Issues with dependencies for toolshed packages

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Issues with dependencies for toolshed packages

Iry Witham
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@...




           

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"
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Re: Issues with dependencies for toolshed packages

Greg Von Kuster
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 <[hidden email]> 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: <a href="x-msg://3425/iry.witham@jax.org">iry.witham@...


<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.
___________________________________________________________
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Re: Issues with dependencies for toolshed packages

Iry Witham
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 <[hidden email]>
Date: Wednesday, August 6, 2014 12:34 PM
To: Iry Witham <[hidden email]>
Cc: "[hidden email]" <[hidden email]>
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 <[hidden email]> 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: <a href="x-msg://3425/iry.witham@jax.org">iry.witham@...


<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:
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Re: Issues with dependencies for toolshed packages

Björn Grüning-3
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 <[hidden email]>:
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 <[hidden email]>
Date: Wednesday, August 6, 2014 12:34 PM
To: Iry Witham <[hidden email]>
Cc: "[hidden email]" <[hidden email]>
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 <[hidden email]> 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: [hidden email]


<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/


___________________________________________________________
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:
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To search Galaxy mailing lists use the unified search at:
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Re: Issues with dependencies for toolshed packages

Iry Witham
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:

snpeff
e8adfc4c0a6b
Error
This tool dependency's required tool dependency snpEff version 3.4 has status Error.
./../shed_tools/tool_dependencies/snpEff/3.4/iuc/snpeff/e8adfc4c0a6b

From: "[hidden email]" <[hidden email]>
Date: Wednesday, August 6, 2014 1:16 PM
To: Iry Witham <[hidden email]>
Cc: Greg Von Kuster <[hidden email]>, "[hidden email]" <[hidden email]>
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 <[hidden email]>:
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 <[hidden email]>
Date: Wednesday, August 6, 2014 12:34 PM
To: Iry Witham <[hidden email]>
Cc: "[hidden email]" <[hidden email]>
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 <[hidden email]> 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: [hidden email]


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___________________________________________________________
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and other Galaxy lists, please use the interface at:
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