Re: [galaxy-dev] tool shed can't install via admin user
Adhemar, Thank you for reporting this issue, it has been resolved in 10562:48191107fd2d. --Dave B. On 09/11/2013 12:10 PM, Adhemar wrote: Hello, I thought it might be a problem related to authentication and decided to run it in a brand new install on my desktop. Same problem: HTTP Error 500 Could you please verify this? Thanks, Adhemar Error Traceback: View as: Interactive http://127.0.0.1:8080/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=c45d6c51a4fcfc6cchangeset_revisions=bf1c3f9f8282# | Text http://127.0.0.1:8080/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=c45d6c51a4fcfc6cchangeset_revisions=bf1c3f9f8282# | XML http://127.0.0.1:8080/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=c45d6c51a4fcfc6cchangeset_revisions=bf1c3f9f8282#(full) http://127.0.0.1:8080/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=c45d6c51a4fcfc6cchangeset_revisions=bf1c3f9f8282# ⇝|HTTPError: HTTP Error 500: Internal Server Error| URL: http://127.0.0.1:8080/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=c45d6c51a4fcfc6cchangeset_revisions=bf1c3f9f8282 Module weberror.evalexception.middleware:*364* in |respond|http://127.0.0.1:8080/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=c45d6c51a4fcfc6cchangeset_revisions=bf1c3f9f8282#http://127.0.0.1:8080/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=c45d6c51a4fcfc6cchangeset_revisions=bf1c3f9f8282#http://127.0.0.1:8080/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=c45d6c51a4fcfc6cchangeset_revisions=bf1c3f9f8282#view http://127.0.0.1:8080/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=c45d6c51a4fcfc6cchangeset_revisions=bf1c3f9f8282# | http://127.0.0.1:8080/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=c45d6c51a4fcfc6cchangeset_revisions=bf1c3f9f8282#||app_iter*=*self||*.*||application||*(*||environ||*,*detect_start_response||*)*| Module paste.recursive:*84* in |__call__|http://127.0.0.1:8080/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=c45d6c51a4fcfc6cchangeset_revisions=bf1c3f9f8282#http://127.0.0.1:8080/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=c45d6c51a4fcfc6cchangeset_revisions=bf1c3f9f8282#http://127.0.0.1:8080/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=c45d6c51a4fcfc6cchangeset_revisions=bf1c3f9f8282#view http://127.0.0.1:8080/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=c45d6c51a4fcfc6cchangeset_revisions=bf1c3f9f8282# | http://127.0.0.1:8080/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=c45d6c51a4fcfc6cchangeset_revisions=bf1c3f9f8282#||*return*self||*.*||application||*(*||environ||*,*start_response||*)*| Module paste.httpexceptions:*633* in |__call__|http://127.0.0.1:8080/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=c45d6c51a4fcfc6cchangeset_revisions=bf1c3f9f8282#http://127.0.0.1:8080/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=c45d6c51a4fcfc6cchangeset_revisions=bf1c3f9f8282#http://127.0.0.1:8080/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=c45d6c51a4fcfc6cchangeset_revisions=bf1c3f9f8282#view http://127.0.0.1:8080/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=c45d6c51a4fcfc6cchangeset_revisions=bf1c3f9f8282# | http://127.0.0.1:8080/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=c45d6c51a4fcfc6cchangeset_revisions=bf1c3f9f8282#||*return*self||*.*||application||*(*||environ||*,*start_response||*)*| Module galaxy.web.framework.base:*132* in |__call__|http://127.0.0.1:8080/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=c45d6c51a4fcfc6cchangeset_revisions=bf1c3f9f8282#http://127.0.0.1:8080/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=c45d6c51a4fcfc6cchangeset_revisions=bf1c3f9f8282#http://127.0.0.1:8080/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=c45d6c51a4fcfc6cchangeset_revisions=bf1c3f9f8282#view http://127.0.0.1:8080/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=c45d6c51a4fcfc6cchangeset_revisions=bf1c3f9f8282# |
[galaxy-dev] tool shed can't install via admin user
