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:g...@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 > > > _url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf7e8d466c&ch > > angeset_revisions=9dabbfd73c8a File > > '/opt/galaxy/galaxy- > dist/lib/galaxy/web/framework/middleware/error.py' > > , line 149 in __call__ app_iter = self.application(environ, > > sr_checker) File > > '/opt/galaxy/galaxy-dist/eggs/Paste-1.7.5.1- > py2.6.egg/paste/recursive. > > py', line 84 in __call__ return self.application(environ, > > start_response) File > > '/opt/galaxy/galaxy-dist/eggs/Paste-1.7.5.1- > py2.6.egg/paste/httpexcept > > ions.py', line 633 in __call__ return self.application(environ, > > start_response) File > > '/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 128 > > in __call__ return self.handle_request( environ, start_response ) > > File '/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line > > 184 in handle_request body = method( trans, **kwargs ) File > > '/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line > > 231 in decorator return func( self, trans, *args, **kwargs ) File > > '/opt/galaxy/galaxy- > dist/lib/galaxy/webapps/galaxy/controllers/admin_t > > oolshed.py', line 894 in prepare_for_install > > common_install_util.get_dependencies_for_repository( trans, > > tool_shed_url, repo_info_dict, includes_tool_dependencies ) File > > '/opt/galaxy/galaxy-dist/lib/tool_shed/util/common_install_util.py', > > line 88 in get_dependencies_for_repository installed_rd, missing_rd > = > > get_installed_and_missing_repository_dependencies_for_new_install( > > trans, repo_info_tuple ) File > > '/opt/galaxy/galaxy-dist/lib/tool_shed/util/common_install_util.py', > > line 192 in > > get_installed_and_missing_repository_dependencies_for_new_install > > tool_shed, name, owner, changeset_revision = rd_tup > > ValueError: too many values to unpack > > > > > > CGI Variables > > ------------- > > CONTENT_LENGTH: '0' > > HTTP_ACCEPT: > 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8' > > HTTP_ACCEPT_ENCODING: 'gzip, deflate' > > HTTP_ACCEPT_LANGUAGE: 'de-de,de;q=0.8,en-us;q=0.5,en;q=0.3' > > HTTP_CACHE_CONTROL: 'max-age=0' > > HTTP_CONNECTION: 'keep-alive' > > HTTP_COOKIE: > 'galaxysession=c6ca0ddb55be603a88fa41dbba7680819dc3ac10c92a6efa6da917af > 7060700e4360e4afb5987baa' > > HTTP_HOST: 'galaxy.jki.bund.de' > > HTTP_REFERER: > 'http://toolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset?re > pository_id=1d92ebdf7e8d466c&changeset_revision=9dabbfd73c8a' > > HTTP_USER_AGENT: 'Mozilla/5.0 (Windows NT 6.1; WOW64; rv:21.0) > Gecko/20100101 Firefox/21.0' > > HTTP_VIA: '1.1 proxy.jki.bund.de:8000 (squid/2.7.STABLE9)' > > HTTP_X_FORWARDED_FOR: '172.31.30.183' > > ORGINAL_REMOTE_ADDR: '172.16.20.52' > > PATH_INFO: '/admin_toolshed/prepare_for_install' > > QUERY_STRING: > 'tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf7e > 8d466c&changeset_revisions=9dabbfd73c8a' > > REMOTE_ADDR: '172.31.30.183' > > REQUEST_METHOD: 'GET' > > SERVER_NAME: '0.0.0.0' > > SERVER_PORT: '8080' > > SERVER_PROTOCOL: 'HTTP/1.0' > > > > > > WSGI Variables > > -------------- > > application: <paste.recursive.RecursiveMiddleware object at > > 0x7c3ed50> > > paste.cookies: (<SimpleCookie: > > > galaxysession='c6ca0ddb55be603a88fa41dbba7680819dc3ac10c92a6efa6da917a > > f7060700e4360e4afb5987baa'>, > > > 'galaxysession=c6ca0ddb55be603a88fa41dbba7680819dc3ac10c92a6efa6da917a > > f7060700e4360e4afb5987baa') > > paste.expected_exceptions: [<class > > 'paste.httpexceptions.HTTPException'>] > > paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler > > object at 0x7c3e710> > > paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at > > 0x7c9ff50> > > paste.parsed_querystring: ([('tool_shed_url', > > 'http://toolshed.g2.bx.psu.edu/'), ('repository_ids', > > '1d92ebdf7e8d466c'), ('changeset_revisions', '9dabbfd73c8a')], > > > 'tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf7 > > e8d466c&changeset_revisions=9dabbfd73c8a') > > paste.recursive.forward: <paste.recursive.Forwarder from /> > > paste.recursive.include: <paste.recursive.Includer from /> > > paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter > > from /> > > paste.recursive.script_name: '' > > paste.throw_errors: True > > request_id: '964a9788c9b511e2bb080050568d0b1f' > > webob._parsed_query_vars: (MultiDict([('tool_shed_url', > > 'http://toolshed.g2.bx.psu.edu/'), ('repository_ids', > > '1d92ebdf7e8d466c'), ('changeset_revisions', '9dabbfd73c8a')]), > > > 'tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf7 > > e8d466c&changeset_revisions=9dabbfd73c8a') > > wsgi process: 'Multithreaded' > > ------------------------------------------------------------ > > > > I would be graetful for any comments. > > > > Best regards, Jens > > > > > >> -----Ursprüngliche Nachricht----- > >> Von: Greg Von Kuster [mailto: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=9dabbfd > >> 73 > >> c8a HTTP/1.0" 500 - > >> > "http://toolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset? > >> re pository_id=1d92ebdf7e8d466c&changeset_revision=9dabbfd73c8a" > >> "Mozilla/5.0 (Windows NT 6.1; WOW64; rv:21.0) Gecko/20100101 > >> Firefox/21.0" > >>> Error - <type 'exceptions.ValueError'>: too many values to unpack > >>> URL: > >>> > >> > http://galaxy.jki.bund.de/admin_toolshed/prepare_for_install?tool_she > >> d > >>> > >> > _url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf7e8d466c&c > >> h > >>> angeset_revisions=9dabbfd73c8a File > >>> '/opt/galaxy/galaxy- > >> dist/lib/galaxy/web/framework/middleware/error.py' > >>> , line 149 in __call__ app_iter = self.application(environ, > >>> sr_checker) File > >>> '/opt/galaxy/galaxy-dist/eggs/Paste-1.7.5.1- > >> py2.6.egg/paste/recursive. > >>> py', line 84 in __call__ return self.application(environ, > >>> start_response) File > >>> '/opt/galaxy/galaxy-dist/eggs/Paste-1.7.5.1- > >> py2.6.egg/paste/httpexcept > >>> ions.py', line 633 in __call__ return self.application(environ, > >>> start_response) File > >>> '/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line > 128 > >>> in __call__ return self.handle_request( environ, start_response ) > >>> File '/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', > >>> line > >>> 184 in handle_request body = method( trans, **kwargs ) File > >>> '/opt/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', > line > >>> 231 in decorator return func( self, trans, *args, **kwargs ) File > >>> '/opt/galaxy/galaxy- > >> dist/lib/galaxy/webapps/galaxy/controllers/admin_t > >>> oolshed.py', line 894 in prepare_for_install > >>> common_install_util.get_dependencies_for_repository( trans, > >>> tool_shed_url, repo_info_dict, includes_tool_dependencies ) File > >>> '/opt/galaxy/galaxy- > dist/lib/tool_shed/util/common_install_util.py', > >>> line 88 in get_dependencies_for_repository installed_rd, > missing_rd > >> = > >>> get_installed_and_missing_repository_dependencies_for_new_install( > >>> trans, repo_info_tuple ) File > >>> '/opt/galaxy/galaxy- > dist/lib/tool_shed/util/common_install_util.py', > >>> line 192 in > >>> get_installed_and_missing_repository_dependencies_for_new_install > >>> tool_shed, name, owner, changeset_revision = rd_tup > >>> ValueError: too many values to unpack > >>> > >>> > >>> CGI Variables > >>> ------------- > >>> CONTENT_LENGTH: '0' > >>> HTTP_ACCEPT: > >> 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8' > >>> HTTP_ACCEPT_ENCODING: 'gzip, deflate' > >>> HTTP_ACCEPT_LANGUAGE: 'de-de,de;q=0.8,en-us;q=0.5,en;q=0.3' > >>> HTTP_CACHE_CONTROL: 'max-age=0' > >>> HTTP_CONNECTION: 'keep-alive' > >>> HTTP_COOKIE: > >> > 'galaxysession=c6ca0ddb55be603a88fa41dbba7680819dc3ac10c92a6efa6da917 > >> af > >> 7060700e4360e4afb5987baa' > >>> HTTP_HOST: 'galaxy.jki.bund.de' > >>> HTTP_REFERER: > >> > 'http://toolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset? > >> re pository_id=1d92ebdf7e8d466c&changeset_revision=9dabbfd73c8a' > >>> HTTP_USER_AGENT: 'Mozilla/5.0 (Windows NT 6.1; WOW64; rv:21.0) > >> Gecko/20100101 Firefox/21.0' > >>> HTTP_VIA: '1.1 proxy.jki.bund.de:8000 (squid/2.7.STABLE9)' > >>> HTTP_X_FORWARDED_FOR: '172.31.30.183' > >>> ORGINAL_REMOTE_ADDR: '172.16.20.52' > >>> PATH_INFO: '/admin_toolshed/prepare_for_install' > >>> QUERY_STRING: > >> > 'tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf > >> 7e 8d466c&changeset_revisions=9dabbfd73c8a' > >>> REMOTE_ADDR: '172.31.30.183' > >>> REQUEST_METHOD: 'GET' > >>> SERVER_NAME: '0.0.0.0' > >>> SERVER_PORT: '8080' > >>> SERVER_PROTOCOL: 'HTTP/1.0' > >>> > >>> > >>> WSGI Variables > >>> -------------- > >>> application: <paste.recursive.RecursiveMiddleware object at > >>> 0x8781210> > >>> paste.cookies: (<SimpleCookie: > >>> > >> > galaxysession='c6ca0ddb55be603a88fa41dbba7680819dc3ac10c92a6efa6da917 > >> a > >>> f7060700e4360e4afb5987baa'>, > >>> > >> > 'galaxysession=c6ca0ddb55be603a88fa41dbba7680819dc3ac10c92a6efa6da917 > >> a > >>> f7060700e4360e4afb5987baa') > >>> paste.expected_exceptions: [<class > >>> 'paste.httpexceptions.HTTPException'>] > >>> paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler > >>> object at 0x8851bd0> > >>> paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object > at > >>> 0x87b2450> > >>> paste.parsed_querystring: ([('tool_shed_url', > >>> 'http://toolshed.g2.bx.psu.edu/'), ('repository_ids', > >>> '1d92ebdf7e8d466c'), ('changeset_revisions', '9dabbfd73c8a')], > >>> > >> > 'tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf > >> 7 > >>> e8d466c&changeset_revisions=9dabbfd73c8a') > >>> paste.recursive.forward: <paste.recursive.Forwarder from /> > >>> paste.recursive.include: <paste.recursive.Includer from /> > >>> paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter > >>> from /> > >>> paste.recursive.script_name: '' > >>> paste.throw_errors: True > >>> request_id: '6905bf7ac8eb11e297ec0050568d0b1f' > >>> webob._parsed_query_vars: (MultiDict([('tool_shed_url', > >>> 'http://toolshed.g2.bx.psu.edu/'), ('repository_ids', > >>> '1d92ebdf7e8d466c'), ('changeset_revisions', '9dabbfd73c8a')]), > >>> > >> > 'tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1d92ebdf > >> 7 > >>> e8d466c&changeset_revisions=9dabbfd73c8a') > >>> wsgi process: 'Multithreaded' > >>> ------------------------------------------------------------ > >>> > >>> However, installing other tools from the tool shed was no problem > so > >> far. > >>> > >>> Best regards, Jens > >>> > >>>> -----Ursprüngliche Nachricht----- > >>>> Von: Greg Von Kuster [mailto: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/ > > ___________________________________________________________ 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/
