Internal Server Error during installation of ncbi_blast_plus

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Internal Server Error during installation of ncbi_blast_plus

Jens
This post was updated on .
Hi guys,

we are currently establishing our own local Galaxy instance. However, when we try to install "Repository 'ncbi_blast_plus'" from the Galaxy main tool shed via the admin pages, we obtain the following error
 
"Internal Server Error
Galaxy was unable to successfully complete your request

An error occurred.
This may be an intermittent problem due to load or other unpredictable factors, reloading the page may address the problem.

The error has been logged to our team."

We tried to install on three different days. Hence, we believe there might be another problem.
 
Thanks for any help.

Best regards, Jens

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Re: Internal Server Error during installation of ncbi_blast_plus

Peter Cock
On Wed, May 29, 2013 at 8:33 AM, Keilwagen, Jens
<[hidden email]> wrote:

> Hi guys,
>
> we are currently estalishing our own local Galaxy instance. However, when we
> try to install "Repository 'ncbi_blast_plus'" from the Galaxy main tool shed via
> the admin pages, we obtain the following error
>
> "Internal Server Error
> Galaxy was unable to sucessfully complete your request
>
> An error occurred.
> This may be an intermittent problem due to load or other unpredictable factors,
> reloading the page may address the problem.
>
> The error has been logged to our team."
>
> We tried to install on three different days. Hence, we believe there might be another problem.
>
> Thanks for any help.
>
> Best regards, Jens

Hi Jens,

The Galaxy team should be able to ask some more targeted questions,
but how far did the process get? Were you asked about the dependencies
(e.g. the blast_dataypes repository or the underlying BLAST+ binaries)?

Peter

P.S. What kind of system are you using? 64 bit Linux? Mac OS X?
___________________________________________________________
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Re: Internal Server Error during installation of ncbi_blast_plus

Greg Von Kuster
Hello Jens,

What does your Galaxy paster log show that is related to the internal server error?

Greg Von Kuster

On May 29, 2013, at 10:13 AM, Peter Cock wrote:

> On Wed, May 29, 2013 at 8:33 AM, Keilwagen, Jens
> <[hidden email]> wrote:
>> Hi guys,
>>
>> we are currently estalishing our own local Galaxy instance. However, when we
>> try to install "Repository 'ncbi_blast_plus'" from the Galaxy main tool shed via
>> the admin pages, we obtain the following error
>>
>> "Internal Server Error
>> Galaxy was unable to sucessfully complete your request
>>
>> An error occurred.
>> This may be an intermittent problem due to load or other unpredictable factors,
>> reloading the page may address the problem.
>>
>> The error has been logged to our team."
>>
>> We tried to install on three different days. Hence, we believe there might be another problem.
>>
>> Thanks for any help.
>>
>> Best regards, Jens
>
> Hi Jens,
>
> The Galaxy team should be able to ask some more targeted questions,
> but how far did the process get? Were you asked about the dependencies
> (e.g. the blast_dataypes repository or the underlying BLAST+ binaries)?
>
> Peter
>
> P.S. What kind of system are you using? 64 bit Linux? Mac OS X?
> ___________________________________________________________
> 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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Re: Internal Server Error during installation of ncbi_blast_plus

Jens
Hi Greg,

here is what the paster.log says:

172.31.30.183 - - [30/May/2013:07:39:54 +0200] "GET /admin_toolshed/browse_tool_shed?tool_shed_url=http%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F HTTP/1.0" 302 - "http://galaxy.jki.bund.de/admin_toolshed/browse_tool_sheds" "Mozilla/5.0 (Windows NT 6.1; WOW64; rv:21.0) Gecko/20100101 Firefox/21.0"
172.31.30.183 - - [30/May/2013:07:40:17 +0200] "GET /admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf7e8d466c&changeset_revisions=9dabbfd73c8a HTTP/1.0" 500 - "http://toolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset?repository_id=1d92ebdf7e8d466c&changeset_revision=9dabbfd73c8a" "Mozilla/5.0 (Windows NT 6.1; WOW64; rv:21.0) Gecko/20100101 Firefox/21.0"
Error - <type 'exceptions.ValueError'>: too many values to unpack
URL: http://galaxy.jki.bund.de/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf7e8d466c&changeset_revisions=9dabbfd73c8a
File '/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__
  app_iter = self.application(environ, sr_checker)
File '/opt/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py', line 84 in __call__
  return self.application(environ, start_response)
File '/opt/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py', line 633 in __call__
  return self.application(environ, start_response)
File '/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 128 in __call__
  return self.handle_request( environ, start_response )
File '/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 184 in handle_request
  body = method( trans, **kwargs )
File '/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 231 in decorator
  return func( self, trans, *args, **kwargs )
File '/opt/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 894 in prepare_for_install
  common_install_util.get_dependencies_for_repository( trans, tool_shed_url, repo_info_dict, includes_tool_dependencies )
File '/opt/galaxy/galaxy-dist/lib/tool_shed/util/common_install_util.py', line 88 in get_dependencies_for_repository
  installed_rd, missing_rd = get_installed_and_missing_repository_dependencies_for_new_install( trans, repo_info_tuple )
File '/opt/galaxy/galaxy-dist/lib/tool_shed/util/common_install_util.py', line 192 in get_installed_and_missing_repository_dependencies_for_new_install
  tool_shed, name, owner, changeset_revision = rd_tup
ValueError: too many values to unpack


CGI Variables
-------------
  CONTENT_LENGTH: '0'
  HTTP_ACCEPT: 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8'
  HTTP_ACCEPT_ENCODING: 'gzip, deflate'
  HTTP_ACCEPT_LANGUAGE: 'de-de,de;q=0.8,en-us;q=0.5,en;q=0.3'
  HTTP_CACHE_CONTROL: 'max-age=0'
  HTTP_CONNECTION: 'keep-alive'
  HTTP_COOKIE: 'galaxysession=c6ca0ddb55be603a88fa41dbba7680819dc3ac10c92a6efa6da917af7060700e4360e4afb5987baa'
  HTTP_HOST: 'galaxy.jki.bund.de'
  HTTP_REFERER: 'http://toolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset?repository_id=1d92ebdf7e8d466c&changeset_revision=9dabbfd73c8a'
  HTTP_USER_AGENT: 'Mozilla/5.0 (Windows NT 6.1; WOW64; rv:21.0) Gecko/20100101 Firefox/21.0'
  HTTP_VIA: '1.1 proxy.jki.bund.de:8000 (squid/2.7.STABLE9)'
  HTTP_X_FORWARDED_FOR: '172.31.30.183'
  ORGINAL_REMOTE_ADDR: '172.16.20.52'
  PATH_INFO: '/admin_toolshed/prepare_for_install'
  QUERY_STRING: 'tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf7e8d466c&changeset_revisions=9dabbfd73c8a'
  REMOTE_ADDR: '172.31.30.183'
  REQUEST_METHOD: 'GET'
  SERVER_NAME: '0.0.0.0'
  SERVER_PORT: '8080'
  SERVER_PROTOCOL: 'HTTP/1.0'


WSGI Variables
--------------
  application: <paste.recursive.RecursiveMiddleware object at 0x8781210>
  paste.cookies: (<SimpleCookie: galaxysession='c6ca0ddb55be603a88fa41dbba7680819dc3ac10c92a6efa6da917af7060700e4360e4afb5987baa'>, 'galaxysession=c6ca0ddb55be603a88fa41dbba7680819dc3ac10c92a6efa6da917af7060700e4360e4afb5987baa')
  paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>]
  paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object at 0x8851bd0>
  paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at 0x87b2450>
  paste.parsed_querystring: ([('tool_shed_url', 'http://toolshed.g2.bx.psu.edu/'), ('repository_ids', '1d92ebdf7e8d466c'), ('changeset_revisions', '9dabbfd73c8a')], 'tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf7e8d466c&changeset_revisions=9dabbfd73c8a')
  paste.recursive.forward: <paste.recursive.Forwarder from />
  paste.recursive.include: <paste.recursive.Includer from />
  paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from />
  paste.recursive.script_name: ''
  paste.throw_errors: True
  request_id: '6905bf7ac8eb11e297ec0050568d0b1f'
  webob._parsed_query_vars: (MultiDict([('tool_shed_url', 'http://toolshed.g2.bx.psu.edu/'), ('repository_ids', '1d92ebdf7e8d466c'), ('changeset_revisions', '9dabbfd73c8a')]), 'tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf7e8d466c&changeset_revisions=9dabbfd73c8a')
  wsgi process: 'Multithreaded'
------------------------------------------------------------

However, installing other tools from the tool shed was no problem so far.

Best regards, Jens

> -----Ursprüngliche Nachricht-----
> Von: Greg Von Kuster [mailto:[hidden email]]
> Gesendet: Mittwoch, 29. Mai 2013 16:45
> An: Keilwagen, Jens
> Cc: Galaxy Dev
> Betreff: Re: [galaxy-dev] Internal Server Error during installation of
> ncbi_blast_plus
>
> Hello Jens,
>
> What does your Galaxy paster log show that is related to the internal
> server error?
>
> Greg Von Kuster
>
> On May 29, 2013, at 10:13 AM, Peter Cock wrote:
>
> > On Wed, May 29, 2013 at 8:33 AM, Keilwagen, Jens
> > <[hidden email]> wrote:
> >> Hi guys,
> >>
> >> we are currently estalishing our own local Galaxy instance. However,
> >> when we try to install "Repository 'ncbi_blast_plus'" from the
> Galaxy
> >> main tool shed via the admin pages, we obtain the following error
> >>
> >> "Internal Server Error
> >> Galaxy was unable to sucessfully complete your request
> >>
> >> An error occurred.
> >> This may be an intermittent problem due to load or other
> >> unpredictable factors, reloading the page may address the problem.
> >>
> >> The error has been logged to our team."
> >>
> >> We tried to install on three different days. Hence, we believe there
> might be another problem.
> >>
> >> Thanks for any help.
> >>
> >> Best regards, Jens
> >
> > Hi Jens,
> >
> > The Galaxy team should be able to ask some more targeted questions,
> > but how far did the process get? Were you asked about the
> dependencies
> > (e.g. the blast_dataypes repository or the underlying BLAST+
> binaries)?
> >
> > Peter
> >
> > P.S. What kind of system are you using? 64 bit Linux? Mac OS X?
> > ___________________________________________________________
> > 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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Re: Internal Server Error during installation of ncbi_blast_plus

Jens
In reply to this post by Peter Cock
Hi Peter,

thanks for your email. Regarding you questions

> The Galaxy team should be able to ask some more targeted questions, but
> how far did the process get?

I get this error immediately after clicking on "Install to Galaxy".

> Were you asked about the dependencies
> (e.g. the blast_dataypes repository or the underlying BLAST+ binaries)?

No, but "blast_datatypes" is already installed.

> P.S. What kind of system are you using? 64 bit Linux? Mac OS X?

galaxy-dist$ more /proc/version
Linux version 2.6.32-5-amd64 (Debian 2.6.32-48squeeze1) ([hidden email]) (gcc version 4.3.5 (Debian 4.3.5-4) ) #1 SMP Mon Feb 2
5 00:26:11 UTC 2013

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Re: Internal Server Error during installation of ncbi_blast_plus

Greg Von Kuster
In reply to this post by Jens
Hello Jens,

It looks like your Galaxy instance is fairly old.  What version of Galaxy are you running?

Thanks,

Greg Von Kuster

On May 30, 2013, at 1:49 AM, Keilwagen, Jens wrote:

> Hi Greg,
>
> here is what the paster.log says:
>
> 172.31.30.183 - - [30/May/2013:07:39:54 +0200] "GET /admin_toolshed/browse_tool_shed?tool_shed_url=http%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F HTTP/1.0" 302 - "http://galaxy.jki.bund.de/admin_toolshed/browse_tool_sheds" "Mozilla/5.0 (Windows NT 6.1; WOW64; rv:21.0) Gecko/20100101 Firefox/21.0"
> 172.31.30.183 - - [30/May/2013:07:40:17 +0200] "GET /admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf7e8d466c&changeset_revisions=9dabbfd73c8a HTTP/1.0" 500 - "http://toolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset?repository_id=1d92ebdf7e8d466c&changeset_revision=9dabbfd73c8a" "Mozilla/5.0 (Windows NT 6.1; WOW64; rv:21.0) Gecko/20100101 Firefox/21.0"
> Error - <type 'exceptions.ValueError'>: too many values to unpack
> URL: http://galaxy.jki.bund.de/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf7e8d466c&changeset_revisions=9dabbfd73c8a
> File '/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__
>  app_iter = self.application(environ, sr_checker)
> File '/opt/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py', line 84 in __call__
>  return self.application(environ, start_response)
> File '/opt/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py', line 633 in __call__
>  return self.application(environ, start_response)
> File '/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 128 in __call__
>  return self.handle_request( environ, start_response )
> File '/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 184 in handle_request
>  body = method( trans, **kwargs )
> File '/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 231 in decorator
>  return func( self, trans, *args, **kwargs )
> File '/opt/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 894 in prepare_for_install
>  common_install_util.get_dependencies_for_repository( trans, tool_shed_url, repo_info_dict, includes_tool_dependencies )
> File '/opt/galaxy/galaxy-dist/lib/tool_shed/util/common_install_util.py', line 88 in get_dependencies_for_repository
>  installed_rd, missing_rd = get_installed_and_missing_repository_dependencies_for_new_install( trans, repo_info_tuple )
> File '/opt/galaxy/galaxy-dist/lib/tool_shed/util/common_install_util.py', line 192 in get_installed_and_missing_repository_dependencies_for_new_install
>  tool_shed, name, owner, changeset_revision = rd_tup
> ValueError: too many values to unpack
>
>
> CGI Variables
> -------------
>  CONTENT_LENGTH: '0'
>  HTTP_ACCEPT: 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8'
>  HTTP_ACCEPT_ENCODING: 'gzip, deflate'
>  HTTP_ACCEPT_LANGUAGE: 'de-de,de;q=0.8,en-us;q=0.5,en;q=0.3'
>  HTTP_CACHE_CONTROL: 'max-age=0'
>  HTTP_CONNECTION: 'keep-alive'
>  HTTP_COOKIE: 'galaxysession=c6ca0ddb55be603a88fa41dbba7680819dc3ac10c92a6efa6da917af7060700e4360e4afb5987baa'
>  HTTP_HOST: 'galaxy.jki.bund.de'
>  HTTP_REFERER: 'http://toolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset?repository_id=1d92ebdf7e8d466c&changeset_revision=9dabbfd73c8a'
>  HTTP_USER_AGENT: 'Mozilla/5.0 (Windows NT 6.1; WOW64; rv:21.0) Gecko/20100101 Firefox/21.0'
>  HTTP_VIA: '1.1 proxy.jki.bund.de:8000 (squid/2.7.STABLE9)'
>  HTTP_X_FORWARDED_FOR: '172.31.30.183'
>  ORGINAL_REMOTE_ADDR: '172.16.20.52'
>  PATH_INFO: '/admin_toolshed/prepare_for_install'
>  QUERY_STRING: 'tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf7e8d466c&changeset_revisions=9dabbfd73c8a'
>  REMOTE_ADDR: '172.31.30.183'
>  REQUEST_METHOD: 'GET'
>  SERVER_NAME: '0.0.0.0'
>  SERVER_PORT: '8080'
>  SERVER_PROTOCOL: 'HTTP/1.0'
>
>
> WSGI Variables
> --------------
>  application: <paste.recursive.RecursiveMiddleware object at 0x8781210>
>  paste.cookies: (<SimpleCookie: galaxysession='c6ca0ddb55be603a88fa41dbba7680819dc3ac10c92a6efa6da917af7060700e4360e4afb5987baa'>, 'galaxysession=c6ca0ddb55be603a88fa41dbba7680819dc3ac10c92a6efa6da917af7060700e4360e4afb5987baa')
>  paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>]
>  paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object at 0x8851bd0>
>  paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at 0x87b2450>
>  paste.parsed_querystring: ([('tool_shed_url', 'http://toolshed.g2.bx.psu.edu/'), ('repository_ids', '1d92ebdf7e8d466c'), ('changeset_revisions', '9dabbfd73c8a')], 'tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf7e8d466c&changeset_revisions=9dabbfd73c8a')
>  paste.recursive.forward: <paste.recursive.Forwarder from />
>  paste.recursive.include: <paste.recursive.Includer from />
>  paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from />
>  paste.recursive.script_name: ''
>  paste.throw_errors: True
>  request_id: '6905bf7ac8eb11e297ec0050568d0b1f'
>  webob._parsed_query_vars: (MultiDict([('tool_shed_url', 'http://toolshed.g2.bx.psu.edu/'), ('repository_ids', '1d92ebdf7e8d466c'), ('changeset_revisions', '9dabbfd73c8a')]), 'tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf7e8d466c&changeset_revisions=9dabbfd73c8a')
>  wsgi process: 'Multithreaded'
> ------------------------------------------------------------
>
> However, installing other tools from the tool shed was no problem so far.
>
> Best regards, Jens
>
>> -----Ursprüngliche Nachricht-----
>> Von: Greg Von Kuster [mailto:[hidden email]]
>> Gesendet: Mittwoch, 29. Mai 2013 16:45
>> An: Keilwagen, Jens
>> Cc: Galaxy Dev
>> Betreff: Re: [galaxy-dev] Internal Server Error during installation of
>> ncbi_blast_plus
>>
>> Hello Jens,
>>
>> What does your Galaxy paster log show that is related to the internal
>> server error?
>>
>> Greg Von Kuster
>>
>> On May 29, 2013, at 10:13 AM, Peter Cock wrote:
>>
>>> On Wed, May 29, 2013 at 8:33 AM, Keilwagen, Jens
>>> <[hidden email]> wrote:
>>>> Hi guys,
>>>>
>>>> we are currently estalishing our own local Galaxy instance. However,
>>>> when we try to install "Repository 'ncbi_blast_plus'" from the
>> Galaxy
>>>> main tool shed via the admin pages, we obtain the following error
>>>>
>>>> "Internal Server Error
>>>> Galaxy was unable to sucessfully complete your request
>>>>
>>>> An error occurred.
>>>> This may be an intermittent problem due to load or other
>>>> unpredictable factors, reloading the page may address the problem.
>>>>
>>>> The error has been logged to our team."
>>>>
>>>> We tried to install on three different days. Hence, we believe there
>> might be another problem.
>>>>
>>>> Thanks for any help.
>>>>
>>>> Best regards, Jens
>>>
>>> Hi Jens,
>>>
>>> The Galaxy team should be able to ask some more targeted questions,
>>> but how far did the process get? Were you asked about the
>> dependencies
>>> (e.g. the blast_dataypes repository or the underlying BLAST+
>> binaries)?
>>>
>>> Peter
>>>
>>> P.S. What kind of system are you using? 64 bit Linux? Mac OS X?
>>> ___________________________________________________________
>>> 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/
>
>


