Installing DeepTools on Cloudman 2.0
<http://ec2-54-226-209-68.compute-1.amazonaws.com/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=8aa7aee9b90e1791&changeset_revisions=1ee0b1ecf500#> app_iter *=* self*.*application*(*environ*,* sr_checker*)* Module paste.recursive:*84* in __call__ <http://ec2-54-226-209-68.compute-1.amazonaws.com/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=8aa7aee9b90e1791&changeset_revisions=1ee0b1ecf500#> *return* self*.*application*(*environ*,* start_response*)* Module paste.httpexceptions:*633* in __call__ <http://ec2-54-226-209-68.compute-1.amazonaws.com/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=8aa7aee9b90e1791&changeset_revisions=1ee0b1ecf500#> *return* self*.*application*(*environ*,* start_response*)* Module galaxy.web.framework.base:*132* in __call__ <http://ec2-54-226-209-68.compute-1.amazonaws.com/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=8aa7aee9b90e1791&changeset_revisions=1ee0b1ecf500#> *return* self*.*handle_request*(* environ*,* start_response *)* Module galaxy.web.framework.base:*190* in handle_request <http://ec2-54-226-209-68.compute-1.amazonaws.com/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=8aa7aee9b90e1791&changeset_revisions=1ee0b1ecf500#>
<http://ec2-54-226-209-68.compute-1.amazonaws.com/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=8aa7aee9b90e1791&changeset_revisions=1ee0b1ecf500#> *return* func*(* self*,* trans*,* ***args*,* ****kwargs *)* Module galaxy.webapps.galaxy.controllers.admin_toolshed:*896* in
<http://ec2-54-226-209-68.compute-1.amazonaws.com/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=8aa7aee9b90e1791&changeset_revisions=1ee0b1ecf500#> common_install_util*.*get_dependencies_for_repository*(* trans*,* tool_shed_url*,* repo_info_dict*,*includes_tool_dependencies *)* Module tool_shed.util.common_install_util:*84* in get_dependencies_for_repository <http://ec2-54-226-209-68.compute-1.amazonaws.com/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=8aa7aee9b90e1791&changeset_revisions=1ee0b1ecf500#> installed_rd*,* missing_rd *=* get_installed_and_missing_repository_dependencies_for_new_install*(*trans*,* repo_info_tuple *)* Module tool_shed.util.common_install_util:*190* in get_installed_and_missing_repository_dependencies_for_new_install <http://ec2-54-226-209-68.compute-1.amazonaws.com/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=8aa7aee9b90e1791&changeset_revisions=1ee0b1ecf500#> tool_shed*,* name*,* owner*,* changeset_revision*,*
Hello, I recently discovered the DeepTools program and have been looking forward to using it with Galaxy Cloudman. Today I attempted to load DeepTools from the Galaxy tool shed on my freshly started Galaxy Cloudman 2.0 instance and got the following error: Internal Server ErrorGalaxy was unable to sucessfully complete your request URL: http://ec2-54-226-209-68.compute-1.amazonaws.com/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=8aa7aee9b90e1791&changeset_revisions=1ee0b1ecf500 Module galaxy.web.framework.middleware.error:*149* in __call__ body *=* method*(* trans*,* ****kwargs *)* Module galaxy.web.framework:*221* in decorator prepare_for_install prior_installation_required *=*suc*.*parse_repository_dependency_tuple*(* rd_tup *)* Module tool_shed.util.shed_util_common:*1106* in parse_repository_dependency_tuple prior_installation_required *=* str*(* prior_installation_required *)* *UnboundLocalError: local variable 'prior_installation_required' referenced before assignment* I got this error when I tried to install either of the three revisions of the tool. Am I doing something wrong? Any guidance is appreciated! Thanks in advance! Cheers, Mo Heydarian PhD candidate The Johns Hopkins School of Medicine Department of Biological Chemistry 725 Wolfe Street 402 Biophysics Baltimore, MD 21205
Hi Mohammed, that seems to be a old Tool Shed bug that is already fixed. Which Galaxy version are you running. Can you update to a more recent version? Thanks for using Galaxy and deepTools, Bjoern
Hello, I recently discovered the DeepTools program and have been looking forward to using it with Galaxy Cloudman. Today I attempted to load DeepTools from the Galaxy tool shed on my freshly started Galaxy Cloudman 2.0 instance and got the following error:
Internal Server Error Galaxy was unable to sucessfully complete your request URL: http://ec2-54-226-209-68.compute-1.amazonaws.com/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=8aa7aee9b90e1791&changeset_revisions=1ee0b1ecf500 Module galaxy.web.framework.middleware.error:149 in __call__
