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 > >> > > > > _______________________________________________ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/