___________________________________________________________
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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

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Re: Internal Server Error during installation of ncbi_blast_plus

Jens
This post was updated on .
Hi Greg,

thanks for your comment. Some days ago, I updated Galaxy following:

http://wiki.galaxyproject.org/News/2013_04_08_Galaxy_Security_Release

Here is what "hg sum" said

parent: 9292:2cc8d10988e0 security_2013.04.08
 controllers/history: use get_history in switch_to_history
Zweig: stable
Übernehme: 10 unbekannt (clean)
Aktualisiere: 11 neue Änderungssätze (Aktualisierung)

(Sorry for the German terms.) I then updated Galaxy by

hg update

obtaining:

parent: 9320:47ddf167c9f1 tip
 Use Galaxy's ErrorMiddleware since Paste's doesn't return start_response.  Fixes downloading tarballs from the Tool Shed when use_debug = false.
Zweig: stable
Übernehme: 10 unbekannt (clean)
Aktualisiere: (aktuell)

I then restarted Galaxy and tried to install again, but it fails again. Even trying for a second time doesn't change the behaviour. Here is what paster.log says:

172.31.30.183 - - [31/May/2013:07:47:32 +0200] "GET /admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf7e8d466c&changeset_revisions=9dabbfd73c8a HTTP/1.0" 500 - "http://toolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset?repository_id=1d92ebdf7e8d466c&changeset_revision=9dabbfd73c8a" "Mozilla/5.0 (Windows NT 6.1; WOW64; rv:21.0) Gecko/20100101 Firefox/21.0"
Error - <type 'exceptions.ValueError'>: too many values to unpack
URL: http://galaxy.jki.bund.de/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf7e8d466c&changeset_revisions=9dabbfd73c8a
File '/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__
  app_iter = self.application(environ, sr_checker)
File '/opt/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py', line 84 in __call__
  return self.application(environ, start_response)
File '/opt/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py', line 633 in __call__
  return self.application(environ, start_response)
File '/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 128 in __call__
  return self.handle_request( environ, start_response )
File '/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 184 in handle_request
  body = method( trans, **kwargs )
File '/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 231 in decorator
  return func( self, trans, *args, **kwargs )
File '/opt/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 894 in prepare_for_install
  common_install_util.get_dependencies_for_repository( trans, tool_shed_url, repo_info_dict, includes_tool_dependencies )
File '/opt/galaxy/galaxy-dist/lib/tool_shed/util/common_install_util.py', line 88 in get_dependencies_for_repository
  installed_rd, missing_rd = get_installed_and_missing_repository_dependencies_for_new_install( trans, repo_info_tuple )
File '/opt/galaxy/galaxy-dist/lib/tool_shed/util/common_install_util.py', line 192 in get_installed_and_missing_repository_dependencies_for_new_install
  tool_shed, name, owner, changeset_revision = rd_tup
ValueError: too many values to unpack


CGI Variables
-------------
  CONTENT_LENGTH: '0'
  HTTP_ACCEPT: 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8'
  HTTP_ACCEPT_ENCODING: 'gzip, deflate'
  HTTP_ACCEPT_LANGUAGE: 'de-de,de;q=0.8,en-us;q=0.5,en;q=0.3'
  HTTP_CACHE_CONTROL: 'max-age=0'
  HTTP_CONNECTION: 'keep-alive'
  HTTP_COOKIE: 'galaxysession=c6ca0ddb55be603a88fa41dbba7680819dc3ac10c92a6efa6da917af7060700e4360e4afb5987baa'
  HTTP_HOST: 'galaxy.jki.bund.de'
  HTTP_REFERER: 'http://toolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset?repository_id=1d92ebdf7e8d466c&changeset_revision=9dabbfd73c8a'
  HTTP_USER_AGENT: 'Mozilla/5.0 (Windows NT 6.1; WOW64; rv:21.0) Gecko/20100101 Firefox/21.0'
  HTTP_VIA: '1.1 proxy.jki.bund.de:8000 (squid/2.7.STABLE9)'
  HTTP_X_FORWARDED_FOR: '172.31.30.183'
  ORGINAL_REMOTE_ADDR: '172.16.20.52'
  PATH_INFO: '/admin_toolshed/prepare_for_install'
  QUERY_STRING: 'tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf7e8d466c&changeset_revisions=9dabbfd73c8a'
  REMOTE_ADDR: '172.31.30.183'
  REQUEST_METHOD: 'GET'
  SERVER_NAME: '0.0.0.0'
  SERVER_PORT: '8080'
  SERVER_PROTOCOL: 'HTTP/1.0'


WSGI Variables
--------------
  application: <paste.recursive.RecursiveMiddleware object at 0x7c3ed50>
  paste.cookies: (<SimpleCookie: galaxysession='c6ca0ddb55be603a88fa41dbba7680819dc3ac10c92a6efa6da917af7060700e4360e4afb5987baa'>, 'galaxysession=c6ca0ddb55be603a88fa41dbba7680819dc3ac10c92a6efa6da917af7060700e4360e4afb5987baa')
  paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>]
  paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object at 0x7c3e710>
  paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at 0x7c9ff50>
  paste.parsed_querystring: ([('tool_shed_url', 'http://toolshed.g2.bx.psu.edu/'), ('repository_ids', '1d92ebdf7e8d466c'), ('changeset_revisions', '9dabbfd73c8a')], 'tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf7e8d466c&changeset_revisions=9dabbfd73c8a')
  paste.recursive.forward: <paste.recursive.Forwarder from />
  paste.recursive.include: <paste.recursive.Includer from />
  paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from />
  paste.recursive.script_name: ''
  paste.throw_errors: True
  request_id: '964a9788c9b511e2bb080050568d0b1f'
  webob._parsed_query_vars: (MultiDict([('tool_shed_url', 'http://toolshed.g2.bx.psu.edu/'), ('repository_ids', '1d92ebdf7e8d466c'), ('changeset_revisions', '9dabbfd73c8a')]), 'tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf7e8d466c&changeset_revisions=9dabbfd73c8a')
  wsgi process: 'Multithreaded'
------------------------------------------------------------

I would be grateful for any comments.

Best regards, Jens


> -----Ursprüngliche Nachricht-----
> Von: Greg Von Kuster [mailto:greg@bx.psu.edu]
> Gesendet: Donnerstag, 30. Mai 2013 15:39
> An: Keilwagen, Jens
> Cc: Galaxy Dev
> Betreff: Re: AW: [galaxy-dev] Internal Server Error during installation
> of ncbi_blast_plus
>
> Hello Jens,
>
> It looks like your Galaxy instance is fairly old.  What version of
> Galaxy are you running?
>
> Thanks,
>
> Greg Von Kuster
>
> On May 30, 2013, at 1:49 AM, Keilwagen, Jens wrote:
>
> > Hi Greg,
> >
> > here is what the paster.log says:
> >
> > 172.31.30.183 - - [30/May/2013:07:39:54 +0200] "GET
> /admin_toolshed/browse_tool_shed?tool_shed_url=http%3A%2F%2Ftoolshed.g2
> .bx.psu.edu%2F HTTP/1.0" 302 -
> "http://galaxy.jki.bund.de/admin_toolshed/browse_tool_sheds"
> "Mozilla/5.0 (Windows NT 6.1; WOW64; rv:21.0) Gecko/20100101
> Firefox/21.0"
> > 172.31.30.183 - - [30/May/2013:07:40:17 +0200] "GET
> /admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx
> .psu.edu/&repository_ids=1d92ebdf7e8d466c&changeset_revisions=9dabbfd73
> c8a HTTP/1.0" 500 -
> "http://toolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset?re
> pository_id=1d92ebdf7e8d466c&changeset_revision=9dabbfd73c8a"
> "Mozilla/5.0 (Windows NT 6.1; WOW64; rv:21.0) Gecko/20100101
> Firefox/21.0"
> > Error - <type 'exceptions.ValueError'>: too many values to unpack
> > URL:
> >
> http://galaxy.jki.bund.de/admin_toolshed/prepare_for_install?tool_shed
> >
> _url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf7e8d466c&ch
> > angeset_revisions=9dabbfd73c8a File
> > '/opt/galaxy/galaxy-
> dist/lib/galaxy/web/framework/middleware/error.py'
> > , line 149 in __call__  app_iter = self.application(environ,
> > sr_checker) File
> > '/opt/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-
> py2.6.egg/paste/recursive.
> > py', line 84 in __call__  return self.application(environ,
> > start_response) File
> > '/opt/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-
> py2.6.egg/paste/httpexcept
> > ions.py', line 633 in __call__  return self.application(environ,
> > start_response) File
> > '/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 128
> > in __call__  return self.handle_request( environ, start_response )
> > File '/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line
> > 184 in handle_request  body = method( trans, **kwargs ) File
> > '/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line
> > 231 in decorator  return func( self, trans, *args, **kwargs ) File
> > '/opt/galaxy/galaxy-
> dist/lib/galaxy/webapps/galaxy/controllers/admin_t
> > oolshed.py', line 894 in prepare_for_install
> > common_install_util.get_dependencies_for_repository( trans,
> > tool_shed_url, repo_info_dict, includes_tool_dependencies ) File
> > '/opt/galaxy/galaxy-dist/lib/tool_shed/util/common_install_util.py',
> > line 88 in get_dependencies_for_repository  installed_rd, missing_rd
> =
> > get_installed_and_missing_repository_dependencies_for_new_install(
> > trans, repo_info_tuple ) File
> > '/opt/galaxy/galaxy-dist/lib/tool_shed/util/common_install_util.py',
> > line 192 in
> > get_installed_and_missing_repository_dependencies_for_new_install
> >  tool_shed, name, owner, changeset_revision = rd_tup
> > ValueError: too many values to unpack
> >
> >
> > CGI Variables
> > -------------
> >  CONTENT_LENGTH: '0'
> >  HTTP_ACCEPT:
> 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8'
> >  HTTP_ACCEPT_ENCODING: 'gzip, deflate'
> >  HTTP_ACCEPT_LANGUAGE: 'de-de,de;q=0.8,en-us;q=0.5,en;q=0.3'
> >  HTTP_CACHE_CONTROL: 'max-age=0'
> >  HTTP_CONNECTION: 'keep-alive'
> >  HTTP_COOKIE:
> 'galaxysession=c6ca0ddb55be603a88fa41dbba7680819dc3ac10c92a6efa6da917af
> 7060700e4360e4afb5987baa'
> >  HTTP_HOST: 'galaxy.jki.bund.de'
> >  HTTP_REFERER:
> 'http://toolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset?re
> pository_id=1d92ebdf7e8d466c&changeset_revision=9dabbfd73c8a'
> >  HTTP_USER_AGENT: 'Mozilla/5.0 (Windows NT 6.1; WOW64; rv:21.0)
> Gecko/20100101 Firefox/21.0'
> >  HTTP_VIA: '1.1 proxy.jki.bund.de:8000 (squid/2.7.STABLE9)'
> >  HTTP_X_FORWARDED_FOR: '172.31.30.183'
> >  ORGINAL_REMOTE_ADDR: '172.16.20.52'
> >  PATH_INFO: '/admin_toolshed/prepare_for_install'
> >  QUERY_STRING:
> 'tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf7e
> 8d466c&changeset_revisions=9dabbfd73c8a'
> >  REMOTE_ADDR: '172.31.30.183'
> >  REQUEST_METHOD: 'GET'
> >  SERVER_NAME: '0.0.0.0'
> >  SERVER_PORT: '8080'
> >  SERVER_PROTOCOL: 'HTTP/1.0'
> >
> >
> > WSGI Variables
> > --------------
> >  application: <paste.recursive.RecursiveMiddleware object at
> > 0x8781210>
> >  paste.cookies: (<SimpleCookie:
> >
> galaxysession='c6ca0ddb55be603a88fa41dbba7680819dc3ac10c92a6efa6da917a
> > f7060700e4360e4afb5987baa'>,
> >
> 'galaxysession=c6ca0ddb55be603a88fa41dbba7680819dc3ac10c92a6efa6da917a
> > f7060700e4360e4afb5987baa')
> >  paste.expected_exceptions: [<class
> > 'paste.httpexceptions.HTTPException'>]
> >  paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler
> > object at 0x8851bd0>
> >  paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at
> > 0x87b2450>
> >  paste.parsed_querystring: ([('tool_shed_url',
> > 'http://toolshed.g2.bx.psu.edu/'), ('repository_ids',
> > '1d92ebdf7e8d466c'), ('changeset_revisions', '9dabbfd73c8a')],
> >
> 'tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf7
> > e8d466c&changeset_revisions=9dabbfd73c8a')
> >  paste.recursive.forward: <paste.recursive.Forwarder from />
> >  paste.recursive.include: <paste.recursive.Includer from />
> >  paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter
> > from />
> >  paste.recursive.script_name: ''
> >  paste.throw_errors: True
> >  request_id: '6905bf7ac8eb11e297ec0050568d0b1f'
> >  webob._parsed_query_vars: (MultiDict([('tool_shed_url',
> > 'http://toolshed.g2.bx.psu.edu/'), ('repository_ids',
> > '1d92ebdf7e8d466c'), ('changeset_revisions', '9dabbfd73c8a')]),
> >
> 'tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf7
> > e8d466c&changeset_revisions=9dabbfd73c8a')
> >  wsgi process: 'Multithreaded'
> > ------------------------------------------------------------
> >
> > However, installing other tools from the tool shed was no problem so
> far.
> >
> > Best regards, Jens
> >
> >> -----Ursprüngliche Nachricht-----
> >> Von: Greg Von Kuster [mailto:greg@bx.psu.edu]
> >> Gesendet: Mittwoch, 29. Mai 2013 16:45
> >> An: Keilwagen, Jens
> >> Cc: Galaxy Dev
> >> Betreff: Re: [galaxy-dev] Internal Server Error during installation
> >> of ncbi_blast_plus
> >>
> >> Hello Jens,
> >>
> >> What does your Galaxy paster log show that is related to the
> internal
> >> server error?
> >>
> >> Greg Von Kuster
> >>
> >> On May 29, 2013, at 10:13 AM, Peter Cock wrote:
> >>
> >>> On Wed, May 29, 2013 at 8:33 AM, Keilwagen, Jens
> >>> <jens.keilwagen@jki.bund.de> wrote:
> >>>> Hi guys,
> >>>>
> >>>> we are currently estalishing our own local Galaxy instance.
> >>>> However, when we try to install "Repository 'ncbi_blast_plus'"
> from
> >>>> the
> >> Galaxy
> >>>> main tool shed via the admin pages, we obtain the following error
> >>>>
> >>>> "Internal Server Error
> >>>> Galaxy was unable to sucessfully complete your request
> >>>>
> >>>> An error occurred.
> >>>> This may be an intermittent problem due to load or other
> >>>> unpredictable factors, reloading the page may address the problem.
> >>>>
> >>>> The error has been logged to our team."
> >>>>
> >>>> We tried to install on three different days. Hence, we believe
> >>>> there
> >> might be another problem.
> >>>>
> >>>> Thanks for any help.
> >>>>
> >>>> Best regards, Jens
> >>>
> >>> Hi Jens,
> >>>
> >>> The Galaxy team should be able to ask some more targeted questions,
> >>> but how far did the process get? Were you asked about the
> >> dependencies
> >>> (e.g. the blast_dataypes repository or the underlying BLAST+
> >> binaries)?
> >>>
> >>> Peter
> >>>
> >>> P.S. What kind of system are you using? 64 bit Linux? Mac OS X?
> >>> ___________________________________________________________
> >>> 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/
> >
> >


