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
> File "/usr/local/lib/python2.5/SocketServer.py", line 341, in
> 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.
> Thank you!
> 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 22.214.171.124, released in 2004. RHEL 4.X
> > apparently ships with zlib 126.96.36.199. 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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