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
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The information in this email, including attachments, may be confidential and is intended
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