___________________________________________________________
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Re: Internal Server Error during installation of ncbi_blast_plus

Greg Von Kuster
Hello Jens.

What is the name of the repository you are trying to install from the tool shed?  Can you run the following sql in your database and reply back with the results?

select id, name, owner, installed_changeset_revision, changeset_revision, deleted, status, error_message from tool_shed_repository where name = '<the name of the repo you are trying to install>';

Thanks,

Greg Von Kuster

On May 31, 2013, at 1:51 AM, Keilwagen, Jens wrote:

> Hi Greg,
>
> thanks for your comment. Some days ago, I updated Galaxy following:
>
> http://wiki.galaxyproject.org/News/2013_04_08_Galaxy_Security_Release
>
> Here is what "hg sum" said
>
> parent: 9292:2cc8d10988e0 security_2013.04.08
> controllers/history: use get_history in switch_to_history
> Zweig: stable
> Übernehme: 10 unbekannt (clean)
> Aktualisiere: 11 neue Änderungssätze (Aktualisierung)
>
> (Sorry for the German terms.) I then updated Galaxy by
>
> hg update
>
> obtaining:
>
> parent: 9320:47ddf167c9f1 tip
> Use Galaxy's ErrorMiddleware since Paste's doesn't return start_response.  Fixes downloading tarballs from the Tool Shed when use_debug = false.
> Zweig: stable
> Übernehme: 10 unbekannt (clean)
> Aktualisiere: (aktuell)
>
> I then restarted Galaxy and tried to install again, but it fails again. Even trying for a second time doesn't change the behaviour. Here is what paster.log says:
>
> 172.31.30.183 - - [31/May/2013:07:47:32 +0200] "GET /admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf7e8d466c&changeset_revisions=9dabbfd73c8a HTTP/1.0" 500 - "http://toolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset?repository_id=1d92ebdf7e8d466c&changeset_revision=9dabbfd73c8a" "Mozilla/5.0 (Windows NT 6.1; WOW64; rv:21.0) Gecko/20100101 Firefox/21.0"
> Error - <type 'exceptions.ValueError'>: too many values to unpack
> URL: http://galaxy.jki.bund.de/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf7e8d466c&changeset_revisions=9dabbfd73c8a
> File '/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__
>  app_iter = self.application(environ, sr_checker)
> File '/opt/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py', line 84 in __call__
>  return self.application(environ, start_response)
> File '/opt/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py', line 633 in __call__
>  return self.application(environ, start_response)
> File '/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 128 in __call__
>  return self.handle_request( environ, start_response )
> File '/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 184 in handle_request
>  body = method( trans, **kwargs )
> File '/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 231 in decorator
>  return func( self, trans, *args, **kwargs )
> File '/opt/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 894 in prepare_for_install
>  common_install_util.get_dependencies_for_repository( trans, tool_shed_url, repo_info_dict, includes_tool_dependencies )
> File '/opt/galaxy/galaxy-dist/lib/tool_shed/util/common_install_util.py', line 88 in get_dependencies_for_repository
>  installed_rd, missing_rd = get_installed_and_missing_repository_dependencies_for_new_install( trans, repo_info_tuple )
> File '/opt/galaxy/galaxy-dist/lib/tool_shed/util/common_install_util.py', line 192 in get_installed_and_missing_repository_dependencies_for_new_install
>  tool_shed, name, owner, changeset_revision = rd_tup
> ValueError: too many values to unpack
>
>
> CGI Variables
> -------------
>  CONTENT_LENGTH: '0'
>  HTTP_ACCEPT: 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8'
>  HTTP_ACCEPT_ENCODING: 'gzip, deflate'
>  HTTP_ACCEPT_LANGUAGE: 'de-de,de;q=0.8,en-us;q=0.5,en;q=0.3'
>  HTTP_CACHE_CONTROL: 'max-age=0'
>  HTTP_CONNECTION: 'keep-alive'
>  HTTP_COOKIE: 'galaxysession=c6ca0ddb55be603a88fa41dbba7680819dc3ac10c92a6efa6da917af7060700e4360e4afb5987baa'
>  HTTP_HOST: 'galaxy.jki.bund.de'
>  HTTP_REFERER: 'http://toolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset?repository_id=1d92ebdf7e8d466c&changeset_revision=9dabbfd73c8a'
>  HTTP_USER_AGENT: 'Mozilla/5.0 (Windows NT 6.1; WOW64; rv:21.0) Gecko/20100101 Firefox/21.0'
>  HTTP_VIA: '1.1 proxy.jki.bund.de:8000 (squid/2.7.STABLE9)'
>  HTTP_X_FORWARDED_FOR: '172.31.30.183'
>  ORGINAL_REMOTE_ADDR: '172.16.20.52'
>  PATH_INFO: '/admin_toolshed/prepare_for_install'
>  QUERY_STRING: 'tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf7e8d466c&changeset_revisions=9dabbfd73c8a'
>  REMOTE_ADDR: '172.31.30.183'
>  REQUEST_METHOD: 'GET'
>  SERVER_NAME: '0.0.0.0'
>  SERVER_PORT: '8080'
>  SERVER_PROTOCOL: 'HTTP/1.0'
>
>
> WSGI Variables
> --------------
>  application: <paste.recursive.RecursiveMiddleware object at 0x7c3ed50>
>  paste.cookies: (<SimpleCookie: galaxysession='c6ca0ddb55be603a88fa41dbba7680819dc3ac10c92a6efa6da917af7060700e4360e4afb5987baa'>, 'galaxysession=c6ca0ddb55be603a88fa41dbba7680819dc3ac10c92a6efa6da917af7060700e4360e4afb5987baa')
>  paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>]
>  paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object at 0x7c3e710>
>  paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at 0x7c9ff50>
>  paste.parsed_querystring: ([('tool_shed_url', 'http://toolshed.g2.bx.psu.edu/'), ('repository_ids', '1d92ebdf7e8d466c'), ('changeset_revisions', '9dabbfd73c8a')], 'tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf7e8d466c&changeset_revisions=9dabbfd73c8a')
>  paste.recursive.forward: <paste.recursive.Forwarder from />
>  paste.recursive.include: <paste.recursive.Includer from />
>  paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from />
>  paste.recursive.script_name: ''
>  paste.throw_errors: True
>  request_id: '964a9788c9b511e2bb080050568d0b1f'
>  webob._parsed_query_vars: (MultiDict([('tool_shed_url', 'http://toolshed.g2.bx.psu.edu/'), ('repository_ids', '1d92ebdf7e8d466c'), ('changeset_revisions', '9dabbfd73c8a')]), 'tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf7e8d466c&changeset_revisions=9dabbfd73c8a')
>  wsgi process: 'Multithreaded'
> ------------------------------------------------------------
>
> I would be graetful for any comments.
>
> Best regards, Jens
>
>
>> -----Ursprüngliche Nachricht-----
>> Von: Greg Von Kuster [mailto:[hidden email]]
>> Gesendet: Donnerstag, 30. Mai 2013 15:39
>> An: Keilwagen, Jens
>> Cc: Galaxy Dev
>> Betreff: Re: AW: [galaxy-dev] Internal Server Error during installation
>> of ncbi_blast_plus
>>
>> Hello Jens,
>>
>> It looks like your Galaxy instance is fairly old.  What version of
>> Galaxy are you running?
>>
>> Thanks,
>>
>> Greg Von Kuster
>>
>> On May 30, 2013, at 1:49 AM, Keilwagen, Jens wrote:
>>
>>> Hi Greg,
>>>
>>> here is what the paster.log says:
>>>
>>> 172.31.30.183 - - [30/May/2013:07:39:54 +0200] "GET
>> /admin_toolshed/browse_tool_shed?tool_shed_url=http%3A%2F%2Ftoolshed.g2
>> .bx.psu.edu%2F HTTP/1.0" 302 -
>> "http://galaxy.jki.bund.de/admin_toolshed/browse_tool_sheds"
>> "Mozilla/5.0 (Windows NT 6.1; WOW64; rv:21.0) Gecko/20100101
>> Firefox/21.0"
>>> 172.31.30.183 - - [30/May/2013:07:40:17 +0200] "GET
>> /admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx
>> .psu.edu/&repository_ids=1d92ebdf7e8d466c&changeset_revisions=9dabbfd73
>> c8a HTTP/1.0" 500 -
>> "http://toolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset?re
>> pository_id=1d92ebdf7e8d466c&changeset_revision=9dabbfd73c8a"
>> "Mozilla/5.0 (Windows NT 6.1; WOW64; rv:21.0) Gecko/20100101
>> Firefox/21.0"
>>> Error - <type 'exceptions.ValueError'>: too many values to unpack
>>> URL:
>>>
>> http://galaxy.jki.bund.de/admin_toolshed/prepare_for_install?tool_shed
>>>
>> _url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf7e8d466c&ch
>>> angeset_revisions=9dabbfd73c8a File
>>> '/opt/galaxy/galaxy-
>> dist/lib/galaxy/web/framework/middleware/error.py'
>>> , line 149 in __call__  app_iter = self.application(environ,
>>> sr_checker) File
>>> '/opt/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-
>> py2.6.egg/paste/recursive.
>>> py', line 84 in __call__  return self.application(environ,
>>> start_response) File
>>> '/opt/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-
>> py2.6.egg/paste/httpexcept
>>> ions.py', line 633 in __call__  return self.application(environ,
>>> start_response) File
>>> '/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 128
>>> in __call__  return self.handle_request( environ, start_response )
>>> File '/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line
>>> 184 in handle_request  body = method( trans, **kwargs ) File
>>> '/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line
>>> 231 in decorator  return func( self, trans, *args, **kwargs ) File
>>> '/opt/galaxy/galaxy-
>> dist/lib/galaxy/webapps/galaxy/controllers/admin_t
>>> oolshed.py', line 894 in prepare_for_install
>>> common_install_util.get_dependencies_for_repository( trans,
>>> tool_shed_url, repo_info_dict, includes_tool_dependencies ) File
>>> '/opt/galaxy/galaxy-dist/lib/tool_shed/util/common_install_util.py',
>>> line 88 in get_dependencies_for_repository  installed_rd, missing_rd
>> =
>>> get_installed_and_missing_repository_dependencies_for_new_install(
>>> trans, repo_info_tuple ) File
>>> '/opt/galaxy/galaxy-dist/lib/tool_shed/util/common_install_util.py',
>>> line 192 in
>>> get_installed_and_missing_repository_dependencies_for_new_install
>>> tool_shed, name, owner, changeset_revision = rd_tup
>>> ValueError: too many values to unpack
>>>
>>>
>>> CGI Variables
>>> -------------
>>> CONTENT_LENGTH: '0'
>>> HTTP_ACCEPT:
>> 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8'
>>> HTTP_ACCEPT_ENCODING: 'gzip, deflate'
>>> HTTP_ACCEPT_LANGUAGE: 'de-de,de;q=0.8,en-us;q=0.5,en;q=0.3'
>>> HTTP_CACHE_CONTROL: 'max-age=0'
>>> HTTP_CONNECTION: 'keep-alive'
>>> HTTP_COOKIE:
>> 'galaxysession=c6ca0ddb55be603a88fa41dbba7680819dc3ac10c92a6efa6da917af
>> 7060700e4360e4afb5987baa'
>>> HTTP_HOST: 'galaxy.jki.bund.de'
>>> HTTP_REFERER:
>> 'http://toolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset?re
>> pository_id=1d92ebdf7e8d466c&changeset_revision=9dabbfd73c8a'
>>> HTTP_USER_AGENT: 'Mozilla/5.0 (Windows NT 6.1; WOW64; rv:21.0)
>> Gecko/20100101 Firefox/21.0'
>>> HTTP_VIA: '1.1 proxy.jki.bund.de:8000 (squid/2.7.STABLE9)'
>>> HTTP_X_FORWARDED_FOR: '172.31.30.183'
>>> ORGINAL_REMOTE_ADDR: '172.16.20.52'
>>> PATH_INFO: '/admin_toolshed/prepare_for_install'
>>> QUERY_STRING:
>> 'tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf7e
>> 8d466c&changeset_revisions=9dabbfd73c8a'
>>> REMOTE_ADDR: '172.31.30.183'
>>> REQUEST_METHOD: 'GET'
>>> SERVER_NAME: '0.0.0.0'
>>> SERVER_PORT: '8080'
>>> SERVER_PROTOCOL: 'HTTP/1.0'
>>>
>>>
>>> WSGI Variables
>>> --------------
>>> application: <paste.recursive.RecursiveMiddleware object at
>>> 0x8781210>
>>> paste.cookies: (<SimpleCookie:
>>>
>> galaxysession='c6ca0ddb55be603a88fa41dbba7680819dc3ac10c92a6efa6da917a
>>> f7060700e4360e4afb5987baa'>,
>>>
>> 'galaxysession=c6ca0ddb55be603a88fa41dbba7680819dc3ac10c92a6efa6da917a
>>> f7060700e4360e4afb5987baa')
>>> paste.expected_exceptions: [<class
>>> 'paste.httpexceptions.HTTPException'>]
>>> paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler
>>> object at 0x8851bd0>
>>> paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at
>>> 0x87b2450>
>>> paste.parsed_querystring: ([('tool_shed_url',
>>> 'http://toolshed.g2.bx.psu.edu/'), ('repository_ids',
>>> '1d92ebdf7e8d466c'), ('changeset_revisions', '9dabbfd73c8a')],
>>>
>> 'tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf7
>>> e8d466c&changeset_revisions=9dabbfd73c8a')
>>> paste.recursive.forward: <paste.recursive.Forwarder from />
>>> paste.recursive.include: <paste.recursive.Includer from />
>>> paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter
>>> from />
>>> paste.recursive.script_name: ''
>>> paste.throw_errors: True
>>> request_id: '6905bf7ac8eb11e297ec0050568d0b1f'
>>> webob._parsed_query_vars: (MultiDict([('tool_shed_url',
>>> 'http://toolshed.g2.bx.psu.edu/'), ('repository_ids',
>>> '1d92ebdf7e8d466c'), ('changeset_revisions', '9dabbfd73c8a')]),
>>>
>> 'tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf7
>>> e8d466c&changeset_revisions=9dabbfd73c8a')
>>> wsgi process: 'Multithreaded'
>>> ------------------------------------------------------------
>>>
>>> However, installing other tools from the tool shed was no problem so
>> far.
>>>
>>> Best regards, Jens
>>>
>>>> -----Ursprüngliche Nachricht-----
>>>> Von: Greg Von Kuster [mailto:[hidden email]]
>>>> Gesendet: Mittwoch, 29. Mai 2013 16:45
>>>> An: Keilwagen, Jens
>>>> Cc: Galaxy Dev
>>>> Betreff: Re: [galaxy-dev] Internal Server Error during installation
>>>> of ncbi_blast_plus
>>>>
>>>> Hello Jens,
>>>>
>>>> What does your Galaxy paster log show that is related to the
>> internal
>>>> server error?
>>>>
>>>> Greg Von Kuster
>>>>
>>>> On May 29, 2013, at 10:13 AM, Peter Cock wrote:
>>>>
>>>>> On Wed, May 29, 2013 at 8:33 AM, Keilwagen, Jens
>>>>> <[hidden email]> wrote:
>>>>>> Hi guys,
>>>>>>
>>>>>> we are currently estalishing our own local Galaxy instance.
>>>>>> However, when we try to install "Repository 'ncbi_blast_plus'"
>> from
>>>>>> the
>>>> Galaxy
>>>>>> main tool shed via the admin pages, we obtain the following error
>>>>>>
>>>>>> "Internal Server Error
>>>>>> Galaxy was unable to sucessfully complete your request
>>>>>>
>>>>>> An error occurred.
>>>>>> This may be an intermittent problem due to load or other
>>>>>> unpredictable factors, reloading the page may address the problem.
>>>>>>
>>>>>> The error has been logged to our team."
>>>>>>
>>>>>> We tried to install on three different days. Hence, we believe
>>>>>> there
>>>> might be another problem.
>>>>>>
>>>>>> Thanks for any help.
>>>>>>
>>>>>> Best regards, Jens
>>>>>
>>>>> Hi Jens,
>>>>>
>>>>> The Galaxy team should be able to ask some more targeted questions,
>>>>> but how far did the process get? Were you asked about the
>>>> dependencies
>>>>> (e.g. the blast_dataypes repository or the underlying BLAST+
>>>> binaries)?
>>>>>
>>>>> Peter
>>>>>
>>>>> P.S. What kind of system are you using? 64 bit Linux? Mac OS X?
>>>>> ___________________________________________________________
>>>>> 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:
>  http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>  http://galaxyproject.org/search/mailinglists/
>


