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