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Also, that repository URL is out of date, I thought we'd updated it.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
> tsa...@gallo.ucsf.edu
> 
> 

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