<http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activat... r+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=activat... r+reinstall&id=88ee2d7021e4dc1a#> environ, self.app) Module paste.wsgilib:539 in intercept_output
<http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activat... r+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=activat... r+reinstall&id=88ee2d7021e4dc1a#> return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__
<http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activat... r+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=activat... r+reinstall&id=88ee2d7021e4dc1a#> body = method( trans, **kwargs ) Module galaxy.web.framework:184 in decorator
<http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activat... r+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=activat... r+reinstall&id=88ee2d7021e4dc1a#> return self.reselect_tool_panel_section(
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+o r+reinstall&id=88ee2d7021e4dc1a Module paste.exceptions.errormiddleware:143 in __call__ trans, **kwd ) Module galaxy.web.framework:184 in decorator
<http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activat... r+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=activat... r+reinstall&id=88ee2d7021e4dc1a#> status=status ) Module galaxy.web.framework:746 in fill_template
<http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activat... r+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=activat... r+reinstall&id=88ee2d7021e4dc1a#> return template.render( **data ) Module mako.template:296 in render
<http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activat... r+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=activat... r+reinstall&id=88ee2d7021e4dc1a#> **_kwargs_for_callable(callable_, data)) Module mako.runtime:692 in _render_context
<http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activat... r+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=activat... r+reinstall&id=88ee2d7021e4dc1a#> callable_(context, *args, **kwargs) Module _base_mako:42 in render_body
<http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activat... r+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=activat... r+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=activat... r+reinstall&id=88ee2d7021e4dc1a#> changeset_revision ) Module posixpath:67 in join
<http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activat... r+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.
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:
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.
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 ³clean² the DB?? (ex. Complete delete of a toolshed tool).. Thanks, On 5/12/12 9:10 PM, "Greg Von Kuster" <greg@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+o... +reinstall&id=88ee2d7021e4dc1a Module paste.exceptions.errormiddleware:143 in __call__
<http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activ ate+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=activ ate+or+reinstall&id=88ee2d7021e4dc1a#> environ, self.app) Module paste.wsgilib:539 in intercept_output
<http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activ ate+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=activ ate+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=activ ate+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=activ ate+or+reinstall&id=88ee2d7021e4dc1a#> body = method( trans, **kwargs ) Module galaxy.web.framework:184 in decorator
<http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activ ate+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=activ ate+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=activ ate+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=activ ate+or+reinstall&id=88ee2d7021e4dc1a#> status=status ) Module galaxy.web.framework:746 in fill_template
<http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activ ate+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=activ ate+or+reinstall&id=88ee2d7021e4dc1a#> return template.render( **data ) Module mako.template:296 in render
<http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activ ate+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=activ ate+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=activ ate+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=activ ate+or+reinstall&id=88ee2d7021e4dc1a#> callable_(context, *args, **kwargs) Module _base_mako:42 in render_body
<http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activ ate+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=activ ate+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=activ ate+or+reinstall&id=88ee2d7021e4dc1a#> changeset_revision ) Module posixpath:67 in join
<http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activ ate+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.
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" <greg@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.
Hi Greg, Thanks a lot for your help. I still get the same error trying to reinstall the tool... Here is the status of the DB: mysql> select name,id,status,deleted,uninstalled from tool_shed_repository where name = 'contra'; +--------+----+-------------+---------+-------------+ | name | id | status | deleted | uninstalled | +--------+----+-------------+---------+-------------+ | contra | 9 | Uninstalled | 1 | 1 | +--------+----+-------------+---------+-------------+ 1 row in set (0.00 sec) select name,status from tool_dependency where tool_shed_repository_id = 9; +----------+-------------+ | name | status | +----------+-------------+ | bedtools | Uninstalled | +----------+-------------+ 1 row in set (0.00 sec) The shed_tool_conf has no contra¹ entry... A complete remove from the DB should help to solve it, but I don¹t want to break possible relationship tables as I¹m not familiar with the schema.. Thanks, Franco On 7/12/12 1:01 AM, "Greg Von Kuster" <greg@bx.psu.edu> wrote:
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:
Re: Re-installing error persists 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 ³clean² the DB?? (ex. Complete delete of a toolshed tool)..