app_iter = self.application(environ, sr_checker) Module paste.recursive:84 in __call__ return self.application(environ, start_response) Module paste.httpexceptions:633 in __call__ return self.application(environ, start_response) Module galaxy.web.framework.base:132 in __call__ return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:190 in handle_request body = method( trans, **kwargs ) Module galaxy.web.framework:221 in decorator return func( self, trans, *args, **kwargs ) Module galaxy.webapps.galaxy.controllers.admin_toolshed:896 in prepare_for_install common_install_util.get_dependencies_for_repository( trans, tool_shed_url, repo_info_dict,includes_tool_dependencies ) Module tool_shed.util.common_install_util:84 in get_dependencies_for_repository installed_rd, missing_rd = get_installed_and_missing_repository_dependencies_for_new_install(trans, repo_info_tuple ) Module tool_shed.util.common_install_util:190 inget_installed_and_missing_repository_dependencies_for_new_install tool_shed, name, owner, changeset_revision, prior_installation_required =suc.parse_repository_dependency_tuple( rd_tup ) Module tool_shed.util.shed_util_common:1106 in parse_repository_dependency_tuple prior_installation_required = str( prior_installation_required ) UnboundLocalError: local variable 'prior_installation_required' referenced before assignment
I got this error when I tried to install either of the three revisions of the tool. Am I doing something wrong?
Any guidance is appreciated! Thanks in advance!
Cheers, Mo Heydarian
PhD candidate The Johns Hopkins School of Medicine Department of Biological Chemistry 725 Wolfe Street 402 Biophysics Baltimore, MD 21205
Hi Bjorn, Thanks for the quick response. I am running version: 10201:ebe87051fadf, when I updated to the latest version, I was able to start the install of DeepTools. The tool seemed to be installing but when I went to refresh the page, I was greeted with this message: "Initializing repository installation failed". Checking on the progress of the installation with the "monitor installing tool shed repositories" page, shows that most of the repositories are "Installing tool dependencies" (yellow box) or "Installed, missing both tool and repository dependencies" (gray box). This is the case even after ~ two hours. I am glad to clarify if my description was unclear, or even share the cloud instance. Thanks in advance for any help! Cheers, Mo Heydarian PhD candidate The Johns Hopkins School of Medicine Department of Biological Chemistry 725 Wolfe Street 402 Biophysics Baltimore, MD 21205 On Tue, Dec 3, 2013 at 1:37 PM, Björn Grüning < bjoern.gruening@pharmazie.uni-freiburg.de> wrote:
Hi Mohammed,
that seems to be a old Tool Shed bug that is already fixed. Which Galaxy version are you running. Can you update to a more recent version?
Thanks for using Galaxy and deepTools, Bjoern
Hello, I recently discovered the DeepTools program and have been looking forward to using it with Galaxy Cloudman. Today I attempted to load DeepTools from the Galaxy tool shed on my freshly started Galaxy Cloudman 2.0 instance and got the following error:
app_iter = self.application(environ, sr_checker) Module paste.recursive:84 in __call__ return self.application(environ, start_response) Module paste.httpexceptions:633 in __call__ return self.application(environ, start_response) Module galaxy.web.framework.base:132 in __call__ return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:190 in handle_request body = method( trans, **kwargs ) Module galaxy.web.framework:221 in decorator return func( self, trans, *args, **kwargs ) Module galaxy.webapps.galaxy.controllers.admin_toolshed:896 in
common_install_util.get_dependencies_for_repository( trans, tool_shed_url, repo_info_dict,includes_tool_dependencies ) Module tool_shed.util.common_install_util:84 in get_dependencies_for_repository installed_rd, missing_rd = get_installed_and_missing_repository_dependencies_for_new_install(trans, repo_info_tuple ) Module tool_shed.util.common_install_util:190 inget_installed_and_missing_repository_dependencies_for_new_install tool_shed, name, owner, changeset_revision,
Internal Server Error Galaxy was unable to sucessfully complete your request URL: http://ec2-54-226-209-68.compute-1.amazonaws.com/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=8aa7aee9b90e1791&changeset_revisions=1ee0b1ecf500 Module galaxy.web.framework.middleware.error:149 in __call__ prepare_for_install prior_installation_required =suc.parse_repository_dependency_tuple( rd_tup ) Module tool_shed.util.shed_util_common:1106 in parse_repository_dependency_tuple
prior_installation_required = str( prior_installation_required ) UnboundLocalError: local variable 'prior_installation_required' referenced before assignment
I got this error when I tried to install either of the three revisions of the tool. Am I doing something wrong?
