Re: [galaxy-dev] Messed up a tool installation from a local toolshed
Hi Greg, Sorry to dig up this unsolved thread from a few months back. Recap of the bug: I have developed a small tool. I have put it in my local Toolshed, and installed it. After applying some changes to the tool, I 'hg push'ed the changes to my repository on my toolshed. I uninstalled the tool, and reinstalled it. Since I work with job handlers, I have to restart Galaxy. Since I had about ~4 committed changes, I have repeated these steps about 4 times. The bug: the tool appears multiple times in the tool management window. 2 times as new, and 1 time as uninstalled (since I uninstalled it). The tool is still available in the toolbox, although it should not. The 2 installed tools have an option 'install', but when I click this I get an internal server error 500. Galaxy version: * [galaxy@galaxy galaxy-dist]$ hg tip changeset: 10411:c42567f43aa7 tag: tip user:greg date:Mon Aug 19 13:19:56 2013 -0400 summary: Filter invalid objects when generating the list of repository_dependencies objects that are associated with a tool shed repository installed into Galaxy. * As per your request: the web log of this internal server error. 193.191.128.2 - - [30/Sep/2013:13:15:19 +0200] GET /admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.bits.vib.be/repository_ids=968205d9ed31733dchangeset_revisions=e08a6d9e97a3 HTTP/1.1 500 - http://galaxy.bits.vib.be/admin_toolshed/browse_repositories; Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Ubuntu Chromium/28.0.1500.71 Chrome/28.0.1500.71 Safari/537.36 Debug at: http://galaxy.bits.vib.be/_debug/view/1380535486 The postgres database shows: galaxydb= select id, tool_shed, name, owner, installed_changeset_revision, status, error_message from tool_shed_repository where name = 'transpose'; id | tool_shed | name| owner | installed_changeset_revision | status| error_message +--+---+-+--+-+--- 45 | toolshed.bits.vib.be | transpose | joachim | cee0157acee1 | Uninstalled | 44 | toolshed.bits.vib.be | transpose | joachim | 2fa0462b9303 | New | 43 | toolshed.bits.vib.be | transpose | joachim | e08a6d9e97a3 | New | (3 rows) How should I proceed ? This is the second time I experience this. On a last note: I have noted also that I managed to get a repository with different branches in this tool shed repository, by mixing 'hg push' and uploading a tarball. There seems no easy way to fixing this. Kind regards, Joachim Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team On 06/14/2013 04:15 PM, Greg Von Kuster wrote: Hello Joachim, What version of Galaxy are your running? What does the tool shed paster go show for the 500 Internal Server Error? Also, run the following sql manually in your Galaxy database and send the results. select id, tool_shed, name, owner, installed_changeset_revision, status, error_message from tool_shed_repository; Thanks, Greg Von Kuster On Jun 14, 2013, at 3:41 AM, Joachim Jacob joachim.ja...@gmail.com mailto:joachim.ja...@gmail.com wrote: Hi all, I have developed a tool in our local Galaxy, and imported it in a local toolshed. I next removed the 'dev' version of the tool in Galaxy, and installed it now via het Tool Shed Manager. I got an error that the dependencies could not be installed. If figured it out that it (needed to add an extra shell_command in the tool_dependencies) (and the mount point on my system needs to have exec permissions of course). So I updated the tool in the toolshed. BUT, then I uninstalled the tool from Galaxy, and reinstalled it from the Tool Shed ... instead of just updating. Anyway, it has happened. Now I have the tool listed in my 'Install Tool Shed Repositories', and when I click on it, it says 'this tool is not installed'. The only action I can apply on this installed tool shed repository is 'Install' (...). But clicking on that 'install' button, leads me to an error page (http error 500). ** URL: http://localhost/admin_toolshed/prepare_for_install?tool_shed_url=http://localhost:9009/repository_ids=84cbaf0b6bf7a1a9changeset_revisions=fc2339abcab7 Module weberror.evalexception.middleware:364 in respond view app_iter = self.application(environ, detect_start_response) Module paste.recursive:84 in __call__ view return self.application(environ, start_response) Module paste.httpexceptions:633 in __call__ view return self.application(environ, start_response) Module galaxy.web.framework.base:132 in __call__ view return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:190 in
Re: [galaxy-dev] Messed up a tool installation from a local toolshed
