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