Tena Sakai wrote:
Hi
I am a developer for a group. I am having a problem with local installation of galaxy. The platform I am using is: $ uname -o GNU/Linux
$ uname -i x86_64
$ uname -v #1 SMP Tue Jul 22 18:01:05 EDT 2008
$ uname -r 2.6.9-78.0.1.ELsmp
Here’s what I did:
$ hg clone http://www.bx.psu.edu/hg/galaxy galaxy_dist grep: http://www.bx.psu.edu/hg/galaxy: No such file or directory grep: galaxy_dist: No such file or directory
Is your 'hg' aliased to something? I am not sure why it appears to be calling grep. Also, that repository URL is out of date, I thought we'd updated it. It should still work, but the URL for the actual repository is: https://bitbucket.org/galaxy/galaxy-dist/ This has been updated in the wiki.
I cut and pasted from your wiki page, and I assume there is no typo...
$ tar xzf galaxy-dist-tip.tar.gz gzip: stdin: unexpected end of file tar: Unexpected EOF in archive tar: Unexpected EOF in archive tar: Error is not recoverable: exiting now
$ gunzip galaxy-dist-tip.tar.gz gunzip: galaxy-dist-tip.tar.gz: unexpected end of file
I guess there is something wrong with this gzipped tar file...
$ rm galaxy-dist-tip.tar.gz $ /bin/rm -rf galaxy-dist
It looks like you're right. I've contacted bitbucket and removed this link from our wiki.
Try it with bz2 file...
$ bunzip2 galaxy-dist-tip.tar.bz2 $ tar xf galaxy-dist-tip.tar $ echo $? 0
$ 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.
Many thanks.
Regards,
Tena Sakai tsakai@gallo.ucsf.edu
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