Hi, I've just updated my galaxy-central version and I can't use the tool shed installer via admin user any more. When I click 'Install to Galaxy' it throws and 500 error. Could you please verify that? I tried the URL from tool_shed_url in the browser and it also doesn't open. Thanks, Adhemar 10.129.9.38, 10.129.0.1 - - [10/Sep/2013:16:05:59 -0200] GET /galaxy/admin_toolshed/prepare_for_install?tool_shed_url= http://toolshed.g2.bx.psu.edu/repository_ids=c45d6c51a4fcfc6cchangeset_revisions=bf1c3f9f8282HTTP/1.0; 500 - http://toolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset?repository_id=c45d6c51a4fcfc6cchangeset_revision=bf1c3f9f8282; Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.95 Safari/537.36 Error - class 'urllib2.HTTPError': HTTP Error 500: Internal Server Error URL: https://www.lmb.cnptia.embrapa.br/galaxy/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=c45d6c51a4fcfc6cchangeset_revisions=bf1c3f9f8282 File '/opt/bioinformatics/share/galaxy20130410/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/usr/lib/python2.6/site-packages/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/opt/bioinformatics/share/galaxy20130410/lib/galaxy/web/framework/middleware/remoteuser.py', line 91 in __call__ return self.app( environ, start_response ) File '/usr/lib/python2.6/site-packages/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/opt/bioinformatics/share/galaxy20130410/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/opt/bioinformatics/share/galaxy20130410/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/opt/bioinformatics/share/galaxy20130410/lib/galaxy/web/framework/__init__.py', line 221 in decorator return func( self, trans, *args, **kwargs ) File '/opt/bioinformatics/share/galaxy20130410/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 908 in prepare_for_install includes_tool_dependencies ) File '/opt/bioinformatics/share/galaxy20130410/lib/tool_shed/util/common_install_util.py', line 130 in get_dependencies_for_repository all_repo_info_dict = get_required_repo_info_dicts( trans, tool_shed_url, util.listify( repo_info_dict ) ) File '/opt/bioinformatics/share/galaxy20130410/lib/tool_shed/util/common_install_util.py', line 360 in get_required_repo_info_dicts response = urllib2.urlopen( request ).read() File '/usr/lib64/python2.6/urllib2.py', line 126 in urlopen return _opener.open(url, data, timeout) File '/usr/lib64/python2.6/urllib2.py', line 397 in open response = meth(req, response) File '/usr/lib64/python2.6/urllib2.py', line 510 in http_response 'http', request, response, code, msg, hdrs) File '/usr/lib64/python2.6/urllib2.py', line 435 in error return self._call_chain(*args) File '/usr/lib64/python2.6/urllib2.py', line 369 in _call_chain result = func(*args) File '/usr/lib64/python2.6/urllib2.py', line 518 in http_error_default raise HTTPError(req.get_full_url(), code, msg, hdrs, fp) HTTPError: HTTP Error 500: Internal Server Error 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,sdch' HTTP_ACCEPT_LANGUAGE: 'pt-BR,pt;q=0.8,en-US;q=0.6,en;q=0.4' HTTP_AUTHORIZATION: 'Basic YWRoZW1hcjpDYWxsIG1lIHRoZSBicmVlemUh' HTTP_COOKIE: 'galaxysession=c6ca0ddb55be603a7b1853fca2041c148b00044fe9cfda0f39abd5fcb4fe71a0bc3b556f2ab9d86b; GUEST_LANGUAGE_ID=pt_BR; COOKIE_SUPPORT=true; JSESSIONID=EC393E44F6CC64AB7CECE0B38408E133' HTTP_HOST: 'www.lmb.cnptia.embrapa.br' HTTP_REFERER: ' http://toolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset?repository_id=c45d6c51a4fcfc6cchangeset_revision=bf1c3f9f8282 ' HTTP_REMOTE_USER: 'adhemar@' HTTP_USER_AGENT: 'Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.95 Safari/537.36' HTTP_X_URL_SCHEME: 'https' PATH_INFO: '/admin_toolshed/prepare_for_install' QUERY_STRING: 'tool_shed_url= http://toolshed.g2.bx.psu.edu/repository_ids=c45d6c51a4fcfc6cchangeset_revisions=bf1c3f9f8282 ' REMOTE_ADDR: '10.129.9.38, 10.129.0.1' REQUEST_METHOD: 'GET' SCRIPT_NAME: '/galaxy' SERVER_NAME: 'www.lmb.cnptia.embrapa.br' SERVER_PORT: '8080' SERVER_PROTOCOL: 'HTTP/1.0' WSGI Variables -- application: paste.recursive.RecursiveMiddleware object at 0x8c58d90 is_api_request: False original_wsgi.url_scheme: 'http' paste.cookies: (SimpleCookie: COOKIE_SUPPORT='true' GUEST_LANGUAGE_ID='pt_BR' JSESSIONID='EC393E44F6CC64AB7CECE0B38408E133' galaxysession='c6ca0ddb55be603a7b1853fca2041c148b00044fe9cfda0f39abd5fcb4fe71a0bc3b556f2ab9d86b',
[galaxy-dev] tool shed can't install via admin user
Hi, I want to install our local Galaxy for more than one users. When I want to install some tools from tool shed via admin user ,and I followed the instructions in the follow link: http://wiki.galaxyproject.org/InstallingRepositoriesToGalaxy#Installing_Galaxy_tool_shed_repository_tools_into_a_local_Galaxy_instance but these are some errors: Server Error URL: http://183.62.232.129:8081/galaxy/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=1ec48b84b33d36d8changeset_revisions=41bba3e648d1 Module paste.exceptions.errormiddleware:143 in __call__ app_iter = self.application(environ, start_response) Module paste.debug.prints:98 in __call__ environ, self.app) Module paste.wsgilib:539 in intercept_output app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ return self.application(environ, start_response) Module galaxy.web.framework.base:160 in __call__ body = method( trans, **kwargs ) Module galaxy.web.framework:208 in decorator return func( self, trans, *args, **kwargs ) Module galaxy.webapps.galaxy.controllers.admin_toolshed:1177 in prepare_for_install response = urllib2.urlopen( url ) Module urllib2:126 in urlopen return _opener.open(url, data, timeout) Module urllib2:391 in open response = self._open(req, data) Module urllib2:409 in _open '_open', req) Module urllib2:369 in _call_chain result = func(*args) Module urllib2:1172 in http_open return self.do_open(httplib.HTTPConnection, req) Module urllib2:1147 in do_open raise URLError(err) Could anyone tell me why ,and how to solve? Thanks shenwiyn___ 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/
