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

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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.witham@jax.org