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 <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 >> > >
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