Hi Nate, I am still not there, though I am getting closer...
I changed the port to 8888 in universe_wsgi.ini and Here's what appears on my screen: galaxy.web.buildapp DEBUG 2011-02-17 13:42:08,285 Enabling 'eval exceptions' middleware galaxy.web.buildapp DEBUG 2011-02-17 13:42:08,286 Enabling 'trans logger' middleware galaxy.web.buildapp DEBUG 2011-02-17 13:42:08,286 Enabling 'config' middleware galaxy.web.buildapp DEBUG 2011-02-17 13:42:08,287 Enabling 'x-forwarded-host' middleware Starting server in PID 28721. serving on http://127.0.0.1:8888 When I try to go there on my browser, the complaint from browser (I used both safari and firefox) is: Firefox can't establish a connection to the server at vixen:8888. Or Safari can¹t open the page ³http://vixen:8888/² because Safari can¹t connect to the server ³vixen². But when I change 8888 to 8080, I do get a page from tomcat. I see that the process is running: $ ps axl | grep 28721 0 1026 28721 28588 15 0 390520 83456 finish Tl pts/9 0:14 python ./scripts/paster.py serve universe_wsgi.ini 0 1026 28781 27316 16 0 51116 668 pipe_w S+ pts/9 0:00 grep 28721 Any clue, why I can't get there by browser? Thank you. Regards, Tena Sakai On 2/17/11 12:57 PM, "Nate Coraor" <[email protected]> wrote: > Tena Sakai wrote: >> Hi Nate, >> >> Thank you for your reply. >> >> I am getting there, but I need a bit more help. >> >> Firstly, yes, I had an alias hg (which was "history | grep $1"). >> I got rid of it and hg is working fine. >> >> Secondly, I installed the latest version of zlib (1.2.5) and >> I can go further with "sh run.sh", but it hangs after it tells >> me: >> File "/usr/local/lib/python2.5/SocketServer.py", line 341, in >> server_bind >> self.socket.bind(self.server_address) >> File "<string>", line 1, in bind >> socket.error: (98, 'Address already in use') >> >> When I point my browser to http://vixen:8080 (vixen is the very >> machine on which I am implementing galaxy), a tomcat page comes >> up (telling me that tomcat is running fine). >> >> Here's my question: Is there a way to run galaxy on ports other >> than 8080? > > Yes, in the file universe_wsgi.ini in the root of the Galaxy directory, > one of the options near the top of the file is 'port ='. This can be > changed to whatever you prefer. > > --nate > >> >> Thank you! >> >> Regards, >> >> Tena Sakai >> >> PS: Thank you for updating the link on wiki page. >> >> On 2/17/11 9:57 AM, "Nate Coraor" <[email protected]> wrote: >> >>> Nate Coraor wrote: >>>>> >>>>> $ uname -v >>>>> #1 SMP Tue Jul 22 18:01:05 EDT 2008 >>>>> >>>>> $ uname -r >>>>> 2.6.9-78.0.1.ELsmp >>> >>> RHEL 4, I believe? >>> >>>>> $ cd galaxy-dist >>>>> $ sh run.sh >>>>> <...lots of lines here...> >>>>> Fetch successful. >>>>> <...more lines here...> >>>>> ysam/csamtools.py", line 6, in __bootstrap__ >>>>> ImportError: >>>>> /home/tsakai/.python-eggs/pysam-0.1.1_kanwei_90e03180969d-py2.5-linux-x86_ >>>>> 64 >>>>> -ucs2.egg-tmp/pysam/csamtools.so: undefined symbol: deflateSetHeader >>>>> >>>>> $ echo $? >>>>> 1 >>>>> >>>>> So, I am lost now. Can somebody please give me a tip as to how to >>>>> proceed? >>>> >>>> I'll dig in to this last bit and get back to you ASAP. >>> >>> It would appear that your zlib does not contain deflateSetHeader, which >>> was added to zlib in version 1.2.2.1, released in 2004. RHEL 4.X >>> apparently ships with zlib 1.2.1.2. If you have a newer zlib installed >>> somewhere, you can work around this problem by setting $LD_LIBRARY_PATH >>> to point to the directory with the newer libz.so.1. LD_LIBRARY_PATH is >>> a hack so this is not ideal, but you may not want to override libz >>> globally by changing something like /etc/ld.so.conf. >>> >>> --nate >> >> _______________________________________________ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
