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" <nate@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