Yan Luo wrote: > Dear Nate, > > It is running, I am a little nervous, hope it is well. By the way, I forgot > set it to the background. If it can start, should I kill the process again, > start screen, and './run.sh'? Do I need any activate and "./run/sh"?
If you close the terminal in which Galaxy is running, Galaxy will stop. You can prevent this using screen as you have suggested, or the --daemon/--stop-daemon method I mentioned in an earlier email. You will need to source `activate` before you run Galaxy if you start a new shell (for example, starting screen). You can see whether it's necessary by looking at the prompt. If your prompt looks like this: kangtu@dscbc-compute:~$ Your virtualenv is not activated. As you can see from the output, once activated your shell prompt will look like: (galaxy_env)kangtu@dscbc-compute:~$ --nate > > Thanks for your help, I hope it is smooth. > > Best Wishes, > > Yan > > On Fri, Feb 11, 2011 at 10:31 AM, Nate Coraor <n...@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 <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/