Hi Franco, Sorry you're still seeing this issue. I assume you updated your Galaxy to the dist release, so not sure how you have rev 8359 - we haven't even reached that rev in development yet. However, since you've updated, the cause of the problem is narrowed down to likely being one of the weaknesses of the mysql database (this is why I always recommend using postgres over mysql).
We don't have a script to execute sql statements to correct problems like this because they do not occur very frequently and they usually turn out to be something very specific to the local environment, However, looking at your contra repository, it looks like it attempts to install only 1 tool dependency (bedtools), so it should be fairly easy to fix manually. Step 1: You need to get the record of the installed tool shed repository named contra from your Galaxy database (you'll need the value for Step 3). This should do it for you. select * from tool_shed_repository where name = 'contra'; (Keep track of the id column value for Step 3 below) Step 2: Now update the row using the following sql statement: update tool_shed_repository set deleted = True, uninstalled = True where name = 'contra'; Step 3: Using the value in the id column from Step 1, execute the following sql, substituting that value - capitalization in the status value is required, so use the exact value. update tool_dependency set status = 'Uninstalled' where tool_shed_repository_id = <value of id column from Step 1>; Step 4: Manually edit the shed_tool_conf.xml file to remove the entry for the contra repository This should be all you need to do. Let me know if you bump into additional issues. Greg Von Kuster On Dec 6, 2012, at 2:08 AM, Franco Caramia wrote: > Hi Greg, > > We have now pulled the lastest revision 8359:c08a5d0d2a4f but the problem > persists. The stack trace remains the same... > Any ideas on what could be happening? > Ideally we would like to be able to fix the problem through the galaxy > interface, but in case we find no solution, do galaxy devs have some repo for > MySQL scripts to “clean” the DB?? (ex. Complete delete of a toolshed tool).. > > > Thanks, > > > On 5/12/12 9:10 PM, "Greg Von Kuster" <g...@bx.psu.edu> wrote: > >> If you have not yet updated your Galaxy instance to the revision from the >> galaxy-dist repository in bitbucket, then that is most likely the cause of >> the behavior you are seeing. >> >> Greg Von Kuster >> >> On Dec 5, 2012, at 12:52 AM, Franco Caramia wrote: >> >>> Re-installing error persists >>> >>> >>> Hi Greg, >>> >>> I have now modified the tool_dependencies.xml thank you for that.. >>> >>> I still have problems re-installing the tool... (need to reinstall to >>> update the tool dependency and test it correctly) >>> >>> Is the reinstalling failure related to my galaxy version?? >>> >>> Here is the error: >>> Server Error >>> URL: >>> http://bioinf-galaxy/admin_toolshed/browse_repositories?operation=activate+or+reinstall&id=88ee2d7021e4dc1a >>> Module paste.exceptions.errormiddleware:143 in __call__ >>> >> >>> >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activate+or+reinstall&id=88ee2d7021e4dc1a#> >>> >> app_iter = self.application(environ, start_response) >>> Module paste.debug.prints:98 in __call__ >>> >> >>> >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activate+or+reinstall&id=88ee2d7021e4dc1a#> >>> >> environ, self.app) >>> Module paste.wsgilib:539 in intercept_output >>> >> >>> >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activate+or+reinstall&id=88ee2d7021e4dc1a#> >>> >> app_iter = application(environ, replacement_start_response) >>> Module paste.recursive:80 in __call__ >>> >> >>> >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activate+or+reinstall&id=88ee2d7021e4dc1a#> >>> >> return self.application(environ, start_response) >>> Module paste.httpexceptions:632 in __call__ >>> >> >>> >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activate+or+reinstall&id=88ee2d7021e4dc1a#> >>> >> return self.application(environ, start_response) >>> Module galaxy.web.framework.base:160 in __call__ >>> >> >>> >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activate+or+reinstall&id=88ee2d7021e4dc1a#> >>> >> body = method( trans, **kwargs ) >>> Module galaxy.web.framework:184 in decorator >>> >> >>> >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activate+or+reinstall&id=88ee2d7021e4dc1a#> >>> >> return func( self, trans, *args, **kwargs ) >>> Module galaxy.web.controllers.admin_toolshed:350 in browse_repositories >>> >> >>> >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activate+or+reinstall&id=88ee2d7021e4dc1a#> >>> >> return self.reselect_tool_panel_section( trans, **kwd ) >>> Module galaxy.web.framework:184 in decorator >>> >> >>> >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activate+or+reinstall&id=88ee2d7021e4dc1a#> >>> >> return func( self, trans, *args, **kwargs ) >>> Module galaxy.web.controllers.admin_toolshed:1352 in >>> reselect_tool_panel_section >>> >> >>> >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activate+or+reinstall&id=88ee2d7021e4dc1a#> >>> >> status=status ) >>> Module galaxy.web.framework:746 in fill_template >>> >> >>> >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activate+or+reinstall&id=88ee2d7021e4dc1a#> >>> >> return self.fill_template_mako( filename, **kwargs ) >>> Module galaxy.web.framework:757 in fill_template_mako >>> >> >>> >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activate+or+reinstall&id=88ee2d7021e4dc1a#> >>> >> return template.render( **data ) >>> Module mako.template:296 in render >>> >> >>> >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activate+or+reinstall&id=88ee2d7021e4dc1a#> >>> >> return runtime._render(self, self.callable_, args, data) >>> Module mako.runtime:660 in _render >>> >> >>> >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activate+or+reinstall&id=88ee2d7021e4dc1a#> >>> >> **_kwargs_for_callable(callable_, data)) >>> Module mako.runtime:692 in _render_context >>> >> >>> >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activate+or+reinstall&id=88ee2d7021e4dc1a#> >>> >> _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) >>> Module mako.runtime:718 in _exec_template >>> >> >>> >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activate+or+reinstall&id=88ee2d7021e4dc1a#> >>> >> callable_(context, *args, **kwargs) >>> Module _base_mako:42 in render_body >>> >> >>> >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activate+or+reinstall&id=88ee2d7021e4dc1a#> >>> >> __M_writer(unicode(next.body())) >>> Module _admin_tool_shed_repository_reselect_tool_panel_section_mako:76 in >>> render_body >>> >> >>> >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activate+or+reinstall&id=88ee2d7021e4dc1a#> >>> >> __M_writer(unicode(render_tool_dependency_section( >>> >> install_tool_dependencies_check_box, [ repo_info_dict ] ))) >>> Module _admin_tool_shed_repository_common_mako:204 in >>> render_render_tool_dependency_section >>> >> >>> >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activate+or+reinstall&id=88ee2d7021e4dc1a#> >>> >> changeset_revision ) >>> Module posixpath:67 in join >>> >> >>> >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activate+or+reinstall&id=88ee2d7021e4dc1a#> >>> >> elif path == '' or path.endswith('/'): >>> AttributeError: 'NoneType' object has no attribute 'endswith' >>> >>> Thanks, >>> >>> Franco >>> >>> >>> This email (including any attachments or links) may contain confidential >>> and/or legally privileged information and is intended only to be read or >>> used by the addressee. If you are not the intended addressee, any use, >>> distribution, disclosure or copying of this email is strictly prohibited. >>> Confidentiality and legal privilege attached to this email (including any >>> attachments) are not waived or lost by reason of its mistaken delivery to >>> you. If you have received this email in error, please delete it and notify >>> us immediately by telephone or email. Peter MacCallum Cancer Centre >>> provides no guarantee that this transmission is free of virus or that it >>> has not been intercepted or altered and will not be liable for any delay in >>> its receipt. >> >> > > This email (including any attachments or links) may contain confidential > and/or legally privileged information and is intended only to be read or used > by the addressee. If you are not the intended addressee, any use, > distribution, disclosure or copying of this email is strictly prohibited. > Confidentiality and legal privilege attached to this email (including any > attachments) are not waived or lost by reason of its mistaken delivery to > you. If you have received this email in error, please delete it and notify us > immediately by telephone or email. Peter MacCallum Cancer Centre provides no > guarantee that this transmission is free of virus or that it has not been > intercepted or altered and will not be liable for any delay in its receipt.
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