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:g...@bx.psu.edu] > Gesendet: Donnerstag, 30. Mai 2013 15:39 > An: Keilwagen, Jens > Cc: Galaxy Dev > Betreff: Re: AW: [galaxy-dev] Internal Server Error during installation > of ncbi_blast_plus > > Hello Jens, > > It looks like your Galaxy instance is fairly old. What version of > Galaxy are you running? > > Thanks, > > Greg Von Kuster > > On May 30, 2013, at 1:49 AM, Keilwagen, Jens wrote: > > > Hi Greg, > > > > here is what the paster.log says: > > > > 172.31.30.183 - - [30/May/2013:07:39:54 +0200] "GET > /admin_toolshed/browse_tool_shed?tool_shed_url=http%3A%2F%2Ftoolshed.g2 > .bx.psu.edu%2F HTTP/1.0" 302 - > "http://galaxy.jki.bund.de/admin_toolshed/browse_tool_sheds"; > "Mozilla/5.0 (Windows NT 6.1; WOW64; rv:21.0) Gecko/20100101 > Firefox/21.0" > > 172.31.30.183 - - [30/May/2013:07:40:17 +0200] "GET > /admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx > .psu.edu/&repository_ids=1d92ebdf7e8d466c&changeset_revisions=9dabbfd73 > c8a HTTP/1.0" 500 - > "http://toolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset?re > pository_id=1d92ebdf7e8d466c&changeset_revision=9dabbfd73c8a" > "Mozilla/5.0 (Windows NT 6.1; WOW64; rv:21.0) Gecko/20100101 > Firefox/21.0" > > Error - <type 'exceptions.ValueError'>: too many values to unpack > > URL: > > > http://galaxy.jki.bund.de/admin_toolshed/prepare_for_install?tool_shed > > > _url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf7e8d466c&ch > > angeset_revisions=9dabbfd73c8a File > > '/opt/galaxy/galaxy- > dist/lib/galaxy/web/framework/middleware/error.py' > > , line 149 in __call__ app_iter = self.application(environ, > > sr_checker) File > > '/opt/galaxy/galaxy-dist/eggs/Paste-1.7.5.1- > py2.6.egg/paste/recursive. > > py', line 84 in __call__ return self.application(environ, > > start_response) File > > '/opt/galaxy/galaxy-dist/eggs/Paste-1.7.5.1- > py2.6.egg/paste/httpexcept > > ions.py', line 633 in __call__ return self.application(environ, > > start_response) File > > '/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 128 > > in __call__ return self.handle_request( environ, start_response ) > > File '/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line > > 184 in handle_request body = method( trans, **kwargs ) File > > '/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line > > 231 in decorator return func( self, trans, *args, **kwargs ) File > > '/opt/galaxy/galaxy- > dist/lib/galaxy/webapps/galaxy/controllers/admin_t > > oolshed.py', line 894 in prepare_for_install > > common_install_util.get_dependencies_for_repository( trans, > > tool_shed_url, repo_info_dict, includes_tool_dependencies ) File > > '/opt/galaxy/galaxy-dist/lib/tool_shed/util/common_install_util.py', > > line 88 in get_dependencies_for_repository installed_rd, missing_rd > = > > get_installed_and_missing_repository_dependencies_for_new_install( > > trans, repo_info_tuple ) File > > '/opt/galaxy/galaxy-dist/lib/tool_shed/util/common_install_util.py', > > line 192 in > > get_installed_and_missing_repository_dependencies_for_new_install > > tool_shed, name, owner, changeset_revision = rd_tup > > ValueError: too many values to unpack > > > > > > CGI Variables > > ------------- > > CONTENT_LENGTH: '0' > > HTTP_ACCEPT: > 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8' > > HTTP_ACCEPT_ENCODING: 'gzip, deflate' > > HTTP_ACCEPT_LANGUAGE: 'de-de,de;q=0.8,en-us;q=0.5,en;q=0.3' > > HTTP_CACHE_CONTROL: 'max-age=0' > > HTTP_CONNECTION: 'keep-alive' > > HTTP_COOKIE: > 'galaxysession=c6ca0ddb55be603a88fa41dbba7680819dc3ac10c92a6efa6da917af > 7060700e4360e4afb5987baa' > > HTTP_HOST: 'galaxy.jki.bund.de' > > HTTP_REFERER: > 'http://toolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset?re > pository_id=1d92ebdf7e8d466c&changeset_revision=9dabbfd73c8a' > > HTTP_USER_AGENT: 'Mozilla/5.0 (Windows NT 6.1; WOW64; rv:21.0) > Gecko/20100101 Firefox/21.0' > > HTTP_VIA: '1.1 proxy.jki.bund.de:8000 (squid/2.7.STABLE9)' > > HTTP_X_FORWARDED_FOR: '172.31.30.183' > > ORGINAL_REMOTE_ADDR: '172.16.20.52' > > PATH_INFO: '/admin_toolshed/prepare_for_install' > > QUERY_STRING: > 'tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf7e > 8d466c&changeset_revisions=9dabbfd73c8a' > > REMOTE_ADDR: '172.31.30.183' > > REQUEST_METHOD: 'GET' > > SERVER_NAME: '0.0.0.0' > > SERVER_PORT: '8080' > > SERVER_PROTOCOL: 'HTTP/1.0' > > > > > > WSGI Variables > > -------------- > > application: <paste.recursive.RecursiveMiddleware object at > > 0x8781210> > > paste.cookies: (<SimpleCookie: > > > galaxysession='c6ca0ddb55be603a88fa41dbba7680819dc3ac10c92a6efa6da917a > > f7060700e4360e4afb5987baa'>, > > > 'galaxysession=c6ca0ddb55be603a88fa41dbba7680819dc3ac10c92a6efa6da917a > > f7060700e4360e4afb5987baa') > > paste.expected_exceptions: [<class > > 'paste.httpexceptions.HTTPException'>] > > paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler > > object at 0x8851bd0> > > paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at > > 0x87b2450> > > paste.parsed_querystring: ([('tool_shed_url', > > 'http://toolshed.g2.bx.psu.edu/'), ('repository_ids', > > '1d92ebdf7e8d466c'), ('changeset_revisions', '9dabbfd73c8a')], > > > 'tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf7 > > e8d466c&changeset_revisions=9dabbfd73c8a') > > paste.recursive.forward: <paste.recursive.Forwarder from /> > > paste.recursive.include: <paste.recursive.Includer from /> > > paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter > > from /> > > paste.recursive.script_name: '' > > paste.throw_errors: True > > request_id: '6905bf7ac8eb11e297ec0050568d0b1f' > > webob._parsed_query_vars: (MultiDict([('tool_shed_url', > > 'http://toolshed.g2.bx.psu.edu/'), ('repository_ids', > > '1d92ebdf7e8d466c'), ('changeset_revisions', '9dabbfd73c8a')]), > > > 'tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf7 > > e8d466c&changeset_revisions=9dabbfd73c8a') > > wsgi process: 'Multithreaded' > > ------------------------------------------------------------ > > > > However, installing other tools from the tool shed was no problem so > far. > > > > Best regards, Jens > > > >> -----Ursprüngliche Nachricht----- > >> Von: Greg Von Kuster [mailto:g...@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.keilwa...@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/ > > > > ___________________________________________________________ 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/