___________________________________________________________
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Re: Internal Server Error during installation of ncbi_blast_plus

Jens
Hi Greg,

Thanks a lot for your email.
I hope, I did do not misunderstand something. We are trying to install "ncbi_blast_plus" from the "Galaxy main tool shed". As we did not manage to install "ncbi_blast_plus" the "where" clause does not make sense to me. Hence, I omit it. Here is the result.

mysql> select id, name, owner,
mysql> installed_changeset_revision,changeset_revision, deleted, status,
mysql> error_message from tool_shed_repository;
+----+------------------------+---------------+------------------------------+--------------------+---------+-----------+---------------+
| id | name                   | owner         | installed_changeset_revision | changeset_revision | deleted | status    | error_message |
+----+------------------------+---------------+------------------------------+--------------------+---------+-----------+---------------+
|  1 | cutadapt               | lparsons      | 2d6671b10919                 | 2d6671b10919       |       0 | Installed | NULL          |
|  2 | mirdeep2_and_targetspy | nikhil-joshi  | 798fe7ba8b5e                 | 798fe7ba8b5e       |       0 | Installed | NULL          |
|  3 | clustalomega           | clustalomega  | bc707542e5de                 | bc707542e5de       |       0 | Installed | NULL          |
|  4 | head_and_tail          | xuebing       | 00dba791c4a2                 | 00dba791c4a2       |       0 | Installed | NULL          |
|  5 | seq_match              | xuebing       | 3fd777932736                 | 3fd777932736       |       0 | Installed | NULL          |
|  6 | dreme                  | xuebing       | 83fb93488cad                 | 83fb93488cad       |       0 | Installed | NULL          |
|  7 | velvet_toolsuite       | edward-kirton | 4afe13ac23b6                 | 4afe13ac23b6       |       0 | Installed | NULL          |
|  8 | velvet_optimiser       | simon-gladman | 43c89d82a7d3                 | 43c89d82a7d3       |       0 | Installed | NULL          |
|  9 | roche454_toolsuite     | edward-kirton | 368a6ebebdde                 | 368a6ebebdde       |       0 | Installed | NULL          |
| 10 | mira_assembler         | peterjc       | 4266cccbb45a                 | 4266cccbb45a       |       0 | Installed | NULL          |
| 11 | abyss_toolsuite        | edward-kirton | 92636934a189                 | 92636934a189       |       0 | Installed | NULL          |
| 12 | bwa_wrappers           | devteam       | 150b3fe44caa                 | 150b3fe44caa       |       0 | Installed | NULL          |
| 13 | mafft                  | dereeper      | d7a735d3625e                 | d7a735d3625e       |       0 | Installed | NULL          |
| 14 | blast_datatypes        | devteam       | b3a3ba0c1d47                 | b3a3ba0c1d47       |       0 | Installed | NULL          |
| 15 | blast                  | edward-kirton | f3ac34855f5e                 | f3ac34855f5e       |       0 | Installed | NULL          |
| 16 | cdf_plot               | xuebing       | 900fd0a7428d                 | 900fd0a7428d       |       0 | Installed | NULL          |
| 17 | plot_distribution      | ynewton       | f180c4ef9128                 | f180c4ef9128       |       0 | Installed | NULL          |
+----+------------------------+---------------+------------------------------+--------------------+---------+-----------+---------------+

Does this help?


