Tena Sakai wrote:
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/%C2%B2 because Safari can¹t connect to the server ³vixen².
See the 'host =' line in universe_wsgi.ini. To listen on the network (instead of just localhost), change the value to:
host = 0.0.0.0
--nate
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" nate@bx.psu.edu 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" nate@bx.psu.edu 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