See attachment. Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team On 09/30/2013 02:15 PM, Peter Cock wrote: On Mon, Sep 30, 2013 at 1:05 PM, Joachim Jacob | VIB | joachim.ja...@vib.be wrote: Hi Greg, Sorry to dig up this unsolved thread from a few months back. Recap of the bug: I have developed a small tool. I have put it in my local Toolshed, and installed it. After applying some changes to the tool, I 'hg push'ed the changes to my repository on my toolshed. I uninstalled the tool, and reinstalled it. Since I work with job handlers, I have to restart Galaxy. Since I had about ~4 committed changes, I have repeated these steps about 4 times. The bug: the tool appears multiple times in the tool management window. 2 times as new, and 1 time as uninstalled (since I uninstalled it). The tool is still available in the toolbox, although it should not. The 2 installed tools have an option 'install', but when I click this I get an internal server error 500. Galaxy version: * [galaxy@galaxy galaxy-dist]$ hg tip changeset: 10411:c42567f43aa7 tag: tip user:greg date:Mon Aug 19 13:19:56 2013 -0400 summary: Filter invalid objects when generating the list of repository_dependencies objects that are associated with a tool shed repository installed into Galaxy. * As per your request: the web log of this internal server error. 193.191.128.2 - - [30/Sep/2013:13:15:19 +0200] GET /admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.bits.vib.be/repository_ids=968205d9ed31733dchangeset_revisions=e08a6d9e97a3 HTTP/1.1 500 - http://galaxy.bits.vib.be/admin_toolshed/browse_repositories; Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Ubuntu Chromium/28.0.1500.71 Chrome/28.0.1500.71 Safari/537.36 Debug at: http://galaxy.bits.vib.be/_debug/view/1380535486 The postgres database shows: galaxydb= select id, tool_shed, name, owner, installed_changeset_revision, status, error_message from tool_shed_repository where name = 'transpose'; id | tool_shed | name| owner | installed_changeset_revision | status| error_message +--+---+-+--+-+--- 45 | toolshed.bits.vib.be | transpose | joachim | cee0157acee1 | Uninstalled | 44 | toolshed.bits.vib.be | transpose | joachim | 2fa0462b9303 | New | 43 | toolshed.bits.vib.be | transpose | joachim | e08a6d9e97a3 | New | (3 rows) How should I proceed ? This is the second time I experience this. On a last note: I have noted also that I managed to get a repository with different branches in this tool shed repository, by mixing 'hg push' and uploading a tarball. There seems no easy way to fixing this. Kind regards, Joachim Hmm - do these New entries show up in white on the Manage installed tool shed repositories admin page? It sounds like a case of what was nicknamed white ghosts, some causes of which have been fixed - but I don't think there was any automated removal of old white ghosts (I still have two on my test system). Peter attachment: Selection_221.png___ 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/
Re: [galaxy-dev] Messed up a tool installation from a local toolshed
| devteam | ffa8aaa14f7c | Installed | 9 | toolshed.g2.bx.psu.edu | picard | devteam | e0232cbac965 | Installed | 11 | toolshed.g2.bx.psu.edu | bowtie_color_wrappers | devteam | fd0914e451c5 | Installed | 12 | toolshed.g2.bx.psu.edu | lastz | devteam | 0801f8207d30 | Installed | 20 | toolshed.g2.bx.psu.edu | htseq_count | lparsons | 62a1de8c8aae | Installed | 21 | toolshed.g2.bx.psu.edu | emboss_datatypes | devteam | a89163f31369 | Installed | 23 | toolshed.g2.bx.psu.edu | trinityrnaseq | bhaas | 177bb1b443db | Installed | 14 | toolshed.g2.bx.psu.edu | fastq_mcf | jjohnson | 217aedbdd0d0 | Installed | 22 | toolshed.g2.bx.psu.edu | emboss_5 | devteam | b45f604a08ac | Installed | 5 | toolshed.g2.bx.psu.edu | deseq_and_sam2counts | nikhil-joshi | 3348f484c49c | Installed | 18 | toolshed.g2.bx.psu.edu | gmap | jjohnson | 93911bac43da | Installed | 19 | toolshed.g2.bx.psu.edu | htseq_count | lparsons | f320093f1e8e | Deactivated | 17 | toolshed.g2.bx.psu.edu | gmap | jjohnson | 6adc485b6dc0 | Uninstalled | 10 | toolshed.g2.bx.psu.edu | bowtie_wrappers | devteam | 0c7e4eadfb3c | Installed | 16 | toolshed.g2.bx.psu.edu | cummerbund | jjohnson | ebb9a992508d | Installed | 24 | toolshed.g2.bx.psu.edu | seq_select_by_id | peterjc | 28d52478ace9 | Installed | 13 | toolshed.g2.bx.psu.edu | lastz_paired_reads | devteam | 96825cee5c25 | Installed | 25 | toolshed.g2.bx.psu.edu | muscle | edward-kirton | 38a28f5f9449 | Installed | 26 | localhost:9009 | hmmer | joachim | fc2339abcab7 | New | 27 | localhost:9009 | hmmer | joachim | d724499758f9 | Uninstalled | 28 | localhost:9009 | blat | joachim | e2b0a830c892 | Installed | 29 | toolshed.g2.bx.psu.edu | prop_venn | idot | cc6707a1e044 | Uninstalled | * Thanks, Joachim Jacob Van: Greg Von Kuster g...