' saved 
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
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:
Whichever it is, do the following:
% . /home/kangtu/data/tools/galaxy_env/bin/activate
% . /home/kangtu/data/tools/galaxy-dist/galaxy_env/bin/activate
% cd ~/Downloads/galaxy-dist % ./run.sh