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 > > > > > > >
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