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?

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, released in 2004.  RHEL 4.X
> apparently ships with zlib  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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