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?reposit... 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<mailto:greg@bx.psu.edu>> Date: Wednesday, August 6, 2014 12:34 PM To: Iry Witham <iry.witham@jax.org<mailto:iry.witham@jax.org>> Cc: "galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>" <galaxy-dev@lists.bx.psu.edu<mailto: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<mailto: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://t... Module galaxy.web.framework.middleware.error:149 in __call__ Module paste.recursive:84 in __call__ Module paste.httpexceptions:633 in __call__ Module galaxy.web.framework.base:132 in __call__ Module galaxy.web.framework.base:190 in handle_request Module galaxy.web.framework:377 in decorator Module galaxy.webapps.galaxy.controllers.admin_toolshed:1035 in prepare_for_install Module tool_shed.util.common_util:310 in tool_shed_get Module urllib2:395 in open Module urllib2:508 in http_response Module urllib2:427 in error Module urllib2:367 in _call_chain Module urllib2:603 in http_error_302 Module urllib2:395 in open Module urllib2:508 in http_response Module urllib2:433 in error Module urllib2:367 in _call_chain Module urllib2:516 in http_error_default HTTPError: HTTP Error 500: Internal Server Error extra data<http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_url=h... full traceback<http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_... text version<http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_ur... 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<x-msg://3425/iry.witham@jax.org> <372D007A-1B00-4668-BA6B-F0527C1F24BE[34][3][1].png> The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible. ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.

Bjoern, I am not getting the same error. However, it is still failing. I get the following banner: This tool dependency is not installed correctly (see the Tool dependency installation error below). Choose Uninstall this tool dependency from the Repository Actions menu, correct problems if necessary, and try installing the dependency again. And the following information is listed: Tool shed repository: snpeff Tool shed repository changeset revision: e8adfc4c0a6b Tool dependency status: Error Tool dependency installation error: This tool dependency's required tool dependency snpEff version 3.4 has status Error. Tool dependency installation directory: ./../shed_tools/tool_dependencies/snpEff/3.4/iuc/snpeff/e8adfc4c0a6b Contents: snpEff<http://galaxy2/admin_toolshed/browse_tool_dependency?repository_id=0dd27a44d4d97a53&operation=browse&tool_dependency_ids=53b036f027c29984#> env.sh<http://galaxy2/admin_toolshed/browse_tool_dependency?repository_id=0dd27a44d4d97a53&operation=browse&tool_dependency_ids=53b036f027c29984#> if [ -f /hpcdata/galaxy-test/galaxy-setup/shed_tools/tool_dependencies/snpEff/3.4/iuc/package_snpeff_3_4/af7ff8187d09/env.sh ] ; then . /hpcdata/galaxy-test/galaxy-setup/shed_tools/tool_dependencies/snpEff/3.4/iuc/package_snpeff_3_4/af7ff8187d09/env.sh ; fi Thanks, Iry From: "bjoern.gruening@googlemail.com<mailto:bjoern.gruening@googlemail.com>" <bjoern.gruening@gmail.com<mailto:bjoern.gruening@gmail.com>> Date: Wednesday, August 6, 2014 1:16 PM To: Iry Witham <iry.witham@jax.org<mailto:iry.witham@jax.org>> Cc: Greg Von Kuster <greg@bx.psu.edu<mailto:greg@bx.psu.edu>>, "galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>" <galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>> Subject: Re: [galaxy-dev] Issues with dependencies for toolshed packages 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.Witham@jax.org<mailto:Iry.Witham@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?reposit... 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<mailto:greg@bx.psu.edu>> Date: Wednesday, August 6, 2014 12:34 PM To: Iry Witham <iry.witham@jax.org<mailto:iry.witham@jax.org>> Cc: "galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>" <galaxy-dev@lists.bx.psu.edu<mailto: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<mailto: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://t... Module galaxy.web.framework.middleware.error:149 in __call__ Module paste.recursive:84 in __call__ Module paste.httpexceptions:633 in __call__ Module galaxy.web.framework.base:132 in __call__ Module galaxy.web.framework.base:190 in handle_request Module galaxy.web.framework:377 in decorator Module galaxy.webapps.galaxy.controllers.admin_toolshed:1035 in prepare_for_install Module tool_shed.util.common_util:310 in tool_shed_get Module urllib2:395 in open Module urllib2:508 in http_response Module urllib2:427 in error Module urllib2:367 in _call_chain Module urllib2:603 in http_error_302 Module urllib2:395 in open Module urllib2:508 in http_response Module urllib2:433 in error Module urllib2:367 in _call_chain Module urllib2:516 in http_error_default HTTPError: HTTP Error 500: Internal Server Error extra data<http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_url=h... full traceback<http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_... text version<http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_ur... 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(a)jax.org <372D007A-1B00-4668-BA6B-F0527C1F24BE[34][3][1].png> The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible. ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible. ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.