Yan Luo wrote: > Dear Nate, > > Sorry for a lot of questions. To set up virtualenv, should I enter the root > folder of "galaxy-dist" and run the commands for steps "a", "b" and "c"? > > For step "b", > I only need to run "python virtualenv.py --no-site-packages galaxy_env > " from root folder of "galaxy-dist"(don't need to run "/usr/bin/python2.6 > virtualenv.py --no-site-packages galaxy_env"), is it right?
Yes. You can just run: % python virtualenv.py --no-site-packages galaxy_env > You mentioned I need to run command from "/home/kangtu/data/tools" > > /home/kangtu/Downloads/Galaxy-dist --> /home/kangtu/data/tools/galaxy-dist/ Using `/home/kangtu/data/tools` was only a suggestion. You may create galaxy_env in whatever directory is most convenient for you. > By the way, I found a folder called "galaxy_env" from root folder of > "galaxy-dist" form the both folder, they are same (date, time, and size ), > can I run step "b" directly from "/home/kangtu/Downloads/Galaxy-dist"? > drwxr-xr-x 5 kangtu admin 36864 2011-01-24 01:49 galaxy_env It would appear that someone already set up a virtualenv, unless this directory is something else. I don't know the specifics of your system or who did what. > For step "c", > is there a space in the beginning? I plan to run it from folder of > "galaxy-dist" > > ". ./galaxy_env/bin/activate" or "../galaxy_env/bin/activate" The space is intentional. The single '.' is analagous to 'source' in Bash but is compatible with other non-bash shells like Bourne and Dash (Debian). See the "SHELL BUILTIN COMMANDS" section of the bash(1) man page for an explanation. You could simply try these commands out as I suggested and then report back if there are any problems. --nate > > Looking forward to hearing from you. > > Best Wishes, > > Yan > > > On Fri, Feb 11, 2011 at 9:00 AM, Yan Luo <luoma...@gmail.com> wrote: > > > Dear Nate, > > > > Thanks for your quick response, my colleagues of a small group are waiting > > for using galaxy, so it is better if we can restart it asap. > > > > 1. If I try to set up a virtualenv, do I need to recompile "bx-python"? I > > am not familiar with "Python", if we need to do it, could you please let me > > know how to do it step by step? > > > > 2. I checked your instruction you mentioned, will I follow the following > > steps (a, b, and c)? If it is, I will try immediately. > > ------------------------------------------- > > (a) download: > > > > nate@weyerbacher% wget > > http://bitbucket.org/ianb/virtualenv/raw/tip/virtualenv.py > > > > --11:18:05-- http://bitbucket.org/ianb/virtualenv/raw/tip/virtualenv.py > > => `virtualenv.py' > > Resolving bitbucket.org... 184.73.244.143, 184.73.226.175 > > > > Connecting to bitbucket.org|184.73.244.143|:80... connected. > > HTTP request sent, awaiting response... 200 OK > > Length: 68,601 (67K) [text/x-python] > > > > 100%[====================================>] 68,601 --.--K/s > > > > 11:18:05 (729.46 KB/s) - `virtualenv.py' saved [68601/68601] > > > > (b) run command as follows > > nate@weyerbacher% /usr/bin/python2.6 virtualenv.py --no-site-packages > > galaxy_env > > New python executable in galaxy_env/bin/python2.6 > > > > Also creating executable in galaxy_env/bin/python > > Installing setuptools...............done. > > > > (c)run the following 3 commands > > nate@weyerbacher% . ./galaxy_env/bin/activate > > nate@weyerbacher% cd galaxy_dist > > > > nate@weyerbacher% sh run.sh > > > > > > ------------------------------------------ > > > > > > Looking forward to hearing from you. > > > > Best Wishes, > > > > Yan > > > > > > > > On Fri, Feb 11, 2011 at 8:45 AM, Nate Coraor <n...@bx.psu.edu> wrote: > > > >> Yan Luo wrote: > >> > Dear Nate, > >> > > >> > Why did you say we have 3 paths? We have a link from > >> > "/home/kangtu/Downloads/galaxy-dist" > >> > > >> > lrwxrwxrwx 1 kangtu admin 36 2010-11-01 17:07 galaxy-dist -> > >> > /home/kangtu/data/tools/galaxy-dist/ > >> > > >> > from "/home/kangtu/data", we have other link as follows. > >> > > >> > lrwxrwxrwx 1 kangtu kangtu 28 2010-10-04 10:25 data -> > >> > /mnt/gluster-vol/home/kangtu > >> > > >> > > >> > They worked well before, when we just restarted, it has such problem, I > >> > couldn't start. By the way, > >> > > >> > 1. I have found some files as "root:root" under > >> > "/home/kangtu/Downloads/galaxy-dist" including its subfolders' files, so > >> I > >> > changed all them as "kangtu/admin", there is only one user right now > >> (we > >> > use postgresql db). > >> > >> Okay, this should be fine. > >> > >> > 2. My colleague told me that he upgraded "numpy" to new version > >> recently, is > >> > it the problem? how can we fix it? I checked online, someone said we > >> need to > >> > recompile something (http://projects.scipy.org/numpy/ticket/1320). > >> > >> You would need to recompile whatever depends on numpy, which in this > >> case is bx-python. However, we provide our own version of numpy 1.3. > >> The reason that version is not being used is due to a bug in our > >> dependency management code which was just fixed. > >> > >> There are two ways to solve this problem. The first would be to set up > >> a virtualenv as suggested in my last email. > >> > >> The second would be to pull our in-development code, but be aware that > >> this has undergone very little testing at this point. You can pull the > >> most recent changes with: > >> > >> % hg pull -u http://bitbucket.org/galaxy/galaxy-central/ > >> > >> --nate > >> > >> > > >> > > >> > Looking forward to hearing from you. > >> > > >> > Thanks, > >> > > >> > Yan > >> > > >> > On Thu, Feb 10, 2011 at 10:26 PM, Nate Coraor <n...@bx.psu.edu> wrote: > >> > > >> > > Yan Luo wrote: > >> > > > Dear Nate, > >> > > > > >> > > > Please find the following errors, it is the newest, and our restart > >> is > >> > > > stopped. I hope we can get the solution from you as soon as > >> possible. > >> > > > >> > > Hi Yan, > >> > > > >> > > Your last 4 messages included 3 different paths to Galaxy. It seems > >> as > >> > > though there are quite a few copies of Galaxy in use here. > >> > > > >> > > To ensure there are no permissions problems, please do the following, > >> > > all as the same non-root user: > >> > > > >> > > 1. Remove the ~/.python-eggs directory and all of its contents. > >> > > 2. Clone a new copy of Galaxy. > >> > > 3. Start Galaxy using `./run.sh` > >> > > > >> > > And report back any errors which persist. If the numpy error below > >> > > remains, I suggest setting up a Python virtualenv as described on: > >> > > > >> > > http://usegalaxy.org/production > >> > > > >> > > --nate > >> > > > >> > > > >> > > > > _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
