Hi Iry,

Sorry for the inconvenience.  The tool shed server was out of space - I've 
corrected the problem and have successfully installed repositories.  Please try 
again and let us know if you encounter problems.

Thanks!

Greg Von Kuster


On Aug 6, 2014, at 12:20 PM, Iry Witham <iry.wit...@jax.org> wrote:

> Hi Team,
> 
> I have been trying to install package_snpEff_3_5 from the Galaxy main tool 
> shed and package_snpEff_3_6 from the Galaxy test tool shed and have the same 
> issue.  Once the installer completes it shows that the dependency snpEff.x.x 
> was not installed.  When I try to install the dependency it reports that the 
> directory 
> /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/tmp/tmp-toolshed-mtdi48tQV/snpEff
>  does not exist.  I have checked to confirm that this is true and discovered 
> that rather then a directory I find a null file named "snpEff and the 
> snpEff_v3.x_core.zip file.  I checked my shedtool dependencies folder and the 
> directory for these tools are empty.  I have since uninstalled the package.  
> I just tried again to install the snpEff tool and am getting the followig 
> error message:
> 
> Internal Server Error
> 
> Galaxy was unable to successfully complete your request
> 
> URL: 
> http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=76ad6cd032d7117e&changeset_revisions=04d2a4f81413
> Module galaxy.web.framework.middleware.error:149 in __call__
> >>  app_iter = self.application(environ, sr_checker)
> Module paste.recursive:84 in __call__
> >>  return self.application(environ, start_response)
> Module paste.httpexceptions:633 in __call__
> >>  return self.application(environ, start_response)
> Module galaxy.web.framework.base:132 in __call__
> >>  return self.handle_request( environ, start_response )
> Module galaxy.web.framework.base:190 in handle_request
> >>  body = method( trans, **kwargs )
> Module galaxy.web.framework:377 in decorator
> >>  return func( self, trans, *args, **kwargs )
> Module galaxy.webapps.galaxy.controllers.admin_toolshed:1035 in 
> prepare_for_install
> >>  raw_text = common_util.tool_shed_get( trans.app, tool_shed_url, url )
> Module tool_shed.util.common_util:310 in tool_shed_get
> >>  response = urlopener.open( uri )
> Module urllib2:395 in open
> >>  response = meth(req, response)
> Module urllib2:508 in http_response
> >>  'http', request, response, code, msg, hdrs)
> Module urllib2:427 in error
> >>  result = self._call_chain(*args)
> Module urllib2:367 in _call_chain
> >>  result = func(*args)
> Module urllib2:603 in http_error_302
> >>  return self.parent.open(new)
> Module urllib2:395 in open
> >>  response = meth(req, response)
> Module urllib2:508 in http_response
> >>  'http', request, response, code, msg, hdrs)
> Module urllib2:433 in error
> >>  return self._call_chain(*args)
> Module urllib2:367 in _call_chain
> >>  result = func(*args)
> Module urllib2:516 in http_error_default
> >>  raise HTTPError(req.get_full_url(), code, msg, hdrs, fp)
> HTTPError: HTTP Error 500: Internal Server Error
> extra data
> 
> full traceback
> 
> text version
> 
> This may be an intermittent problem due to load or other unpredictable 
> factors, reloading the page may address the problem.
> 
> I appreciate any possible assistance,
> 
> Regards,
> __________________________________
> Iry T. Witham
> Scientific Applications Administrator
> Scientific Computing Group
> Computational Sciences Dept.
> The Jackson Laboratory
> 600 Main Street
> Bar Harbor, ME  04609
> Phone: 207-288-6744
> email: iry.wit...@jax.org
> 
> 
> <372D007A-1B00-4668-BA6B-F0527C1F24BE[34][3][1].png>
> 
>            
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