Hi Greg,

That resolved the internal server error issue.  Now I need to figure out the issue with the dependencies.  I was unable to post the actual error message previously, but am doing so now.  Here is the error I get for the dependency installation:

Name	Version	Type	Status	Error
snpEff	3.6	package	Error	File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", line 110, in install_and_build_package_via_fabric     tool_dependency = self.install_and_build_package( app, tool_shed_repository, tool_dependency, actions_dict )   File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", line 103, in install_and_build_package     dir = tmp_dir   File "/usr/lib64/python2.6/contextlib.py", line 34, in __exit__     self.gen.throw(type, value, traceback)   File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Fabric-1.7.0-py2.6.egg/fabric/context_managers.py", line 142, in _setenv     yield   File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", line 68, in install_and_build_package     initial_download=True )   File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py", line 32, in execute_step     initial_download=initial_download )   File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 397, in execute_step     dir = td_common_util.url_download( work_dir, downloaded_filename, url, extract=True )   File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py", line 560, in url_download     extraction_path = archive.extract( install_dir )   File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py", line 60, in extract     self.archive.extractall( os.path.join( path ) )   File "/usr/lib64/python2.6/zipfile.py", line 940, in extractall     self.extract(zipinfo, path, pwd)   File "/usr/lib64/python2.6/zipfile.py", line 928, in extract     return self._extract_member(member, path, pwd)   File "/usr/lib64/python2.6/zipfile.py", line 965, in _extract_member     target = file(targetpath, "wb") [Errno 20] Not a directory: 'database/tmp/tmp-toolshed-mtdCAL19a/snpEff/snpEff.config'

This current package is owned by jjohnson and is located in the test toolshed.  

Thanks,

Iry

From: Greg Von Kuster <greg@bx.psu.edu>
Date: Wednesday, August 6, 2014 12:34 PM
To: Iry Witham <iry.witham@jax.org>
Cc: "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu>
Subject: Re: [galaxy-dev] Issues with dependencies for toolshed packages

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.Witham@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.witham@jax.org

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