Iry,

are you seeing the same error with:
 https://toolshed.g2.bx.psu.edu/view/iuc/snpeff

Cheers,
Bjoern



2014-08-06 19:12 GMT+02:00 Iry Witham <iry.wit...@jax.org>:

>  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
> <http://galaxy2/admin_toolshed/manage_repository_tool_dependencies?repository_id=b1254334b8763c9c&operation=browse&tool_dependency_ids=81424a9b99396c5a>
> 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 <g...@bx.psu.edu>
> Date: Wednesday, August 6, 2014 12:34 PM
> To: Iry Witham <iry.wit...@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.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__
> >>
> <http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=76ad6cd032d7117e&changeset_revisions=04d2a4f81413#>
> app_iter *=* self*.*application*(*environ*,*sr_checker*)*
> Module paste.recursive:*84* in __call__
> >>
> <http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=76ad6cd032d7117e&changeset_revisions=04d2a4f81413#>
> *return* self*.*application*(*environ*,*start_response*)*
> Module paste.httpexceptions:*633* in __call__
> >>
> <http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=76ad6cd032d7117e&changeset_revisions=04d2a4f81413#>
> *return* self*.*application*(*environ*,*start_response*)*
> Module galaxy.web.framework.base:*132* in __call__
> >>
> <http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=76ad6cd032d7117e&changeset_revisions=04d2a4f81413#>
> *return* self*.*handle_request*(*environ*,* start_response*)*
> Module galaxy.web.framework.base:*190* in handle_request
> >>
> <http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=76ad6cd032d7117e&changeset_revisions=04d2a4f81413#>
> body *=* method*(*trans*,* ****kwargs*)*
> Module galaxy.web.framework:*377* in decorator
> >>
> <http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=76ad6cd032d7117e&changeset_revisions=04d2a4f81413#>
> *return* func*(*self*,* trans*,****args*,* ****kwargs*)*
> Module galaxy.webapps.galaxy.controllers.admin_toolshed:*1035* in
> prepare_for_install
> >>
> <http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=76ad6cd032d7117e&changeset_revisions=04d2a4f81413#>
> raw_text *=* common_util*.*tool_shed_get*(*trans*.*app*,*tool_shed_url*,*
> url*)*
> Module tool_shed.util.common_util:*310* in tool_shed_get
> >>
> <http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=76ad6cd032d7117e&changeset_revisions=04d2a4f81413#>
> response *=* urlopener*.*open*(*uri *)*
>
> Module urllib2:*395* in open
> >>
> <http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=76ad6cd032d7117e&changeset_revisions=04d2a4f81413#>
> response *=* meth*(*req*,*response*)*
> Module urllib2:*508* in http_response
> >>
> <http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=76ad6cd032d7117e&changeset_revisions=04d2a4f81413#>
> 'http'*,* request*,*response*,* code*,*msg*,* hdrs*)*
>
> Module urllib2:*427* in error
> >>
> <http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=76ad6cd032d7117e&changeset_revisions=04d2a4f81413#>
> result *=* self*.*_call_chain*(****args*)*
> Module urllib2:*367* in _call_chain
> >>
> <http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=76ad6cd032d7117e&changeset_revisions=04d2a4f81413#>
> result *=* func*(****args*)*
> Module urllib2:*603* in http_error_302
> >>
> <http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=76ad6cd032d7117e&changeset_revisions=04d2a4f81413#>
> *return* self*.*parent*.*open*(*new*)*
> Module urllib2:*395* in open
> >>
> <http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=76ad6cd032d7117e&changeset_revisions=04d2a4f81413#>
> response *=* meth*(*req*,*response*)*
> Module urllib2:*508* in http_response
> >>
> <http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=76ad6cd032d7117e&changeset_revisions=04d2a4f81413#>
> 'http'*,* request*,*response*,* code*,*msg*,* hdrs*)*
>
> Module urllib2:*433* in error
> >>
> <http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=76ad6cd032d7117e&changeset_revisions=04d2a4f81413#>
> *return* self*.*_call_chain*(****args*)*
> Module urllib2:*367* in _call_chain
> >>
> <http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=76ad6cd032d7117e&changeset_revisions=04d2a4f81413#>
> result *=* func*(****args*)*
> Module urllib2:*516* in http_error_default
> >>
> <http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=76ad6cd032d7117e&changeset_revisions=04d2a4f81413#>
> *raise* HTTPError*(*req*.*get_full_url*(**)**,*code*,* msg*,*hdrs*,* fp*)*
>
> *HTTPError: HTTP Error 500: Internal Server Error*
> extra data
> <http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=76ad6cd032d7117e&changeset_revisions=04d2a4f81413#extra_data>
>
> full traceback
> <http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=76ad6cd032d7117e&changeset_revisions=04d2a4f81413#full_traceback>
>
> text version
> <http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=76ad6cd032d7117e&changeset_revisions=04d2a4f81413#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>
>
>
> The information in this email, including attachments, may be confidential
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