Hi Nate,

Please ignore my previous post.  I got it working.
I changed an entry in universe_wsgi.ini file.
>From "#host = 127.0.0.1" to "host = vixen.egcrc.org".
It appears to be working.

Many thanks for your help.

Regards,

Tena Sakai


On 2/17/11 1:48 PM, "Tena Sakai" <tsa...@gallo.ucsf.edu> 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:8888/² 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" <n...@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" <n...@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
>>> 
>>> 
> 
> 
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