Re: [galaxy-dev] tool shed can't install via admin user
Shenwiyn, I have not been able to duplicate that error message in my local environment, what changeset revision of Galaxy are you running, and how is your server environment configured? --Dave B. On 3/4/13 10:41:36.000, shenwiyn wrote: Hi, I want to install our local Galaxy for more than one users. When I want to install some tools from tool shed via admin user ,and I followed the instructions in the follow link: http://wiki.galaxyproject.org/InstallingRepositoriesToGalaxy#Installing_Galaxy_tool_shed_repository_tools_into_a_local_Galaxy_instance but these are some errors: Server Error URL: http://183.62.232.129:8081/galaxy/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=1ec48b84b33d36d8changeset_revisions=41bba3e648d1 Module paste.exceptions.errormiddleware:*143* in |__call__| | http://183.62.232.129:8081/galaxy/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=1ec48b84b33d36d8changeset_revisions=41bba3e648d1#app_iter *=* self*.*application*(*environ*,* start_response*)*| Module paste.debug.prints:*98* in |__call__| | http://183.62.232.129:8081/galaxy/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=1ec48b84b33d36d8changeset_revisions=41bba3e648d1#environ*,* self*.*app*)*| Module paste.wsgilib:*539* in |intercept_output| | http://183.62.232.129:8081/galaxy/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=1ec48b84b33d36d8changeset_revisions=41bba3e648d1#app_iter *=* application*(*environ*,* replacement_start_response*)*| Module paste.recursive:*80* in |__call__| | http://183.62.232.129:8081/galaxy/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=1ec48b84b33d36d8changeset_revisions=41bba3e648d1#*return* self*.*application*(*environ*,* start_response*)*| Module paste.httpexceptions:*632* in |__call__| | http://183.62.232.129:8081/galaxy/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=1ec48b84b33d36d8changeset_revisions=41bba3e648d1#*return* self*.*application*(*environ*,* start_response*)*| Module galaxy.web.framework.base:*160* in |__call__| | http://183.62.232.129:8081/galaxy/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=1ec48b84b33d36d8changeset_revisions=41bba3e648d1#body *=* method*(* trans*,* kwargs *)*| Module galaxy.web.framework:*208* in |decorator| | http://183.62.232.129:8081/galaxy/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=1ec48b84b33d36d8changeset_revisions=41bba3e648d1#*return* func*(* self*,* trans*,* ***args*,* kwargs *)*| Module galaxy.webapps.galaxy.controllers.admin_toolshed:*1177* in |prepare_for_install| | http://183.62.232.129:8081/galaxy/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=1ec48b84b33d36d8changeset_revisions=41bba3e648d1#response *=* urllib2*.*urlopen*(* url *)*| Module urllib2:*126* in |urlopen| | http://183.62.232.129:8081/galaxy/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=1ec48b84b33d36d8changeset_revisions=41bba3e648d1#*return* _opener*.*open*(*url*,* data*,* timeout*)*| Module urllib2:*391* in |open| | http://183.62.232.129:8081/galaxy/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=1ec48b84b33d36d8changeset_revisions=41bba3e648d1#response *=* self*.*_open*(*req*,* data*)*| Module urllib2:*409* in |_open| | http://183.62.232.129:8081/galaxy/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=1ec48b84b33d36d8changeset_revisions=41bba3e648d1#'_open'*,* req*)*| Module urllib2:*369* in |_call_chain| | http://183.62.232.129:8081/galaxy/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=1ec48b84b33d36d8changeset_revisions=41bba3e648d1#result *=* func*(args*)*| Module urllib2:*1172* in |http_open| | http://183.62.232.129:8081/galaxy/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=1ec48b84b33d36d8changeset_revisions=41bba3e648d1#*return* self*.*do_open*(*httplib*.*HTTPConnection*,* req*)*| Module urllib2:*1147* in |do_open| | http://183.62.232.129:8081/galaxy/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=1ec48b84b33d36d8changeset_revisions=41bba3e648d1#*raise* URLError*(*err*)*| Could anyone tell me why ,and how to solve? Thanks shenwiyn ___ 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/