Thanks,
On 5/12/12 9:10 PM, "Greg Von Kuster" <greg@bx.psu.edu <x-msg://14/greg@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=act ivate+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=act ivate+or+reinstall&id=88ee2d7021e4dc1a#> environ, self.app) Module paste.wsgilib:539 in intercept_output >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=act ivate+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=act ivate+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=act ivate+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=act ivate+or+reinstall&id=88ee2d7021e4dc1a#> body = method( trans, **kwargs ) Module galaxy.web.framework:184 in decorator >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=act ivate+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=act ivate+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=act ivate+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=act ivate+or+reinstall&id=88ee2d7021e4dc1a#> status=status ) Module galaxy.web.framework:746 in fill_template >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=act ivate+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=act ivate+or+reinstall&id=88ee2d7021e4dc1a#> return template.render( **data ) Module mako.template:296 in render >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=act ivate+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=act ivate+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=act ivate+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=act ivate+or+reinstall&id=88ee2d7021e4dc1a#> callable_(context, *args, **kwargs) Module _base_mako:42 in render_body >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=act ivate+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=act ivate+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=act ivate+or+reinstall&id=88ee2d7021e4dc1a#> changeset_revision ) Module posixpath:67 in join >> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=act ivate+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.
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.
Hi Greg, list When installing a tool dependency, and the Installation Status shows : Error In what log would the actual error be specified?? Thanks, Franco On 5/12/12 9:10 PM, "Greg Von Kuster" <greg@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+o... +reinstall&id=88ee2d7021e4dc1a Module paste.exceptions.errormiddleware:143 in __call__
<http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activ ate+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=activ ate+or+reinstall&id=88ee2d7021e4dc1a#> environ, self.app) Module paste.wsgilib:539 in intercept_output
<http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activ ate+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=activ ate+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=activ ate+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=activ ate+or+reinstall&id=88ee2d7021e4dc1a#> body = method( trans, **kwargs ) Module galaxy.web.framework:184 in decorator
<http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activ ate+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=activ ate+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=activ ate+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=activ ate+or+reinstall&id=88ee2d7021e4dc1a#> status=status ) Module galaxy.web.framework:746 in fill_template
<http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activ ate+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=activ ate+or+reinstall&id=88ee2d7021e4dc1a#> return template.render( **data ) Module mako.template:296 in render
<http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activ ate+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=activ ate+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=activ ate+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=activ ate+or+reinstall&id=88ee2d7021e4dc1a#> callable_(context, *args, **kwargs) Module _base_mako:42 in render_body
<http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activ ate+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=activ ate+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=activ ate+or+reinstall&id=88ee2d7021e4dc1a#> changeset_revision ) Module posixpath:67 in join
<http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=activ ate+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.
Never mind, the INSTALLATION .log is in the repository browser... Sorry, Franco On 11/12/12 4:17 PM, "Franco Caramia" <franco.caramia@petermac.org> wrote:
Hi Greg, list
When installing a tool dependency, and the Installation Status shows : Error
In what log would the actual error be specified??
Thanks,
Franco
On 5/12/12 9:10 PM, "Greg Von Kuster" <greg@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+o r+reinstall&id=88ee2d7021e4dc1a Module paste.exceptions.errormiddleware:143 in __call__
> <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=acti vate+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=acti vate+or+reinstall&id=88ee2d7021e4dc1a#> environ, self.app) Module paste.wsgilib:539 in intercept_output > <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=acti vate+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=acti vate+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=acti vate+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=acti vate+or+reinstall&id=88ee2d7021e4dc1a#> body = method( trans, **kwargs ) Module galaxy.web.framework:184 in decorator > <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=acti vate+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=acti vate+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=acti vate+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=acti vate+or+reinstall&id=88ee2d7021e4dc1a#> status=status ) Module galaxy.web.framework:746 in fill_template > <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=acti vate+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=acti vate+or+reinstall&id=88ee2d7021e4dc1a#> return template.render( **data ) Module mako.template:296 in render > <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=acti vate+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=acti vate+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=acti vate+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=acti vate+or+reinstall&id=88ee2d7021e4dc1a#> callable_(context, *args, **kwargs) Module _base_mako:42 in render_body > <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=acti vate+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=acti vate+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=acti vate+or+reinstall&id=88ee2d7021e4dc1a#> changeset_revision ) Module posixpath:67 in join > <http://bioinf-galaxy:83/admin_toolshed/browse_repositories?operation=acti vate+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.
Hi Franco, I'm not quite sure what page you'r eon, but if you're looking at the page that has the tool dependency with the error status, you should be able to click the link of the tool dependency and see the error, log, etc. If this is not the page you're referring to, then I'll have to take a look and see if I can reproduce this. I'm swamped right now, but I'll get to this as soon as possible. Greg Von Kuster On Dec 11, 2012, at 1:17 AM, Franco Caramia wrote:
Hi Greg, list
When installing a tool dependency, and the Installation Status shows : Error
In what log would the actual error be specified??
Thanks,
Franco
On 5/12/12 9:10 PM, "Greg Von Kuster" <greg@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
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participants (2)
-
Franco Caramia -
Greg Von Kuster