@bx.psu.edu mailto:g...@bx.psu.edu Datum: 14-jun.-2013 16:15 Onderwerp: Re: [galaxy-dev] Messed up a tool installation from a local toolshed Aan: Joachim Jacob joachim.ja...@gmail.com mailto:joachim.ja...@gmail.com Cc: galaxy-...@bx.psu.edu mailto:galaxy-...@bx.psu.edu Hello Joachim, What version of Galaxy are your running? What does the tool shed paster go show for the 500 Internal Server Error? Also, run the following sql manually in your Galaxy database and send the results. select id, tool_shed, name, owner, installed_changeset_revision, status, error_message from tool_shed_repository; Thanks, Greg Von Kuster Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team On 06/14/2013 09:38 AM, Joachim Jacob | VIB | wrote: Hi all, I have developed a tool in our local Galaxy, and imported it in a local toolshed. I next removed the 'dev' version of the tool in Galaxy, and installed it now via het Tool Shed Manager. I got an error that the dependencies could not be installed. If figured it out that it (needed to add an extra shell_command in the tool_dependencies) (and the mount point on my system needs to have exec permissions of course). So I updated the tool in the toolshed. BUT, then I uninstalled the tool from Galaxy, and reinstalled it from the Tool Shed ... instead of just updating. Anyway, it has happened. Now I have the tool listed in my 'Install Tool Shed Repositories', and when I click on it, it says 'this tool is not installed'. The only action I can apply on this installed tool shed repository is 'Install'. Clicking on that 'install' button, leads me to an error page (http error 500). ** URL: http://localhost/admin_toolshed/prepare_for_install?tool_shed_url=http://localhost:9009/repository_ids=84cbaf0b6bf7a1a9changeset_revisions=fc2339abcab7 Module weberror.evalexception.middleware:364 in respond view app_iter = self.application(environ, detect_start_response) Module paste.recursive:84 in __call__ view return self.application(environ, start_response) Module paste.httpexceptions:633 in __call__ view return self.application(environ, start_response) Module galaxy.web.framework.base:132 in __call__ view return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:190 in handle_request view body = method( trans, **kwargs ) Module galaxy.web.framework:221 in decorator view return func( self, trans, *args, **kwargs ) Module galaxy.webapps.galaxy.controllers.admin_toolshed:825 in prepare_for_install view raw_text = common_util.tool_shed_get( trans.app, tool_shed_url, url ) Module tool_shed.util.common_util:110 in tool_shed_get view response = urlopener.open( uri ) Module urllib2:397 in open view response = meth(req, response) Module urllib2:510 in http_response view 'http', request, response, code, msg, hdrs) Module urllib2:435 in error view return self._call_chain(*args) Module urllib2:369 in _call_chain view result = func(*args) Module urllib2:518 in http_error_default view raise HTTPError(req.get_full_url
Re: [galaxy-dev] Messed up a tool installation from a local toolshed
-jun.-2013 16:15 Onderwerp: Re: [galaxy-dev] Messed up a tool installation from a local toolshed Aan: Joachim Jacob joachim.ja...@gmail.com mailto:joachim.ja...@gmail.com Cc: galaxy-...@bx.psu.edu mailto:galaxy-...@bx.psu.edu Hello Joachim, What version of Galaxy are your running? What does the tool shed paster go show for the 500 Internal Server Error? Also, run the following sql manually in your Galaxy database and send the results. select id, tool_shed, name, owner, installed_changeset_revision, status, error_message from tool_shed_repository; Thanks, Greg Von Kuster Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team On 06/14/2013 09:38 AM, Joachim Jacob | VIB | wrote: Hi all, I have developed a tool in our local Galaxy, and imported it in a local toolshed. I next removed the 'dev' version of the tool in Galaxy, and installed it now via het Tool Shed Manager. I got an error that the dependencies could not be installed. If figured it out that it (needed to add an extra shell_command in the tool_dependencies) (and the mount point on my system needs to have exec permissions of course). So I updated the tool in the toolshed. BUT, then I uninstalled the tool from Galaxy, and reinstalled it from the Tool Shed ... instead of just updating. Anyway, it has happened. Now I have the tool listed in my 'Install Tool Shed Repositories', and when I click on it, it says 'this tool is not installed'. The only action I can apply on this installed tool shed repository is 'Install'. Clicking on that 'install' button, leads me to an error page (http