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?
Thank you!
Regards,
Tena Sakai
PS: Thank you for updating the link on wiki page.
On 2/17/11 9:57 AM, "Nate Coraor" <[email protected]> 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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