Best regards, Jens

> -----Ursprüngliche Nachricht-----
> Von: Greg Von Kuster [mailto:[hidden email]]
> Gesendet: Dienstag, 4. Juni 2013 15:29
> An: Keilwagen, Jens
> Cc: Galaxy Dev
> Betreff: Re: [galaxy-dev] Internal Server Error during installation of
> ncbi_blast_plus
>
> Hello Jens.
>
> What is the name of the repository you are trying to install from the
> tool shed?  Can you run the following sql in your database and reply
> back with the results?
>
> select id, name, owner, installed_changeset_revision,
> changeset_revision, deleted, status, error_message from
> tool_shed_repository where name = '<the name of the repo you are trying
> to install>';
>
> Thanks,
>
> Greg Von Kuster
>
> On May 31, 2013, at 1:51 AM, Keilwagen, Jens wrote:
>
> > Hi Greg,
> >
> > thanks for your comment. Some days ago, I updated Galaxy following:
> >
> > http://wiki.galaxyproject.org/News/2013_04_08_Galaxy_Security_Release
> >
> > Here is what "hg sum" said
> >
> > parent: 9292:2cc8d10988e0 security_2013.04.08
> > controllers/history: use get_history in switch_to_history
> > Zweig: stable
> > Übernehme: 10 unbekannt (clean)
> > Aktualisiere: 11 neue Änderungssätze (Aktualisierung)
> >
> > (Sorry for the German terms.) I then updated Galaxy by
> >
> > hg update
> >
> > obtaining:
> >
> > parent: 9320:47ddf167c9f1 tip
> > Use Galaxy's ErrorMiddleware since Paste's doesn't return
> start_response.  Fixes downloading tarballs from the Tool Shed when
> use_debug = false.
> > Zweig: stable
> > Übernehme: 10 unbekannt (clean)
> > Aktualisiere: (aktuell)
> >
> > I then restarted Galaxy and tried to install again, but it fails
> again. Even trying for a second time doesn't change the behaviour. Here
> is what paster.log says:
> >
> > 172.31.30.183 - - [31/May/2013:07:47:32 +0200] "GET
> /admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx
> .psu.edu/&repository_ids=1d92ebdf7e8d466c&changeset_revisions=9dabbfd73
> c8a HTTP/1.0" 500 -
> "http://toolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset?re
> pository_id=1d92ebdf7e8d466c&changeset_revision=9dabbfd73c8a"
> "Mozilla/5.0 (Windows NT 6.1; WOW64; rv:21.0) Gecko/20100101
> Firefox/21.0"
> > Error - <type 'exceptions.ValueError'>: too many values to unpack
> > URL:
> >
> http://galaxy.jki.bund.de/admin_toolshed/prepare_for_install?tool_shed
> >
> _url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf7e8d466c&ch
> > angeset_revisions=9dabbfd73c8a File
> > '/opt/galaxy/galaxy-
> dist/lib/galaxy/web/framework/middleware/error.py'
> > , line 149 in __call__  app_iter = self.application(environ,
> > sr_checker) File
> > '/opt/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-
> py2.6.egg/paste/recursive.
> > py', line 84 in __call__  return self.application(environ,
> > start_response) File
> > '/opt/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-
> py2.6.egg/paste/httpexcept
> > ions.py', line 633 in __call__  return self.application(environ,
> > start_response) File
> > '/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 128
> > in __call__  return self.handle_request( environ, start_response )
> > File '/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line
> > 184 in handle_request  body = method( trans, **kwargs ) File
> > '/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line
> > 231 in decorator  return func( self, trans, *args, **kwargs ) File
> > '/opt/galaxy/galaxy-
> dist/lib/galaxy/webapps/galaxy/controllers/admin_t
> > oolshed.py', line 894 in prepare_for_install
> > common_install_util.get_dependencies_for_repository( trans,
> > tool_shed_url, repo_info_dict, includes_tool_dependencies ) File
> > '/opt/galaxy/galaxy-dist/lib/tool_shed/util/common_install_util.py',
> > line 88 in get_dependencies_for_repository  installed_rd, missing_rd
> =
> > get_installed_and_missing_repository_dependencies_for_new_install(
> > trans, repo_info_tuple ) File
> > '/opt/galaxy/galaxy-dist/lib/tool_shed/util/common_install_util.py',
> > line 192 in
> > get_installed_and_missing_repository_dependencies_for_new_install
> >  tool_shed, name, owner, changeset_revision = rd_tup
> > ValueError: too many values to unpack
> >
> >
> > CGI Variables
> > -------------
> >  CONTENT_LENGTH: '0'
> >  HTTP_ACCEPT:
> 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8'
> >  HTTP_ACCEPT_ENCODING: 'gzip, deflate'
> >  HTTP_ACCEPT_LANGUAGE: 'de-de,de;q=0.8,en-us;q=0.5,en;q=0.3'
> >  HTTP_CACHE_CONTROL: 'max-age=0'
> >  HTTP_CONNECTION: 'keep-alive'
> >  HTTP_COOKIE:
> 'galaxysession=c6ca0ddb55be603a88fa41dbba7680819dc3ac10c92a6efa6da917af
> 7060700e4360e4afb5987baa'
> >  HTTP_HOST: 'galaxy.jki.bund.de'
> >  HTTP_REFERER:
> 'http://toolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset?re
> pository_id=1d92ebdf7e8d466c&changeset_revision=9dabbfd73c8a'
> >  HTTP_USER_AGENT: 'Mozilla/5.0 (Windows NT 6.1; WOW64; rv:21.0)
> Gecko/20100101 Firefox/21.0'
> >  HTTP_VIA: '1.1 proxy.jki.bund.de:8000 (squid/2.7.STABLE9)'
> >  HTTP_X_FORWARDED_FOR: '172.31.30.183'
> >  ORGINAL_REMOTE_ADDR: '172.16.20.52'
> >  PATH_INFO: '/admin_toolshed/prepare_for_install'
> >  QUERY_STRING:
> 'tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf7e
> 8d466c&changeset_revisions=9dabbfd73c8a'
> >  REMOTE_ADDR: '172.31.30.183'
> >  REQUEST_METHOD: 'GET'
> >  SERVER_NAME: '0.0.0.0'
> >  SERVER_PORT: '8080'
> >  SERVER_PROTOCOL: 'HTTP/1.0'
> >
> >
> > WSGI Variables
> > --------------
> >  application: <paste.recursive.RecursiveMiddleware object at
> > 0x7c3ed50>
> >  paste.cookies: (<SimpleCookie:
> >
> galaxysession='c6ca0ddb55be603a88fa41dbba7680819dc3ac10c92a6efa6da917a
> > f7060700e4360e4afb5987baa'>,
> >
> 'galaxysession=c6ca0ddb55be603a88fa41dbba7680819dc3ac10c92a6efa6da917a
> > f7060700e4360e4afb5987baa')
> >  paste.expected_exceptions: [<class
> > 'paste.httpexceptions.HTTPException'>]
> >  paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler
> > object at 0x7c3e710>
> >  paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at
> > 0x7c9ff50>
> >  paste.parsed_querystring: ([('tool_shed_url',
> > 'http://toolshed.g2.bx.psu.edu/'), ('repository_ids',
> > '1d92ebdf7e8d466c'), ('changeset_revisions', '9dabbfd73c8a')],
> >
> 'tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf7
> > e8d466c&changeset_revisions=9dabbfd73c8a')
> >  paste.recursive.forward: <paste.recursive.Forwarder from />
> >  paste.recursive.include: <paste.recursive.Includer from />
> >  paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter
> > from />
> >  paste.recursive.script_name: ''
> >  paste.throw_errors: True
> >  request_id: '964a9788c9b511e2bb080050568d0b1f'
> >  webob._parsed_query_vars: (MultiDict([('tool_shed_url',
> > 'http://toolshed.g2.bx.psu.edu/'), ('repository_ids',
> > '1d92ebdf7e8d466c'), ('changeset_revisions', '9dabbfd73c8a')]),
> >
> 'tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf7
> > e8d466c&changeset_revisions=9dabbfd73c8a')
> >  wsgi process: 'Multithreaded'
> > ------------------------------------------------------------
> >
> > I would be graetful for any comments.
> >
> > Best regards, Jens
> >
> >
> >> -----Ursprüngliche Nachricht-----
> >> Von: Greg Von Kuster [mailto:[hidden email]]
> >> Gesendet: Donnerstag, 30. Mai 2013 15:39
> >> An: Keilwagen, Jens
> >> Cc: Galaxy Dev
> >> Betreff: Re: AW: [galaxy-dev] Internal Server Error during
> >> installation of ncbi_blast_plus
> >>
> >> Hello Jens,
> >>
> >> It looks like your Galaxy instance is fairly old.  What version of
> >> Galaxy are you running?
> >>
> >> Thanks,
> >>
> >> Greg Von Kuster
> >>
> >> On May 30, 2013, at 1:49 AM, Keilwagen, Jens wrote:
> >>
> >>> Hi Greg,
> >>>
> >>> here is what the paster.log says:
> >>>
> >>> 172.31.30.183 - - [30/May/2013:07:39:54 +0200] "GET
> >>
> /admin_toolshed/browse_tool_shed?tool_shed_url=http%3A%2F%2Ftoolshed.
> >> g2
> >> .bx.psu.edu%2F HTTP/1.0" 302 -
> >> "http://galaxy.jki.bund.de/admin_toolshed/browse_tool_sheds"
> >> "Mozilla/5.0 (Windows NT 6.1; WOW64; rv:21.0) Gecko/20100101
> >> Firefox/21.0"
> >>> 172.31.30.183 - - [30/May/2013:07:40:17 +0200] "GET
> >>
> /admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.
> >> bx
> >>
> .psu.edu/&repository_ids=1d92ebdf7e8d466c&changeset_revisions=9dabbfd
> >> 73
> >> c8a HTTP/1.0" 500 -
> >>
> "http://toolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset?
> >> re pository_id=1d92ebdf7e8d466c&changeset_revision=9dabbfd73c8a"
> >> "Mozilla/5.0 (Windows NT 6.1; WOW64; rv:21.0) Gecko/20100101
> >> Firefox/21.0"
> >>> Error - <type 'exceptions.ValueError'>: too many values to unpack
> >>> URL:
> >>>
> >>
> http://galaxy.jki.bund.de/admin_toolshed/prepare_for_install?tool_she
> >> d
> >>>
> >>
> _url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf7e8d466c&c
> >> h
> >>> angeset_revisions=9dabbfd73c8a File
> >>> '/opt/galaxy/galaxy-
> >> dist/lib/galaxy/web/framework/middleware/error.py'
> >>> , line 149 in __call__  app_iter = self.application(environ,
> >>> sr_checker) File
> >>> '/opt/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-
> >> py2.6.egg/paste/recursive.
> >>> py', line 84 in __call__  return self.application(environ,
> >>> start_response) File
> >>> '/opt/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-
> >> py2.6.egg/paste/httpexcept
> >>> ions.py', line 633 in __call__  return self.application(environ,
> >>> start_response) File
> >>> '/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line
> 128
> >>> in __call__  return self.handle_request( environ, start_response )
> >>> File '/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py',
> >>> line
> >>> 184 in handle_request  body = method( trans, **kwargs ) File
> >>> '/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py',
> line
> >>> 231 in decorator  return func( self, trans, *args, **kwargs ) File
> >>> '/opt/galaxy/galaxy-
> >> dist/lib/galaxy/webapps/galaxy/controllers/admin_t
> >>> oolshed.py', line 894 in prepare_for_install
> >>> common_install_util.get_dependencies_for_repository( trans,
> >>> tool_shed_url, repo_info_dict, includes_tool_dependencies ) File
> >>> '/opt/galaxy/galaxy-
> dist/lib/tool_shed/util/common_install_util.py',
> >>> line 88 in get_dependencies_for_repository  installed_rd,
> missing_rd
> >> =
> >>> get_installed_and_missing_repository_dependencies_for_new_install(
> >>> trans, repo_info_tuple ) File
> >>> '/opt/galaxy/galaxy-
> dist/lib/tool_shed/util/common_install_util.py',
> >>> line 192 in
> >>> get_installed_and_missing_repository_dependencies_for_new_install
> >>> tool_shed, name, owner, changeset_revision = rd_tup
> >>> ValueError: too many values to unpack
> >>>
> >>>
> >>> CGI Variables
> >>> -------------
> >>> CONTENT_LENGTH: '0'
> >>> HTTP_ACCEPT:
> >> 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8'
> >>> HTTP_ACCEPT_ENCODING: 'gzip, deflate'
> >>> HTTP_ACCEPT_LANGUAGE: 'de-de,de;q=0.8,en-us;q=0.5,en;q=0.3'
> >>> HTTP_CACHE_CONTROL: 'max-age=0'
> >>> HTTP_CONNECTION: 'keep-alive'
> >>> HTTP_COOKIE:
> >>
> 'galaxysession=c6ca0ddb55be603a88fa41dbba7680819dc3ac10c92a6efa6da917
> >> af
> >> 7060700e4360e4afb5987baa'
> >>> HTTP_HOST: 'galaxy.jki.bund.de'
> >>> HTTP_REFERER:
> >>
> 'http://toolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset?
> >> re pository_id=1d92ebdf7e8d466c&changeset_revision=9dabbfd73c8a'
> >>> HTTP_USER_AGENT: 'Mozilla/5.0 (Windows NT 6.1; WOW64; rv:21.0)
> >> Gecko/20100101 Firefox/21.0'
> >>> HTTP_VIA: '1.1 proxy.jki.bund.de:8000 (squid/2.7.STABLE9)'
> >>> HTTP_X_FORWARDED_FOR: '172.31.30.183'
> >>> ORGINAL_REMOTE_ADDR: '172.16.20.52'
> >>> PATH_INFO: '/admin_toolshed/prepare_for_install'
> >>> QUERY_STRING:
> >>
> 'tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf
> >> 7e 8d466c&changeset_revisions=9dabbfd73c8a'
> >>> REMOTE_ADDR: '172.31.30.183'
> >>> REQUEST_METHOD: 'GET'
> >>> SERVER_NAME: '0.0.0.0'
> >>> SERVER_PORT: '8080'
> >>> SERVER_PROTOCOL: 'HTTP/1.0'
> >>>
> >>>
> >>> WSGI Variables
> >>> --------------
> >>> application: <paste.recursive.RecursiveMiddleware object at
> >>> 0x8781210>
> >>> paste.cookies: (<SimpleCookie:
> >>>
> >>
> galaxysession='c6ca0ddb55be603a88fa41dbba7680819dc3ac10c92a6efa6da917
> >> a
> >>> f7060700e4360e4afb5987baa'>,
> >>>
> >>
> 'galaxysession=c6ca0ddb55be603a88fa41dbba7680819dc3ac10c92a6efa6da917
> >> a
> >>> f7060700e4360e4afb5987baa')
> >>> paste.expected_exceptions: [<class
> >>> 'paste.httpexceptions.HTTPException'>]
> >>> paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler
> >>> object at 0x8851bd0>
> >>> paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object
> at
> >>> 0x87b2450>
> >>> paste.parsed_querystring: ([('tool_shed_url',
> >>> 'http://toolshed.g2.bx.psu.edu/'), ('repository_ids',
> >>> '1d92ebdf7e8d466c'), ('changeset_revisions', '9dabbfd73c8a')],
> >>>
> >>
> 'tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf
> >> 7
> >>> e8d466c&changeset_revisions=9dabbfd73c8a')
> >>> paste.recursive.forward: <paste.recursive.Forwarder from />
> >>> paste.recursive.include: <paste.recursive.Includer from />
> >>> paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter
> >>> from />
> >>> paste.recursive.script_name: ''
> >>> paste.throw_errors: True
> >>> request_id: '6905bf7ac8eb11e297ec0050568d0b1f'
> >>> webob._parsed_query_vars: (MultiDict([('tool_shed_url',
> >>> 'http://toolshed.g2.bx.psu.edu/'), ('repository_ids',
> >>> '1d92ebdf7e8d466c'), ('changeset_revisions', '9dabbfd73c8a')]),
> >>>
> >>
> 'tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf
> >> 7
> >>> e8d466c&changeset_revisions=9dabbfd73c8a')
> >>> wsgi process: 'Multithreaded'
> >>> ------------------------------------------------------------
> >>>
> >>> However, installing other tools from the tool shed was no problem
> so
> >> far.
> >>>
> >>> Best regards, Jens
> >>>
> >>>> -----Ursprüngliche Nachricht-----
> >>>> Von: Greg Von Kuster [mailto:[hidden email]]
> >>>> Gesendet: Mittwoch, 29. Mai 2013 16:45
> >>>> An: Keilwagen, Jens
> >>>> Cc: Galaxy Dev
> >>>> Betreff: Re: [galaxy-dev] Internal Server Error during
> installation
> >>>> of ncbi_blast_plus
> >>>>
> >>>> Hello Jens,
> >>>>
> >>>> What does your Galaxy paster log show that is related to the
> >> internal
> >>>> server error?
> >>>>
> >>>> Greg Von Kuster
> >>>>
> >>>> On May 29, 2013, at 10:13 AM, Peter Cock wrote:
> >>>>
> >>>>> On Wed, May 29, 2013 at 8:33 AM, Keilwagen, Jens
> >>>>> <[hidden email]> wrote:
> >>>>>> Hi guys,
> >>>>>>
> >>>>>> we are currently estalishing our own local Galaxy instance.
> >>>>>> However, when we try to install "Repository 'ncbi_blast_plus'"
> >> from
> >>>>>> the
> >>>> Galaxy
> >>>>>> main tool shed via the admin pages, we obtain the following
> error
> >>>>>>
> >>>>>> "Internal Server Error
> >>>>>> Galaxy was unable to sucessfully complete your request
> >>>>>>
> >>>>>> An error occurred.
> >>>>>> This may be an intermittent problem due to load or other
> >>>>>> unpredictable factors, reloading the page may address the
> problem.
> >>>>>>
> >>>>>> The error has been logged to our team."
> >>>>>>
> >>>>>> We tried to install on three different days. Hence, we believe
> >>>>>> there
> >>>> might be another problem.
> >>>>>>
> >>>>>> Thanks for any help.
> >>>>>>
> >>>>>> Best regards, Jens
> >>>>>
> >>>>> Hi Jens,
> >>>>>
> >>>>> The Galaxy team should be able to ask some more targeted
> >>>>> questions, but how far did the process get? Were you asked about
> >>>>> the
> >>>> dependencies
> >>>>> (e.g. the blast_dataypes repository or the underlying BLAST+
> >>>> binaries)?
> >>>>>
> >>>>> Peter
> >>>>>
> >>>>> P.S. What kind of system are you using? 64 bit Linux? Mac OS X?
> >>>>> ___________________________________________________________
> >>>>> 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:
> >  http://lists.bx.psu.edu/
> >
> > To search Galaxy mailing lists use the unified search at:
> >  http://galaxyproject.org/search/mailinglists/
> >


___________________________________________________________
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Re: Internal Server Error during installation of ncbi_blast_plus

Greg Von Kuster
Hi Jens,

Thanks for the information, but it doesn't help determine what is causing this behavior in your environment.  It's strange that you have never installed the ncbi_blast_plus repository (so it is not currently in some error state), and yet you cannot install it.  I am not able to reproduce this behavior, so I have no idea of it's cause or how to resolve it.  

We just completed the latest Galaxy release yesterday, so when it is convenient perhaps you could update your Galaxy environment again, although I don't believe your Galaxy version is the issue either.  

Sorry to not be of much help here, but this is unusual behavior that has not been seen in the community, so it's unclear how to resolve it.

Greg Von Kuster

On Jun 4, 2013, at 9:47 AM, Keilwagen, Jens wrote:

> Hi Greg,
>
> Thanks a lot for your email.
> I hope, I did do not misunderstand something. We are trying to install "ncbi_blast_plus" from the "Galaxy main tool shed". As we did not manage to install "ncbi_blast_plus" the "where" clause does not make sense to me. Hence, I omit it. Here is the result.
>
> mysql> select id, name, owner,
> mysql> installed_changeset_revision,changeset_revision, deleted, status,
> mysql> error_message from tool_shed_repository;
> +----+------------------------+---------------+------------------------------+--------------------+---------+-----------+---------------+
> | id | name                   | owner         | installed_changeset_revision | changeset_revision | deleted | status    | error_message |
> +----+------------------------+---------------+------------------------------+--------------------+---------+-----------+---------------+
> |  1 | cutadapt               | lparsons      | 2d6671b10919                 | 2d6671b10919       |       0 | Installed | NULL          |
> |  2 | mirdeep2_and_targetspy | nikhil-joshi  | 798fe7ba8b5e                 | 798fe7ba8b5e       |       0 | Installed | NULL          |
> |  3 | clustalomega           | clustalomega  | bc707542e5de                 | bc707542e5de       |       0 | Installed | NULL          |
> |  4 | head_and_tail          | xuebing       | 00dba791c4a2                 | 00dba791c4a2       |       0 | Installed | NULL          |
> |  5 | seq_match              | xuebing       | 3fd777932736                 | 3fd777932736       |       0 | Installed | NULL          |
> |  6 | dreme                  | xuebing       | 83fb93488cad                 | 83fb93488cad       |       0 | Installed | NULL          |
> |  7 | velvet_toolsuite       | edward-kirton | 4afe13ac23b6                 | 4afe13ac23b6       |       0 | Installed | NULL          |
> |  8 | velvet_optimiser       | simon-gladman | 43c89d82a7d3                 | 43c89d82a7d3       |       0 | Installed | NULL          |
> |  9 | roche454_toolsuite     | edward-kirton | 368a6ebebdde                 | 368a6ebebdde       |       0 | Installed | NULL          |
> | 10 | mira_assembler         | peterjc       | 4266cccbb45a                 | 4266cccbb45a       |       0 | Installed | NULL          |
> | 11 | abyss_toolsuite        | edward-kirton | 92636934a189                 | 92636934a189       |       0 | Installed | NULL          |
> | 12 | bwa_wrappers           | devteam       | 150b3fe44caa                 | 150b3fe44caa       |       0 | Installed | NULL          |
> | 13 | mafft                  | dereeper      | d7a735d3625e                 | d7a735d3625e       |       0 | Installed | NULL          |
> | 14 | blast_datatypes        | devteam       | b3a3ba0c1d47                 | b3a3ba0c1d47       |       0 | Installed | NULL          |
> | 15 | blast                  | edward-kirton | f3ac34855f5e                 | f3ac34855f5e       |       0 | Installed | NULL          |
> | 16 | cdf_plot               | xuebing       | 900fd0a7428d                 | 900fd0a7428d       |       0 | Installed | NULL          |
> | 17 | plot_distribution      | ynewton       | f180c4ef9128                 | f180c4ef9128       |       0 | Installed | NULL          |
> +----+------------------------+---------------+------------------------------+--------------------+---------+-----------+---------------+
>
> Does this help?
>
>
> Best regards, Jens
>
>> -----Ursprüngliche Nachricht-----
>> Von: Greg Von Kuster [mailto:[hidden email]]
>> Gesendet: Dienstag, 4. Juni 2013 15:29
>> An: Keilwagen, Jens
>> Cc: Galaxy Dev
>> Betreff: Re: [galaxy-dev] Internal Server Error during installation of
>> ncbi_blast_plus
>>
>> Hello Jens.
>>
>> What is the name of the repository you are trying to install from the
>> tool shed?  Can you run the following sql in your database and reply
>> back with the results?
>>
>> select id, name, owner, installed_changeset_revision,
>> changeset_revision, deleted, status, error_message from
>> tool_shed_repository where name = '<the name of the repo you are trying
>> to install>';
>>
>> Thanks,
>>
>> Greg Von Kuster
>>
>> On May 31, 2013, at 1:51 AM, Keilwagen, Jens wrote:
>>
>>> Hi Greg,
>>>
>>> thanks for your comment. Some days ago, I updated Galaxy following:
>>>
>>> http://wiki.galaxyproject.org/News/2013_04_08_Galaxy_Security_Release
>>>
>>> Here is what "hg sum" said
>>>
>>> parent: 9292:2cc8d10988e0 security_2013.04.08
>>> controllers/history: use get_history in switch_to_history
>>> Zweig: stable
>>> Übernehme: 10 unbekannt (clean)
>>> Aktualisiere: 11 neue Änderungssätze (Aktualisierung)
>>>
>>> (Sorry for the German terms.) I then updated Galaxy by
>>>
>>> hg update
>>>
>>> obtaining:
>>>
>>> parent: 9320:47ddf167c9f1 tip
>>> Use Galaxy's ErrorMiddleware since Paste's doesn't return
>> start_response.  Fixes downloading tarballs from the Tool Shed when
>> use_debug = false.
>>> Zweig: stable
>>> Übernehme: 10 unbekannt (clean)
>>> Aktualisiere: (aktuell)
>>>
>>> I then restarted Galaxy and tried to install again, but it fails
>> again. Even trying for a second time doesn't change the behaviour. Here
>> is what paster.log says:
>>>
>>> 172.31.30.183 - - [31/May/2013:07:47:32 +0200] "GET
>> /admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx
>> .psu.edu/&repository_ids=1d92ebdf7e8d466c&changeset_revisions=9dabbfd73
>> c8a HTTP/1.0" 500 -
>> "http://toolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset?re
>> pository_id=1d92ebdf7e8d466c&changeset_revision=9dabbfd73c8a"
>> "Mozilla/5.0 (Windows NT 6.1; WOW64; rv:21.0) Gecko/20100101
>> Firefox/21.0"
>>> Error - <type 'exceptions.ValueError'>: too many values to unpack
>>> URL:
>>>
>> http://galaxy.jki.bund.de/admin_toolshed/prepare_for_install?tool_shed
>>>
>> _url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf7e8d466c&ch
>>> angeset_revisions=9dabbfd73c8a File
>>> '/opt/galaxy/galaxy-
>> dist/lib/galaxy/web/framework/middleware/error.py'
>>> , line 149 in __call__  app_iter = self.application(environ,
>>> sr_checker) File
>>> '/opt/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-
>> py2.6.egg/paste/recursive.
>>> py', line 84 in __call__  return self.application(environ,
>>> start_response) File
>>> '/opt/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-
>> py2.6.egg/paste/httpexcept
>>> ions.py', line 633 in __call__  return self.application(environ,
>>> start_response) File
>>> '/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 128
>>> in __call__  return self.handle_request( environ, start_response )
>>> File '/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line
>>> 184 in handle_request  body = method( trans, **kwargs ) File
>>> '/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line
>>> 231 in decorator  return func( self, trans, *args, **kwargs ) File
>>> '/opt/galaxy/galaxy-
>> dist/lib/galaxy/webapps/galaxy/controllers/admin_t
>>> oolshed.py', line 894 in prepare_for_install
>>> common_install_util.get_dependencies_for_repository( trans,
>>> tool_shed_url, repo_info_dict, includes_tool_dependencies ) File
>>> '/opt/galaxy/galaxy-dist/lib/tool_shed/util/common_install_util.py',
>>> line 88 in get_dependencies_for_repository  installed_rd, missing_rd
>> =
>>> get_installed_and_missing_repository_dependencies_for_new_install(
>>> trans, repo_info_tuple ) File
>>> '/opt/galaxy/galaxy-dist/lib/tool_shed/util/common_install_util.py',
>>> line 192 in
>>> get_installed_and_missing_repository_dependencies_for_new_install
>>> tool_shed, name, owner, changeset_revision = rd_tup
>>> ValueError: too many values to unpack
>>>
>>>
>>> CGI Variables
>>> -------------
>>> CONTENT_LENGTH: '0'
>>> HTTP_ACCEPT:
>> 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8'
>>> HTTP_ACCEPT_ENCODING: 'gzip, deflate'
>>> HTTP_ACCEPT_LANGUAGE: 'de-de,de;q=0.8,en-us;q=0.5,en;q=0.3'
>>> HTTP_CACHE_CONTROL: 'max-age=0'
>>> HTTP_CONNECTION: 'keep-alive'
>>> HTTP_COOKIE:
>> 'galaxysession=c6ca0ddb55be603a88fa41dbba7680819dc3ac10c92a6efa6da917af
>> 7060700e4360e4afb5987baa'
>>> HTTP_HOST: 'galaxy.jki.bund.de'
>>> HTTP_REFERER:
>> 'http://toolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset?re
>> pository_id=1d92ebdf7e8d466c&changeset_revision=9dabbfd73c8a'
>>> HTTP_USER_AGENT: 'Mozilla/5.0 (Windows NT 6.1; WOW64; rv:21.0)
>> Gecko/20100101 Firefox/21.0'
>>> HTTP_VIA: '1.1 proxy.jki.bund.de:8000 (squid/2.7.STABLE9)'
>>> HTTP_X_FORWARDED_FOR: '172.31.30.183'
>>> ORGINAL_REMOTE_ADDR: '172.16.20.52'
>>> PATH_INFO: '/admin_toolshed/prepare_for_install'
>>> QUERY_STRING:
>> 'tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf7e
>> 8d466c&changeset_revisions=9dabbfd73c8a'
>>> REMOTE_ADDR: '172.31.30.183'
>>> REQUEST_METHOD: 'GET'
>>> SERVER_NAME: '0.0.0.0'
>>> SERVER_PORT: '8080'
>>> SERVER_PROTOCOL: 'HTTP/1.0'
>>>
>>>
>>> WSGI Variables
>>> --------------
>>> application: <paste.recursive.RecursiveMiddleware object at
>>> 0x7c3ed50>
>>> paste.cookies: (<SimpleCookie:
>>>
>> galaxysession='c6ca0ddb55be603a88fa41dbba7680819dc3ac10c92a6efa6da917a
>>> f7060700e4360e4afb5987baa'>,
>>>
>> 'galaxysession=c6ca0ddb55be603a88fa41dbba7680819dc3ac10c92a6efa6da917a
>>> f7060700e4360e4afb5987baa')
>>> paste.expected_exceptions: [<class
>>> 'paste.httpexceptions.HTTPException'>]
>>> paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler
>>> object at 0x7c3e710>
>>> paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at
>>> 0x7c9ff50>
>>> paste.parsed_querystring: ([('tool_shed_url',
>>> 'http://toolshed.g2.bx.psu.edu/'), ('repository_ids',
>>> '1d92ebdf7e8d466c'), ('changeset_revisions', '9dabbfd73c8a')],
>>>
>> 'tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf7
>>> e8d466c&changeset_revisions=9dabbfd73c8a')
>>> paste.recursive.forward: <paste.recursive.Forwarder from />
>>> paste.recursive.include: <paste.recursive.Includer from />
>>> paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter
>>> from />
>>> paste.recursive.script_name: ''
>>> paste.throw_errors: True
>>> request_id: '964a9788c9b511e2bb080050568d0b1f'
>>> webob._parsed_query_vars: (MultiDict([('tool_shed_url',
>>> 'http://toolshed.g2.bx.psu.edu/'), ('repository_ids',
>>> '1d92ebdf7e8d466c'), ('changeset_revisions', '9dabbfd73c8a')]),
>>>
>> 'tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf7
>>> e8d466c&changeset_revisions=9dabbfd73c8a')
>>> wsgi process: 'Multithreaded'
>>> ------------------------------------------------------------
>>>
>>> I would be graetful for any comments.
>>>
>>> Best regards, Jens
>>>
>>>
>>>> -----Ursprüngliche Nachricht-----
>>>> Von: Greg Von Kuster [mailto:[hidden email]]
>>>> Gesendet: Donnerstag, 30. Mai 2013 15:39
>>>> An: Keilwagen, Jens
>>>> Cc: Galaxy Dev
>>>> Betreff: Re: AW: [galaxy-dev] Internal Server Error during
>>>> installation of ncbi_blast_plus
>>>>
>>>> Hello Jens,
>>>>
>>>> It looks like your Galaxy instance is fairly old.  What version of
>>>> Galaxy are you running?
>>>>
>>>> Thanks,
>>>>
>>>> Greg Von Kuster
>>>>
>>>> On May 30, 2013, at 1:49 AM, Keilwagen, Jens wrote:
>>>>
>>>>> Hi Greg,
>>>>>
>>>>> here is what the paster.log says:
>>>>>
>>>>> 172.31.30.183 - - [30/May/2013:07:39:54 +0200] "GET
>>>>
>> /admin_toolshed/browse_tool_shed?tool_shed_url=http%3A%2F%2Ftoolshed.
>>>> g2
>>>> .bx.psu.edu%2F HTTP/1.0" 302 -
>>>> "http://galaxy.jki.bund.de/admin_toolshed/browse_tool_sheds"
>>>> "Mozilla/5.0 (Windows NT 6.1; WOW64; rv:21.0) Gecko/20100101
>>>> Firefox/21.0"
>>>>> 172.31.30.183 - - [30/May/2013:07:40:17 +0200] "GET
>>>>
>> /admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.
>>>> bx
>>>>
>> .psu.edu/&repository_ids=1d92ebdf7e8d466c&changeset_revisions=9dabbfd
>>>> 73
>>>> c8a HTTP/1.0" 500 -
>>>>
>> "http://toolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset?
>>>> re pository_id=1d92ebdf7e8d466c&changeset_revision=9dabbfd73c8a"
>>>> "Mozilla/5.0 (Windows NT 6.1; WOW64; rv:21.0) Gecko/20100101
>>>> Firefox/21.0"
>>>>> Error - <type 'exceptions.ValueError'>: too many values to unpack
>>>>> URL:
>>>>>
>>>>
>> http://galaxy.jki.bund.de/admin_toolshed/prepare_for_install?tool_she
>>>> d
>>>>>
>>>>
>> _url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf7e8d466c&c
>>>> h
>>>>> angeset_revisions=9dabbfd73c8a File
>>>>> '/opt/galaxy/galaxy-
>>>> dist/lib/galaxy/web/framework/middleware/error.py'
>>>>> , line 149 in __call__  app_iter = self.application(environ,
>>>>> sr_checker) File
>>>>> '/opt/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-
>>>> py2.6.egg/paste/recursive.
>>>>> py', line 84 in __call__  return self.application(environ,
>>>>> start_response) File
>>>>> '/opt/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-
>>>> py2.6.egg/paste/httpexcept
>>>>> ions.py', line 633 in __call__  return self.application(environ,
>>>>> start_response) File
>>>>> '/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line
>> 128
>>>>> in __call__  return self.handle_request( environ, start_response )
>>>>> File '/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py',
>>>>> line
>>>>> 184 in handle_request  body = method( trans, **kwargs ) File
>>>>> '/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py',
>> line
>>>>> 231 in decorator  return func( self, trans, *args, **kwargs ) File
>>>>> '/opt/galaxy/galaxy-
>>>> dist/lib/galaxy/webapps/galaxy/controllers/admin_t
>>>>> oolshed.py', line 894 in prepare_for_install
>>>>> common_install_util.get_dependencies_for_repository( trans,
>>>>> tool_shed_url, repo_info_dict, includes_tool_dependencies ) File
>>>>> '/opt/galaxy/galaxy-
>> dist/lib/tool_shed/util/common_install_util.py',
>>>>> line 88 in get_dependencies_for_repository  installed_rd,
>> missing_rd
>>>> =
>>>>> get_installed_and_missing_repository_dependencies_for_new_install(
>>>>> trans, repo_info_tuple ) File
>>>>> '/opt/galaxy/galaxy-
>> dist/lib/tool_shed/util/common_install_util.py',
>>>>> line 192 in
>>>>> get_installed_and_missing_repository_dependencies_for_new_install
>>>>> tool_shed, name, owner, changeset_revision = rd_tup
>>>>> ValueError: too many values to unpack
>>>>>
>>>>>
>>>>> CGI Variables
>>>>> -------------
>>>>> CONTENT_LENGTH: '0'
>>>>> HTTP_ACCEPT:
>>>> 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8'
>>>>> HTTP_ACCEPT_ENCODING: 'gzip, deflate'
>>>>> HTTP_ACCEPT_LANGUAGE: 'de-de,de;q=0.8,en-us;q=0.5,en;q=0.3'
>>>>> HTTP_CACHE_CONTROL: 'max-age=0'
>>>>> HTTP_CONNECTION: 'keep-alive'
>>>>> HTTP_COOKIE:
>>>>
>> 'galaxysession=c6ca0ddb55be603a88fa41dbba7680819dc3ac10c92a6efa6da917
>>>> af
>>>> 7060700e4360e4afb5987baa'
>>>>> HTTP_HOST: 'galaxy.jki.bund.de'
>>>>> HTTP_REFERER:
>>>>
>> 'http://toolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset?
>>>> re pository_id=1d92ebdf7e8d466c&changeset_revision=9dabbfd73c8a'
>>>>> HTTP_USER_AGENT: 'Mozilla/5.0 (Windows NT 6.1; WOW64; rv:21.0)
>>>> Gecko/20100101 Firefox/21.0'
>>>>> HTTP_VIA: '1.1 proxy.jki.bund.de:8000 (squid/2.7.STABLE9)'
>>>>> HTTP_X_FORWARDED_FOR: '172.31.30.183'
>>>>> ORGINAL_REMOTE_ADDR: '172.16.20.52'
>>>>> PATH_INFO: '/admin_toolshed/prepare_for_install'
>>>>> QUERY_STRING:
>>>>
>> 'tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf
>>>> 7e 8d466c&changeset_revisions=9dabbfd73c8a'
>>>>> REMOTE_ADDR: '172.31.30.183'
>>>>> REQUEST_METHOD: 'GET'
>>>>> SERVER_NAME: '0.0.0.0'
>>>>> SERVER_PORT: '8080'
>>>>> SERVER_PROTOCOL: 'HTTP/1.0'
>>>>>
>>>>>
>>>>> WSGI Variables
>>>>> --------------
>>>>> application: <paste.recursive.RecursiveMiddleware object at
>>>>> 0x8781210>
>>>>> paste.cookies: (<SimpleCookie:
>>>>>
>>>>
>> galaxysession='c6ca0ddb55be603a88fa41dbba7680819dc3ac10c92a6efa6da917
>>>> a
>>>>> f7060700e4360e4afb5987baa'>,
>>>>>
>>>>
>> 'galaxysession=c6ca0ddb55be603a88fa41dbba7680819dc3ac10c92a6efa6da917
>>>> a
>>>>> f7060700e4360e4afb5987baa')
>>>>> paste.expected_exceptions: [<class
>>>>> 'paste.httpexceptions.HTTPException'>]
>>>>> paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler
>>>>> object at 0x8851bd0>
>>>>> paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object
>> at
>>>>> 0x87b2450>
>>>>> paste.parsed_querystring: ([('tool_shed_url',
>>>>> 'http://toolshed.g2.bx.psu.edu/'), ('repository_ids',
>>>>> '1d92ebdf7e8d466c'), ('changeset_revisions', '9dabbfd73c8a')],
>>>>>
>>>>
>> 'tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf
>>>> 7
>>>>> e8d466c&changeset_revisions=9dabbfd73c8a')
>>>>> paste.recursive.forward: <paste.recursive.Forwarder from />
>>>>> paste.recursive.include: <paste.recursive.Includer from />
>>>>> paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter
>>>>> from />
>>>>> paste.recursive.script_name: ''
>>>>> paste.throw_errors: True
>>>>> request_id: '6905bf7ac8eb11e297ec0050568d0b1f'
>>>>> webob._parsed_query_vars: (MultiDict([('tool_shed_url',
>>>>> 'http://toolshed.g2.bx.psu.edu/'), ('repository_ids',
>>>>> '1d92ebdf7e8d466c'), ('changeset_revisions', '9dabbfd73c8a')]),
>>>>>
>>>>
>> 'tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf
>>>> 7
>>>>> e8d466c&changeset_revisions=9dabbfd73c8a')
>>>>> wsgi process: 'Multithreaded'
>>>>> ------------------------------------------------------------
>>>>>
>>>>> However, installing other tools from the tool shed was no problem
>> so
>>>> far.
>>>>>
>>>>> Best regards, Jens
>>>>>
>>>>>> -----Ursprüngliche Nachricht-----
>>>>>> Von: Greg Von Kuster [mailto:[hidden email]]
>>>>>> Gesendet: Mittwoch, 29. Mai 2013 16:45
>>>>>> An: Keilwagen, Jens
>>>>>> Cc: Galaxy Dev
>>>>>> Betreff: Re: [galaxy-dev] Internal Server Error during
>> installation
>>>>>> of ncbi_blast_plus
>>>>>>
>>>>>> Hello Jens,
>>>>>>
>>>>>> What does your Galaxy paster log show that is related to the
>>>> internal
>>>>>> server error?
>>>>>>
>>>>>> Greg Von Kuster
>>>>>>
>>>>>> On May 29, 2013, at 10:13 AM, Peter Cock wrote:
>>>>>>
>>>>>>> On Wed, May 29, 2013 at 8:33 AM, Keilwagen, Jens
>>>>>>> <[hidden email]> wrote:
>>>>>>>> Hi guys,
>>>>>>>>
>>>>>>>> we are currently estalishing our own local Galaxy instance.
>>>>>>>> However, when we try to install "Repository 'ncbi_blast_plus'"
>>>> from
>>>>>>>> the
>>>>>> Galaxy
>>>>>>>> main tool shed via the admin pages, we obtain the following
>> error
>>>>>>>>
>>>>>>>> "Internal Server Error
>>>>>>>> Galaxy was unable to sucessfully complete your request
>>>>>>>>
>>>>>>>> An error occurred.
>>>>>>>> This may be an intermittent problem due to load or other
>>>>>>>> unpredictable factors, reloading the page may address the
>> problem.
>>>>>>>>
>>>>>>>> The error has been logged to our team."
>>>>>>>>
>>>>>>>> We tried to install on three different days. Hence, we believe
>>>>>>>> there
>>>>>> might be another problem.
>>>>>>>>
>>>>>>>> Thanks for any help.
>>>>>>>>
>>>>>>>> Best regards, Jens
>>>>>>>
>>>>>>> Hi Jens,
>>>>>>>
>>>>>>> The Galaxy team should be able to ask some more targeted
>>>>>>> questions, but how far did the process get? Were you asked about
>>>>>>> the
>>>>>> dependencies
>>>>>>> (e.g. the blast_dataypes repository or the underlying BLAST+
>>>>>> binaries)?
>>>>>>>
>>>>>>> Peter
>>>>>>>
>>>>>>> P.S. What kind of system are you using? 64 bit Linux? Mac OS X?
>>>>>>> ___________________________________________________________
>>>>>>> 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:
>>> http://lists.bx.psu.edu/
>>>
>>> To search Galaxy mailing lists use the unified search at:
>>> http://galaxyproject.org/search/mailinglists/
>>>
>
>


