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 > > _______________________________________________ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