error 500). ** URL: http://localhost/admin_toolshed/prepare_for_install?tool_shed_url=http://localhost:9009/repository_ids=84cbaf0b6bf7a1a9changeset_revisions=fc2339abcab7 Module weberror.evalexception.middleware:364 in respond view app_iter = self.application(environ, detect_start_response) Module paste.recursive:84 in __call__ view return self.application(environ, start_response) Module paste.httpexceptions:633 in __call__ view return self.application(environ, start_response) Module galaxy.web.framework.base:132 in __call__ view return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:190 in handle_request view body = method( trans, **kwargs ) Module galaxy.web.framework:221 in decorator view return func( self, trans, *args, **kwargs ) Module galaxy.webapps.galaxy.controllers.admin_toolshed:825 in prepare_for_install view raw_text = common_util.tool_shed_get( trans.app, tool_shed_url, url ) Module tool_shed.util.common_util:110 in tool_shed_get view response = urlopener.open( uri ) Module urllib2:397 in open view response = meth(req, response) Module urllib2:510 in http_response view 'http', request, response, code, msg, hdrs) Module urllib2:435 in error view return self._call_chain(*args) Module urllib2:369 in _call_chain view result = func(*args) Module urllib2:518 in http_error_default view raise HTTPError(req.get_full_url(), code, msg, hdrs, fp) HTTPError: HTTP Error 500: Internal Server Error The same happens when I go to the Tool Shed, and try to install the tool from there: Galaxy detects that the tool has been installed before, and points me to that 500 error page. Any help is heartily appreciated, Thanks, Joachim ___ 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/
Re: [galaxy-dev] Messed up a tool installation from a local toolshed
| hmmer | joachim | d724499758f9 | Uninstalled | 28 | localhost:9009 | blat | joachim | e2b0a830c892 | Installed | 29 | toolshed.g2.bx.psu.edu | prop_venn | idot | cc6707a1e044 | Uninstalled | * Thanks, Joachim Jacob Van: Greg Von Kuster g...@bx.psu.edu mailto:g...@bx.psu.edu Datum: 14-jun.-2013 16:15 Onderwerp: Re: [galaxy-dev] Messed up a tool installation from a local toolshed Aan: Joachim Jacob joachim.ja...@gmail.com mailto:joachim.ja...@gmail.com Cc: galaxy-...@bx.psu.edu mailto:galaxy-...@bx.psu.edu Hello Joachim, What version of Galaxy are your running? What does the tool shed paster go show for the 500 Internal Server Error? Also, run the following sql manually in your Galaxy database and send the results. select id, tool_shed, name, owner, installed_changeset_revision, status, error_message from tool_shed_repository; Thanks, Greg Von Kuster Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team On 06/14/2013 09:38 AM, Joachim Jacob | VIB | wrote: Hi all, I have developed a tool in our local Galaxy, and imported it in a local toolshed. I next removed the 'dev' version of the tool in Galaxy, and installed it now via het Tool Shed Manager. I got an error that the dependencies could not be installed. If figured it out that it (needed to add an extra shell_command in the tool_dependencies) (and the mount point on my system needs to have exec permissions of course). So I updated the tool in the toolshed. BUT, then I uninstalled the tool from Galaxy, and reinstalled it from the Tool Shed ... instead of just updating. Anyway, it has happened. Now I have the tool listed in my 'Install Tool Shed Repositories', and when I click on it, it says 'this tool is not installed'. The only action I can apply on this installed tool shed repository is 'Install'. Clicking on that 'install' button, leads me to an error page (http error 500). ** URL: http://localhost/admin_toolshed/prepare_for_install?tool_shed_url=http://localhost:9009/repository_ids=84cbaf0b6bf7a1a9changeset_revisions=fc2339abcab7 Module weberror.evalexception.middleware:364 in respond view app_iter = self.application(environ, detect_start_response) Module paste.recursive:84 in __call__ view return self.application(environ, start_response) Module paste.httpexceptions:633 in __call__ view return self.application(environ, start_response) Module galaxy.web.framework.base:132 in __call__ view return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:190 in handle_request view body = method( trans, **kwargs ) Module galaxy.web.framework:221 in decorator view return func( self, trans, *args, **kwargs ) Module galaxy.webapps.galaxy.controllers.admin_toolshed:825 in prepare_for_install view raw_text = common_util.tool_shed_get( trans.app, tool_shed_url, url ) Module tool_shed.util.common_util:110 in tool_shed_get view response = urlopener.open( uri ) Module urllib2:397 in open view response = meth(req, response) Module urllib2:510 in http_response view 'http', request, response, code, msg, hdrs) Module urllib2:435 in error view return self._call_chain(*args) Module urllib2:369 in _call_chain view result = func(*args) Module urllib2:518 in http_error_default view raise HTTPError(req.get_full_url(), code, msg, hdrs, fp) HTTPError: HTTP Error 500: Internal Server Error The same happens when I go to the Tool Shed, and try to install the tool from there: Galaxy detects that the tool has been installed before, and points me to that 500 error page. Any help is heartily appreciated, Thanks, Joachim ___ 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/