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Re: Internal Server Error during installation of ncbi_blast_plus

Jens
Hi Greg,

I just updated our instance:

hg pull
hg update
sh manage_db.sh upgrade

and checked the current version

parent: 9944:cea3ddf6cdda tip
 Update tag for stable_2013.06.03
Zweig: stable
Ãbernehme: 16 unbekannt (clean)
Aktualisiere: (aktuell)

Subsequently, I tried again  .... and it took a while, but it works. Thank you very much.

All the best, Jens

> -----Ursprüngliche Nachricht-----
> Von: Greg Von Kuster [mailto:[hidden email]]
> Gesendet: Dienstag, 4. Juni 2013 15:58
> An: Keilwagen, Jens
> Cc: Galaxy Dev
> Betreff: Re: AW: [galaxy-dev] Internal Server Error during installation
> of ncbi_blast_plus
>
> Hi Jens,
>
> Thanks for the information, but it doesn't help determine what is
> causing this behavior in your environment.  It's strange that you have
> never installed the ncbi_blast_plus repository (so it is not currently
> in some error state), and yet you cannot install it.  I am not able to
> reproduce this behavior, so I have no idea of it's cause or how to
> resolve it.
>
> We just completed the latest Galaxy release yesterday, so when it is
> convenient perhaps you could update your Galaxy environment again,
> although I don't believe your Galaxy version is the issue either.
>
> Sorry to not be of much help here, but this is unusual behavior that
> has not been seen in the community, so it's unclear how to resolve it.
>
> Greg Von Kuster
>
> On Jun 4, 2013, at 9:47 AM, Keilwagen, Jens wrote:
>
> > Hi Greg,
> >
> > Thanks a lot for your email.
> > I hope, I did do not misunderstand something. We are trying to
> install "ncbi_blast_plus" from the "Galaxy main tool shed". As we did
> not manage to install "ncbi_blast_plus" the "where" clause does not
> make sense to me. Hence, I omit it. Here is the result.
> >
> > mysql> select id, name, owner,
> > mysql> installed_changeset_revision,changeset_revision, deleted,
> > mysql> status, error_message from tool_shed_repository;
> > +----+------------------------+---------------+----------------------
> --------+--------------------+---------+-----------+---------------+
> > | id | name                   | owner         |
> installed_changeset_revision | changeset_revision | deleted | status
> | error_message |
> > +----+------------------------+---------------+----------------------
> --------+--------------------+---------+-----------+---------------+
> > |  1 | cutadapt               | lparsons      | 2d6671b10919
> | 2d6671b10919       |       0 | Installed | NULL          |
> > |  2 | mirdeep2_and_targetspy | nikhil-joshi  | 798fe7ba8b5e
> | 798fe7ba8b5e       |       0 | Installed | NULL          |
> > |  3 | clustalomega           | clustalomega  | bc707542e5de
> | bc707542e5de       |       0 | Installed | NULL          |
> > |  4 | head_and_tail          | xuebing       | 00dba791c4a2
> | 00dba791c4a2       |       0 | Installed | NULL          |
> > |  5 | seq_match              | xuebing       | 3fd777932736
> | 3fd777932736       |       0 | Installed | NULL          |
> > |  6 | dreme                  | xuebing       | 83fb93488cad
> | 83fb93488cad       |       0 | Installed | NULL          |
> > |  7 | velvet_toolsuite       | edward-kirton | 4afe13ac23b6
> | 4afe13ac23b6       |       0 | Installed | NULL          |
> > |  8 | velvet_optimiser       | simon-gladman | 43c89d82a7d3
> | 43c89d82a7d3       |       0 | Installed | NULL          |
> > |  9 | roche454_toolsuite     | edward-kirton | 368a6ebebdde
> | 368a6ebebdde       |       0 | Installed | NULL          |
> > | 10 | mira_assembler         | peterjc       | 4266cccbb45a
> | 4266cccbb45a       |       0 | Installed | NULL          |
> > | 11 | abyss_toolsuite        | edward-kirton | 92636934a189
> | 92636934a189       |       0 | Installed | NULL          |
> > | 12 | bwa_wrappers           | devteam       | 150b3fe44caa
> | 150b3fe44caa       |       0 | Installed | NULL          |
> > | 13 | mafft                  | dereeper      | d7a735d3625e
> | d7a735d3625e       |       0 | Installed | NULL          |
> > | 14 | blast_datatypes        | devteam       | b3a3ba0c1d47
> | b3a3ba0c1d47       |       0 | Installed | NULL          |
> > | 15 | blast                  | edward-kirton | f3ac34855f5e
> | f3ac34855f5e       |       0 | Installed | NULL          |
> > | 16 | cdf_plot               | xuebing       | 900fd0a7428d
> | 900fd0a7428d       |       0 | Installed | NULL          |
> > | 17 | plot_distribution      | ynewton       | f180c4ef9128
> | f180c4ef9128       |       0 | Installed | NULL          |
> > +----+------------------------+---------------+----------------------
> --------+--------------------+---------+-----------+---------------+
> >
> > Does this help?
> >
> >
> > Best regards, Jens
> >
> >> -----Ursprüngliche Nachricht-----
> >> Von: Greg Von Kuster [mailto:[hidden email]]
> >> Gesendet: Dienstag, 4. Juni 2013 15:29
> >> An: Keilwagen, Jens
> >> Cc: Galaxy Dev
> >> Betreff: Re: [galaxy-dev] Internal Server Error during installation
> >> of ncbi_blast_plus
> >>
> >> Hello Jens.
> >>
> >> What is the name of the repository you are trying to install from
> the
> >> tool shed?  Can you run the following sql in your database and reply
> >> back with the results?
> >>
> >> select id, name, owner, installed_changeset_revision,
> >> changeset_revision, deleted, status, error_message from
> >> tool_shed_repository where name = '<the name of the repo you are
> >> trying to install>';
> >>
> >> Thanks,
> >>
> >> Greg Von Kuster
> >>
> >> On May 31, 2013, at 1:51 AM, Keilwagen, Jens wrote:
> >>
> >>> Hi Greg,
> >>>
> >>> thanks for your comment. Some days ago, I updated Galaxy following:
> >>>
> >>>
> http://wiki.galaxyproject.org/News/2013_04_08_Galaxy_Security_Releas
> >>> e
> >>>
> >>> Here is what "hg sum" said
> >>>
> >>> parent: 9292:2cc8d10988e0 security_2013.04.08
> >>> controllers/history: use get_history in switch_to_history
> >>> Zweig: stable
> >>> Übernehme: 10 unbekannt (clean)
> >>> Aktualisiere: 11 neue Änderungssätze (Aktualisierung)
> >>>
> >>> (Sorry for the German terms.) I then updated Galaxy by
> >>>
> >>> hg update
> >>>
> >>> obtaining:
> >>>
> >>> parent: 9320:47ddf167c9f1 tip
> >>> Use Galaxy's ErrorMiddleware since Paste's doesn't return
> >> start_response.  Fixes downloading tarballs from the Tool Shed when
> >> use_debug = false.
> >>> Zweig: stable
> >>> Übernehme: 10 unbekannt (clean)
> >>> Aktualisiere: (aktuell)
> >>>
> >>> I then restarted Galaxy and tried to install again, but it fails
> >> again. Even trying for a second time doesn't change the behaviour.
> >> Here is what paster.log says:
> >>>
> >>> 172.31.30.183 - - [31/May/2013:07:47:32 +0200] "GET
> >>
> /admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.
> >> bx
> >>
> .psu.edu/&repository_ids=1d92ebdf7e8d466c&changeset_revisions=9dabbfd
> >> 73
> >> c8a HTTP/1.0" 500 -
> >>
> "http://toolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset?
> >> re pository_id=1d92ebdf7e8d466c&changeset_revision=9dabbfd73c8a"
> >> "Mozilla/5.0 (Windows NT 6.1; WOW64; rv:21.0) Gecko/20100101
> >> Firefox/21.0"
> >>> Error - <type 'exceptions.ValueError'>: too many values to unpack
> >>> URL:
> >>>
> >>
> http://galaxy.jki.bund.de/admin_toolshed/prepare_for_install?tool_she
> >> d
> >>>
> >>
> _url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf7e8d466c&c
> >> h
> >>> angeset_revisions=9dabbfd73c8a File
> >>> '/opt/galaxy/galaxy-
> >> dist/lib/galaxy/web/framework/middleware/error.py'
> >>> , line 149 in __call__  app_iter = self.application(environ,
> >>> sr_checker) File
> >>> '/opt/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-
> >> py2.6.egg/paste/recursive.
> >>> py', line 84 in __call__  return self.application(environ,
> >>> start_response) File
> >>> '/opt/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-
> >> py2.6.egg/paste/httpexcept
> >>> ions.py', line 633 in __call__  return self.application(environ,
> >>> start_response) File
> >>> '/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line
> 128
> >>> in __call__  return self.handle_request( environ, start_response )
> >>> File '/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py',
> >>> line
> >>> 184 in handle_request  body = method( trans, **kwargs ) File
> >>> '/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py',
> line
> >>> 231 in decorator  return func( self, trans, *args, **kwargs ) File
> >>> '/opt/galaxy/galaxy-
> >> dist/lib/galaxy/webapps/galaxy/controllers/admin_t
> >>> oolshed.py', line 894 in prepare_for_install
> >>> common_install_util.get_dependencies_for_repository( trans,
> >>> tool_shed_url, repo_info_dict, includes_tool_dependencies ) File
> >>> '/opt/galaxy/galaxy-
> dist/lib/tool_shed/util/common_install_util.py',
> >>> line 88 in get_dependencies_for_repository  installed_rd,
> missing_rd
> >> =
> >>> get_installed_and_missing_repository_dependencies_for_new_install(
> >>> trans, repo_info_tuple ) File
> >>> '/opt/galaxy/galaxy-
> dist/lib/tool_shed/util/common_install_util.py',
> >>> line 192 in
> >>> get_installed_and_missing_repository_dependencies_for_new_install
> >>> tool_shed, name, owner, changeset_revision = rd_tup
> >>> ValueError: too many values to unpack
> >>>
> >>>
> >>> CGI Variables
> >>> -------------
> >>> CONTENT_LENGTH: '0'
> >>> HTTP_ACCEPT:
> >> 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8'
> >>> HTTP_ACCEPT_ENCODING: 'gzip, deflate'
> >>> HTTP_ACCEPT_LANGUAGE: 'de-de,de;q=0.8,en-us;q=0.5,en;q=0.3'
> >>> HTTP_CACHE_CONTROL: 'max-age=0'
> >>> HTTP_CONNECTION: 'keep-alive'
> >>> HTTP_COOKIE:
> >>
> 'galaxysession=c6ca0ddb55be603a88fa41dbba7680819dc3ac10c92a6efa6da917
> >> af
> >> 7060700e4360e4afb5987baa'
> >>> HTTP_HOST: 'galaxy.jki.bund.de'
> >>> HTTP_REFERER:
> >>
> 'http://toolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset?
> >> re pository_id=1d92ebdf7e8d466c&changeset_revision=9dabbfd73c8a'
> >>> HTTP_USER_AGENT: 'Mozilla/5.0 (Windows NT 6.1; WOW64; rv:21.0)
> >> Gecko/20100101 Firefox/21.0'
> >>> HTTP_VIA: '1.1 proxy.jki.bund.de:8000 (squid/2.7.STABLE9)'
> >>> HTTP_X_FORWARDED_FOR: '172.31.30.183'
> >>> ORGINAL_REMOTE_ADDR: '172.16.20.52'
> >>> PATH_INFO: '/admin_toolshed/prepare_for_install'
> >>> QUERY_STRING:
> >>
> 'tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf
> >> 7e 8d466c&changeset_revisions=9dabbfd73c8a'
> >>> REMOTE_ADDR: '172.31.30.183'
> >>> REQUEST_METHOD: 'GET'
> >>> SERVER_NAME: '0.0.0.0'
> >>> SERVER_PORT: '8080'
> >>> SERVER_PROTOCOL: 'HTTP/1.0'
> >>>
> >>>
> >>> WSGI Variables
> >>> --------------
> >>> application: <paste.recursive.RecursiveMiddleware object at
> >>> 0x7c3ed50>
> >>> paste.cookies: (<SimpleCookie:
> >>>
> >>
> galaxysession='c6ca0ddb55be603a88fa41dbba7680819dc3ac10c92a6efa6da917
> >> a