Any guidance is appreciated! Thanks in advance!
Cheers, Mo Heydarian
PhD candidate The Johns Hopkins School of Medicine Department of Biological Chemistry 725 Wolfe Street 402 Biophysics Baltimore, MD 21205
Am Dienstag, den 03.12.2013, 16:19 -0500 schrieb Mohammad Heydarian:
Hi Bjorn, Thanks for the quick response.
I am running version: 10201:ebe87051fadf, when I updated to the latest version, I was able to start the install of DeepTools. The tool seemed to be installing but when I went to refresh the page, I was greeted with this message: "Initializing repository installation failed".
That one should not scare you. Its not an error, I need to fill a trello card about that. But it nothing to worry about.
Checking on the progress of the installation with the "monitor installing tool shed repositories" page, shows that most of the repositories are "Installing tool dependencies" (yellow box) or "Installed, missing both tool and repository dependencies" (gray box). This is the case even after ~ two hours.
Probably due to the error before. Can you please visit the deepTools repository and choose the 'repair repository' under 'repository actions'. That should fix all previous errors. You can also remove and reinstall deepTools and all packages in the 'Installing' state. Hope that helps! Bjoern
I am glad to clarify if my description was unclear, or even share the cloud instance.
Thanks in advance for any help!
Cheers, Mo Heydarian
PhD candidate The Johns Hopkins School of Medicine Department of Biological Chemistry 725 Wolfe Street 402 Biophysics Baltimore, MD 21205
On Tue, Dec 3, 2013 at 1:37 PM, Björn Grüning <bjoern.gruening@pharmazie.uni-freiburg.de> wrote: Hi Mohammed,
that seems to be a old Tool Shed bug that is already fixed. Which Galaxy version are you running. Can you update to a more recent version?
Thanks for using Galaxy and deepTools, Bjoern
> Hello, > I recently discovered the DeepTools program and have been looking > forward to using it with Galaxy Cloudman. Today I attempted to load > DeepTools from the Galaxy tool shed on my freshly started Galaxy > Cloudman 2.0 instance and got the following error: > > Internal Server Error > Galaxy was unable to sucessfully complete your request > URL: http://ec2-54-226-209-68.compute-1.amazonaws.com/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=8aa7aee9b90e1791&changeset_revisions=1ee0b1ecf500 > Module galaxy.web.framework.middleware.error:149 in __call__ > >> app_iter = self.application(environ, sr_checker) > Module paste.recursive:84 in __call__ > >> return self.application(environ, start_response) > Module paste.httpexceptions:633 in __call__ > >> return self.application(environ, start_response) > Module galaxy.web.framework.base:132 in __call__ > >> return self.handle_request( environ, start_response ) > Module galaxy.web.framework.base:190 in handle_request > >> body = method( trans, **kwargs ) > Module galaxy.web.framework:221 in decorator > >> return func( self, trans, *args, **kwargs ) > Module galaxy.webapps.galaxy.controllers.admin_toolshed:896 in prepare_for_install > >> common_install_util.get_dependencies_for_repository( trans, tool_shed_url, repo_info_dict,includes_tool_dependencies ) > Module tool_shed.util.common_install_util:84 in get_dependencies_for_repository > >> installed_rd, missing_rd = get_installed_and_missing_repository_dependencies_for_new_install(trans, repo_info_tuple ) > Module tool_shed.util.common_install_util:190 inget_installed_and_missing_repository_dependencies_for_new_install > >> tool_shed, name, owner, changeset_revision, prior_installation_required =suc.parse_repository_dependency_tuple( rd_tup ) > Module tool_shed.util.shed_util_common:1106 in parse_repository_dependency_tuple > >> prior_installation_required = str( prior_installation_required ) > UnboundLocalError: local variable 'prior_installation_required' > referenced before assignment > > > I got this error when I tried to install either of the three revisions > of the tool. Am I doing something wrong? > > > > > Any guidance is appreciated! Thanks in advance! > > > Cheers, > Mo Heydarian > > PhD candidate > The Johns Hopkins School of Medicine > Department of Biological Chemistry > 725 Wolfe Street > 402 Biophysics > Baltimore, MD 21205
That did the trick! Thanks, Bjoern! Cheers, Mo Heydarian PhD candidate The Johns Hopkins School of Medicine Department of Biological Chemistry 725 Wolfe Street 402 Biophysics Baltimore, MD 21205 On Tue, Dec 3, 2013 at 5:14 PM, Björn Grüning < bjoern.gruening@pharmazie.uni-freiburg.de> wrote:
Am Dienstag, den 03.12.2013, 16:19 -0500 schrieb Mohammad Heydarian:
Hi Bjorn, Thanks for the quick response.
