Internal Server Error during installation of ncbi_blast_plus
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
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?
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/
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: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/
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: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/
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: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
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-
py', line 84 in __call__ return self.application(environ, start_response) File '/opt/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-
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
_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf7e8d466c&ch py2.6.egg/paste/recursive. py2.6.egg/paste/httpexcept 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/
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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: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
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-
py', line 84 in __call__ return self.application(environ, start_response) File '/opt/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-
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
_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf7e8d466c&ch py2.6.egg/paste/recursive. py2.6.egg/paste/httpexcept 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/
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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:greg@bx.psu.edu] 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
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-
py', line 84 in __call__ return self.application(environ, start_response) File '/opt/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-
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
_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf7e8d466c&ch py2.6.egg/paste/recursive. py2.6.egg/paste/httpexcept 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')]),
e8d466c&changeset_revisions=9dabbfd73c8a') wsgi process: 'Multithreaded' ------------------------------------------------------------
I would be graetful 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=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
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-
py', line 84 in __call__ return self.application(environ, start_response) File '/opt/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-
h py2.6.egg/paste/recursive. 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',
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: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
'tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf7 line 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/
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:greg@bx.psu.edu] 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
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-
py', line 84 in __call__ return self.application(environ, start_response) File '/opt/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-
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
_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf7e8d466c&ch py2.6.egg/paste/recursive. py2.6.egg/paste/httpexcept 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')]),
e8d466c&changeset_revisions=9dabbfd73c8a') wsgi process: 'Multithreaded' ------------------------------------------------------------
I would be graetful 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=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
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-
py', line 84 in __call__ return self.application(environ, start_response) File '/opt/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-
h py2.6.egg/paste/recursive. 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',
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: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
'tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf7 line 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/
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:greg@bx.psu.edu] 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:greg@bx.psu.edu] 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
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-
py', line 84 in __call__ return self.application(environ, start_response) File '/opt/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-
h py2.6.egg/paste/recursive. 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',
_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf7e8d466c&c 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: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=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
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-
py', line 84 in __call__ return self.application(environ, start_response) File '/opt/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-
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',
h py2.6.egg/paste/recursive. py2.6.egg/paste/httpexcept 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
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
7 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/
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) (dannf@debian.org) (gcc version 4.3.5 (Debian 4.3.5-4) ) #1 SMP Mon Feb 2 5 00:26:11 UTC 2013
participants (3)
-
Greg Von Kuster -
Keilwagen, Jens -
Peter Cock