> >>> f7060700e4360e4afb5987baa'>,
> >>>
> >>
> 'galaxysession=c6ca0ddb55be603a88fa41dbba7680819dc3ac10c92a6efa6da917
> >> a
> >>> f7060700e4360e4afb5987baa')
> >>> paste.expected_exceptions: [<class
> >>> 'paste.httpexceptions.HTTPException'>]
> >>> paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler
> >>> object at 0x7c3e710>
> >>> paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object
> at
> >>> 0x7c9ff50>
> >>> paste.parsed_querystring: ([('tool_shed_url',
> >>> 'http://toolshed.g2.bx.psu.edu/'), ('repository_ids',
> >>> '1d92ebdf7e8d466c'), ('changeset_revisions', '9dabbfd73c8a')],
> >>>
> >>
> 'tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf
> >> 7
> >>> e8d466c&changeset_revisions=9dabbfd73c8a')
> >>> paste.recursive.forward: <paste.recursive.Forwarder from />
> >>> paste.recursive.include: <paste.recursive.Includer from />
> >>> paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter
> >>> from />
> >>> paste.recursive.script_name: ''
> >>> paste.throw_errors: True
> >>> request_id: '964a9788c9b511e2bb080050568d0b1f'
> >>> webob._parsed_query_vars: (MultiDict([('tool_shed_url',
> >>> 'http://toolshed.g2.bx.psu.edu/'), ('repository_ids',
> >>> '1d92ebdf7e8d466c'), ('changeset_revisions', '9dabbfd73c8a')]),
> >>>
> >>
> 'tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf
> >> 7
> >>> e8d466c&changeset_revisions=9dabbfd73c8a')
> >>> wsgi process: 'Multithreaded'
> >>> ------------------------------------------------------------
> >>>
> >>> I would be graetful for any comments.
> >>>
> >>> Best regards, Jens
> >>>
> >>>
> >>>> -----Ursprüngliche Nachricht-----
> >>>> Von: Greg Von Kuster [mailto:[hidden email]]
> >>>> Gesendet: Donnerstag, 30. Mai 2013 15:39
> >>>> An: Keilwagen, Jens
> >>>> Cc: Galaxy Dev
> >>>> Betreff: Re: AW: [galaxy-dev] Internal Server Error during
> >>>> installation of ncbi_blast_plus
> >>>>
> >>>> Hello Jens,
> >>>>
> >>>> It looks like your Galaxy instance is fairly old.  What version of
> >>>> Galaxy are you running?
> >>>>
> >>>> Thanks,
> >>>>
> >>>> Greg Von Kuster
> >>>>
> >>>> On May 30, 2013, at 1:49 AM, Keilwagen, Jens wrote:
> >>>>
> >>>>> Hi Greg,
> >>>>>
> >>>>> here is what the paster.log says:
> >>>>>
> >>>>> 172.31.30.183 - - [30/May/2013:07:39:54 +0200] "GET
> >>>>
> >>
> /admin_toolshed/browse_tool_shed?tool_shed_url=http%3A%2F%2Ftoolshed.
> >>>> g2
> >>>> .bx.psu.edu%2F HTTP/1.0" 302 -
> >>>> "http://galaxy.jki.bund.de/admin_toolshed/browse_tool_sheds"
> >>>> "Mozilla/5.0 (Windows NT 6.1; WOW64; rv:21.0) Gecko/20100101
> >>>> Firefox/21.0"
> >>>>> 172.31.30.183 - - [30/May/2013:07:40:17 +0200] "GET
> >>>>
> >>
> /admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.
> >>>> bx
> >>>>
> >>
> .psu.edu/&repository_ids=1d92ebdf7e8d466c&changeset_revisions=9dabbfd
> >>>> 73
> >>>> c8a HTTP/1.0" 500 -
> >>>>
> >>
> "http://toolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset?
> >>>> re pository_id=1d92ebdf7e8d466c&changeset_revision=9dabbfd73c8a"
> >>>> "Mozilla/5.0 (Windows NT 6.1; WOW64; rv:21.0) Gecko/20100101
> >>>> Firefox/21.0"
> >>>>> Error - <type 'exceptions.ValueError'>: too many values to unpack
> >>>>> URL:
> >>>>>
> >>>>
> >>
> http://galaxy.jki.bund.de/admin_toolshed/prepare_for_install?tool_she
> >>>> d
> >>>>>
> >>>>
> >>
> _url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf7e8d466c&c
> >>>> h
> >>>>> angeset_revisions=9dabbfd73c8a File
> >>>>> '/opt/galaxy/galaxy-
> >>>> dist/lib/galaxy/web/framework/middleware/error.py'
> >>>>> , line 149 in __call__  app_iter = self.application(environ,
> >>>>> sr_checker) File
> >>>>> '/opt/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-
> >>>> py2.6.egg/paste/recursive.
> >>>>> py', line 84 in __call__  return self.application(environ,
> >>>>> start_response) File
> >>>>> '/opt/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-
> >>>> py2.6.egg/paste/httpexcept
> >>>>> ions.py', line 633 in __call__  return self.application(environ,
> >>>>> start_response) File
> >>>>> '/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line
> >> 128
> >>>>> in __call__  return self.handle_request( environ, start_response
> )
> >>>>> File '/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py',
> >>>>> line
> >>>>> 184 in handle_request  body = method( trans, **kwargs ) File
> >>>>> '/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py',
> >> line
> >>>>> 231 in decorator  return func( self, trans, *args, **kwargs )
> File
> >>>>> '/opt/galaxy/galaxy-
> >>>> dist/lib/galaxy/webapps/galaxy/controllers/admin_t
> >>>>> oolshed.py', line 894 in prepare_for_install
> >>>>> common_install_util.get_dependencies_for_repository( trans,
> >>>>> tool_shed_url, repo_info_dict, includes_tool_dependencies ) File
> >>>>> '/opt/galaxy/galaxy-
> >> dist/lib/tool_shed/util/common_install_util.py',
> >>>>> line 88 in get_dependencies_for_repository  installed_rd,
> >> missing_rd
> >>>> =
> >>>>>
> get_installed_and_missing_repository_dependencies_for_new_install(
> >>>>> trans, repo_info_tuple ) File
> >>>>> '/opt/galaxy/galaxy-
> >> dist/lib/tool_shed/util/common_install_util.py',
> >>>>> line 192 in
> >>>>> get_installed_and_missing_repository_dependencies_for_new_install
> >>>>> tool_shed, name, owner, changeset_revision = rd_tup
> >>>>> ValueError: too many values to unpack
> >>>>>
> >>>>>
> >>>>> CGI Variables
> >>>>> -------------
> >>>>> CONTENT_LENGTH: '0'
> >>>>> HTTP_ACCEPT:
> >>>> 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8'
> >>>>> HTTP_ACCEPT_ENCODING: 'gzip, deflate'
> >>>>> HTTP_ACCEPT_LANGUAGE: 'de-de,de;q=0.8,en-us;q=0.5,en;q=0.3'
> >>>>> HTTP_CACHE_CONTROL: 'max-age=0'
> >>>>> HTTP_CONNECTION: 'keep-alive'
> >>>>> HTTP_COOKIE:
> >>>>
> >>
> 'galaxysession=c6ca0ddb55be603a88fa41dbba7680819dc3ac10c92a6efa6da917
> >>>> af
> >>>> 7060700e4360e4afb5987baa'
> >>>>> HTTP_HOST: 'galaxy.jki.bund.de'
> >>>>> HTTP_REFERER:
> >>>>
> >>
> 'http://toolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset?
> >>>> re pository_id=1d92ebdf7e8d466c&changeset_revision=9dabbfd73c8a'
> >>>>> HTTP_USER_AGENT: 'Mozilla/5.0 (Windows NT 6.1; WOW64; rv:21.0)
> >>>> Gecko/20100101 Firefox/21.0'
> >>>>> HTTP_VIA: '1.1 proxy.jki.bund.de:8000 (squid/2.7.STABLE9)'
> >>>>> HTTP_X_FORWARDED_FOR: '172.31.30.183'
> >>>>> ORGINAL_REMOTE_ADDR: '172.16.20.52'
> >>>>> PATH_INFO: '/admin_toolshed/prepare_for_install'
> >>>>> QUERY_STRING:
> >>>>
> >>
> 'tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf
> >>>> 7e 8d466c&changeset_revisions=9dabbfd73c8a'
> >>>>> REMOTE_ADDR: '172.31.30.183'
> >>>>> REQUEST_METHOD: 'GET'
> >>>>> SERVER_NAME: '0.0.0.0'
> >>>>> SERVER_PORT: '8080'
> >>>>> SERVER_PROTOCOL: 'HTTP/1.0'
> >>>>>
> >>>>>
> >>>>> WSGI Variables
> >>>>> --------------
> >>>>> application: <paste.recursive.RecursiveMiddleware object at
> >>>>> 0x8781210>
> >>>>> paste.cookies: (<SimpleCookie:
> >>>>>
> >>>>
> >>
> galaxysession='c6ca0ddb55be603a88fa41dbba7680819dc3ac10c92a6efa6da917
> >>>> a
> >>>>> f7060700e4360e4afb5987baa'>,
> >>>>>
> >>>>
> >>
> 'galaxysession=c6ca0ddb55be603a88fa41dbba7680819dc3ac10c92a6efa6da917
> >>>> a
> >>>>> f7060700e4360e4afb5987baa')
> >>>>> paste.expected_exceptions: [<class
> >>>>> 'paste.httpexceptions.HTTPException'>]
> >>>>> paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler
> >>>>> object at 0x8851bd0>
> >>>>> paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object
> >> at
> >>>>> 0x87b2450>
> >>>>> paste.parsed_querystring: ([('tool_shed_url',
> >>>>> 'http://toolshed.g2.bx.psu.edu/'), ('repository_ids',
> >>>>> '1d92ebdf7e8d466c'), ('changeset_revisions', '9dabbfd73c8a')],
> >>>>>
> >>>>
> >>
> 'tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf
> >>>> 7
> >>>>> e8d466c&changeset_revisions=9dabbfd73c8a')
> >>>>> paste.recursive.forward: <paste.recursive.Forwarder from />
> >>>>> paste.recursive.include: <paste.recursive.Includer from />
> >>>>> paste.recursive.include_app_iter:
> <paste.recursive.IncluderAppIter
> >>>>> from />
> >>>>> paste.recursive.script_name: ''
> >>>>> paste.throw_errors: True
> >>>>> request_id: '6905bf7ac8eb11e297ec0050568d0b1f'
> >>>>> webob._parsed_query_vars: (MultiDict([('tool_shed_url',
> >>>>> 'http://toolshed.g2.bx.psu.edu/'), ('repository_ids',
> >>>>> '1d92ebdf7e8d466c'), ('changeset_revisions', '9dabbfd73c8a')]),
> >>>>>
> >>>>
> >>
> 'tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf
> >>>> 7
> >>>>> e8d466c&changeset_revisions=9dabbfd73c8a')
> >>>>> wsgi process: 'Multithreaded'
> >>>>> ------------------------------------------------------------
> >>>>>
> >>>>> However, installing other tools from the tool shed was no problem
> >> so
> >>>> far.
> >>>>>
> >>>>> Best regards, Jens
> >>>>>
> >>>>>> -----Ursprüngliche Nachricht-----
> >>>>>> Von: Greg Von Kuster [mailto:[hidden email]]
> >>>>>> Gesendet: Mittwoch, 29. Mai 2013 16:45
> >>>>>> An: Keilwagen, Jens
> >>>>>> Cc: Galaxy Dev
> >>>>>> Betreff: Re: [galaxy-dev] Internal Server Error during
> >> installation
> >>>>>> of ncbi_blast_plus
> >>>>>>
> >>>>>> Hello Jens,
> >>>>>>
> >>>>>> What does your Galaxy paster log show that is related to the
> >>>> internal
> >>>>>> server error?
> >>>>>>
> >>>>>> Greg Von Kuster
> >>>>>>
> >>>>>> On May 29, 2013, at 10:13 AM, Peter Cock wrote:
> >>>>>>
> >>>>>>> On Wed, May 29, 2013 at 8:33 AM, Keilwagen, Jens
> >>>>>>> <[hidden email]> wrote:
> >>>>>>>> Hi guys,
> >>>>>>>>
> >>>>>>>> we are currently estalishing our own local Galaxy instance.
> >>>>>>>> However, when we try to install "Repository 'ncbi_blast_plus'"
> >>>> from
> >>>>>>>> the
> >>>>>> Galaxy
> >>>>>>>> main tool shed via the admin pages, we obtain the following
> >> error
> >>>>>>>>
> >>>>>>>> "Internal Server Error
> >>>>>>>> Galaxy was unable to sucessfully complete your request
> >>>>>>>>
> >>>>>>>> An error occurred.
> >>>>>>>> This may be an intermittent problem due to load or other
> >>>>>>>> unpredictable factors, reloading the page may address the
> >> problem.
> >>>>>>>>
> >>>>>>>> The error has been logged to our team."
> >>>>>>>>
> >>>>>>>> We tried to install on three different days. Hence, we believe
> >>>>>>>> there
> >>>>>> might be another problem.
> >>>>>>>>
> >>>>>>>> Thanks for any help.
> >>>>>>>>
> >>>>>>>> Best regards, Jens
> >>>>>>>
> >>>>>>> Hi Jens,
> >>>>>>>
> >>>>>>> The Galaxy team should be able to ask some more targeted
> >>>>>>> questions, but how far did the process get? Were you asked
> about
> >>>>>>> the
> >>>>>> dependencies
> >>>>>>> (e.g. the blast_dataypes repository or the underlying BLAST+
> >>>>>> binaries)?
> >>>>>>>
> >>>>>>> Peter
> >>>>>>>
> >>>>>>> P.S. What kind of system are you using? 64 bit Linux? Mac OS X?
> >>>>>>> ___________________________________________________________
> >>>>>>> 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:
> >>> 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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