[galaxy-dev] Messed up a tool installation from a local toolshed
Hi all, I have developed a tool in our local Galaxy, and imported it in a local toolshed. I next removed the 'dev' version of the tool in Galaxy, and installed it now via het Tool Shed Manager. I got an error that the dependencies could not be installed. If figured it out that it (needed to add an extra shell_command in the tool_dependencies) (and the mount point on my system needs to have exec permissions of course). So I updated the tool in the toolshed. BUT, then I uninstalled the tool from Galaxy, and reinstalled it from the Tool Shed ... instead of just updating. Anyway, it has happened. Now I have the tool listed in my 'Install Tool Shed Repositories', and when I click on it, it says 'this tool is not installed'. The only action I can apply on this installed tool shed repository is 'Install'. Clicking on that 'install' button, leads me to an error page (http error 500). ** URL: http://localhost/admin_toolshed/prepare_for_install?tool_shed_url=http://localhost:9009/repository_ids=84cbaf0b6bf7a1a9changeset_revisions=fc2339abcab7 Module weberror.evalexception.middleware:364 in respond view app_iter = self.application(environ, detect_start_response) Module paste.recursive:84 in __call__ view return self.application(environ, start_response) Module paste.httpexceptions:633 in __call__ view return self.application(environ, start_response) Module galaxy.web.framework.base:132 in __call__ view return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:190 in handle_request view body = method( trans, **kwargs ) Module galaxy.web.framework:221 in decorator view return func( self, trans, *args, **kwargs ) Module galaxy.webapps.galaxy.controllers.admin_toolshed:825 in prepare_for_install view raw_text = common_util.tool_shed_get( trans.app, tool_shed_url, url ) Module tool_shed.util.common_util:110 in tool_shed_get view response = urlopener.open( uri ) Module urllib2:397 in open view response = meth(req, response) Module urllib2:510 in http_response view 'http', request, response, code, msg, hdrs) Module urllib2:435 in error view return self._call_chain(*args) Module urllib2:369 in _call_chain view result = func(*args) Module urllib2:518 in http_error_default view raise HTTPError(req.get_full_url(), code, msg, hdrs, fp) HTTPError: HTTP Error 500: Internal Server Error The same happens when I go to the Tool Shed, and try to install the tool from there: Galaxy detects that the tool has been installed before, and points me to that 500 error page. Any help is heartily appreciated, Thanks, Joachim -- Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team ___ 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/
[galaxy-dev] Messed up a tool installation from a local toolshed
Hi all, I have developed a tool in our local Galaxy, and imported it in a local toolshed. I next removed the 'dev' version of the tool in Galaxy, and installed it now via het Tool Shed Manager. I got an error that the dependencies could not be installed. If figured it out that it (needed to add an extra shell_command in the tool_dependencies) (and the mount point on my system needs to have exec permissions of course). So I updated the tool in the toolshed. BUT, then I uninstalled the tool from Galaxy, and reinstalled it from the Tool Shed ... instead of just updating. Anyway, it has happened. Now I have the tool listed in my 'Install Tool Shed Repositories', and when I click on it, it says 'this tool is not installed'. The only action I can apply on this installed tool shed repository is 'Install' (...). But clicking on that 'install' button, leads me to an error page (http error 500). ** URL: http://localhost/admin_toolshed/prepare_for_install?tool_shed_url=http://localhost:9009/repository_ids=84cbaf0b6bf7a1a9changeset_revisions=fc2339abcab7 Module weberror.evalexception.middleware:364 in respond view app_iter = self.application(environ, detect_start_response) Module