I am running version: 10201:ebe87051fadf, when I updated to the latest version, I was able to start the install of DeepTools. The tool seemed to be installing but when I went to refresh the page, I was greeted with this message: "Initializing repository installation failed".
That one should not scare you. Its not an error, I need to fill a trello card about that. But it nothing to worry about.
Checking on the progress of the installation with the "monitor installing tool shed repositories" page, shows that most of the repositories are "Installing tool dependencies" (yellow box) or "Installed, missing both tool and repository dependencies" (gray box). This is the case even after ~ two hours.
Probably due to the error before. Can you please visit the deepTools repository and choose the 'repair repository' under 'repository actions'. That should fix all previous errors. You can also remove and reinstall deepTools and all packages in the 'Installing' state.
Hope that helps! Bjoern
I am glad to clarify if my description was unclear, or even share the cloud instance.
Thanks in advance for any help!
Cheers, Mo Heydarian
PhD candidate The Johns Hopkins School of Medicine Department of Biological Chemistry 725 Wolfe Street 402 Biophysics Baltimore, MD 21205
On Tue, Dec 3, 2013 at 1:37 PM, Björn Grüning <bjoern.gruening@pharmazie.uni-freiburg.de> wrote: Hi Mohammed,
that seems to be a old Tool Shed bug that is already fixed. Which Galaxy version are you running. Can you update to a more recent version?
Thanks for using Galaxy and deepTools, Bjoern
> Hello, > I recently discovered the DeepTools program and have been looking > forward to using it with Galaxy Cloudman. Today I attempted to load > DeepTools from the Galaxy tool shed on my freshly started Galaxy > Cloudman 2.0 instance and got the following error: > > Internal Server Error > Galaxy was unable to sucessfully complete your request > URL:
> Module galaxy.web.framework.middleware.error:149 in __call__ > >> app_iter = self.application(environ, sr_checker) > Module paste.recursive:84 in __call__ > >> return self.application(environ, start_response) > Module paste.httpexceptions:633 in __call__ > >> return self.application(environ, start_response) > Module galaxy.web.framework.base:132 in __call__ > >> return self.handle_request( environ, start_response ) > Module galaxy.web.framework.base:190 in handle_request > >> body = method( trans, **kwargs ) > Module galaxy.web.framework:221 in decorator > >> return func( self, trans, *args, **kwargs ) > Module galaxy.webapps.galaxy.controllers.admin_toolshed:896 in prepare_for_install > >> common_install_util.get_dependencies_for_repository( trans, tool_shed_url, repo_info_dict,includes_tool_dependencies ) > Module tool_shed.util.common_install_util:84 in get_dependencies_for_repository > >> installed_rd, missing_rd =
get_installed_and_missing_repository_dependencies_for_new_install(trans, repo_info_tuple )
> Module tool_shed.util.common_install_util:190
inget_installed_and_missing_repository_dependencies_for_new_install
> >> tool_shed, name, owner, changeset_revision, prior_installation_required =suc.parse_repository_dependency_tuple( rd_tup ) > Module tool_shed.util.shed_util_common:1106 in parse_repository_dependency_tuple > >> prior_installation_required = str( prior_installation_required ) > UnboundLocalError: local variable 'prior_installation_required' > referenced before assignment > > > I got this error when I tried to install either of the three revisions > of the tool. Am I doing something wrong? > > > > > Any guidance is appreciated! Thanks in advance! > > > Cheers, > Mo Heydarian > > PhD candidate > The Johns Hopkins School of Medicine > Department of Biological Chemistry > 725 Wolfe Street > 402 Biophysics > Baltimore, MD 21205
participants (2)
-
Björn Grüning -
Mohammad Heydarian