paste.recursive:84 in __call__ view return self.application(environ, start_response) Module paste.httpexceptions:633 in __call__ view return self.application(environ, start_response) Module galaxy.web.framework.base:132 in __call__ view return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:190 in handle_request view body = method( trans, **kwargs ) Module galaxy.web.framework:221 in decorator view return func( self, trans, *args, **kwargs ) Module galaxy.webapps.galaxy.controllers.admin_toolshed:825 in prepare_for_install view raw_text = common_util.tool_shed_get( trans.app, tool_shed_url, url ) Module tool_shed.util.common_util:110 in tool_shed_get view response = urlopener.open( uri ) Module urllib2:397 in open view response = meth(req, response) Module urllib2:510 in http_response view 'http', request, response, code, msg, hdrs) Module urllib2:435 in error view return self._call_chain(*args) Module urllib2:369 in _call_chain view result = func(*args) Module urllib2:518 in http_error_default view raise HTTPError(req.get_full_url(), code, msg, hdrs, fp) HTTPError: HTTP Error 500: Internal Server Error The same happens when I go to the Tool Shed, and try to install the tool from there: Galaxy detects that the tool has been installed before, and points me to that 500 error page. Any help is heartily appreciated, Thanks, Joachim -- Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team -- @joachimjacob ___ 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/
Re: [galaxy-dev] Messed up a tool installation from a local toolshed
Hello Joachim, What version of Galaxy are your running? What does the tool shed paster go show for the 500 Internal Server Error? Also, run the following sql manually in your Galaxy database and send the results. select id, tool_shed, name, owner, installed_changeset_revision, status, error_message from tool_shed_repository; Thanks, Greg Von Kuster On Jun 14, 2013, at 3:41 AM, Joachim Jacob joachim.ja...@gmail.com wrote: Hi all, I have developed a tool in our local Galaxy, and imported it in a local toolshed. I next removed the 'dev' version of the tool in Galaxy, and installed it now via het Tool Shed Manager. I got an error that the dependencies could not be installed. If figured it out that it (needed to add an extra shell_command in the tool_dependencies) (and the mount point on my system needs to have exec permissions of course). So I updated the tool in the toolshed. BUT, then I uninstalled the tool from Galaxy, and reinstalled it from the Tool Shed ... instead of just updating. Anyway, it has happened. Now I have the tool listed in my 'Install Tool Shed Repositories', and when I click on it, it says 'this tool is not installed'. The only action I can apply on this installed tool shed repository is 'Install' (...). But clicking on that 'install' button, leads me to an error page (http error 500). ** URL: http://localhost/admin_toolshed/prepare_for_install?tool_shed_url=http://localhost:9009/repository_ids=84cbaf0b6bf7a1a9changeset_revisions=fc2339abcab7 Module weberror.evalexception.middleware:364 in respond view app_iter = self.application(environ, detect_start_response) Module paste.recursive:84 in __call__ view return self.application(environ, start_response) Module paste.httpexceptions:633 in __call__ view return self.application(environ, start_response) Module galaxy.web.framework.base:132 in __call__ view return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:190 in handle_request view body = method( trans, **kwargs ) Module galaxy.web.framework:221 in decorator view return func( self, trans, *args, **kwargs ) Module galaxy.webapps.galaxy.controllers.admin_toolshed:825 in prepare_for_install view raw_text = common_util.tool_shed_get( trans.app, tool_shed_url, url ) Module tool_shed.util.common_util:110 in tool_shed_get view response = urlopener.open( uri ) Module urllib2:397 in open view response = meth(req, response) Module urllib2:510 in http_response view 'http', request, response, code, msg, hdrs) Module urllib2:435 in error view return self._call_chain(*args) Module urllib2:369 in _call_chain view result = func(*args) Module urllib2:518 in http_error_default view raise HTTPError(req.get_full_url(), code, msg, hdrs, fp) HTTPError: HTTP Error 500: Internal Server Error The same happens when I go to the Tool Shed, and try to install the tool from there: Galaxy detects that the tool has been installed before, and points me to that 500 error page. Any help is heartily appreciated, Thanks, Joachim -- Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team -- @joachimjacob ___ 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/
