Hello Franco,
The tool dependency installation fails due to BEDTools.v2.17.0.tar.gz extracting into a directory named bedtools-2.17.0, rather than BEDTools.v2.17.0. Also, you following tag is not optimal since it assumes a specific os platform.
<action type="shell_command">cp bin/* $INSTALL_DIR/bin</action>
You'll need to change your tool_dependency.xml definition to use the "target_file" option, and correct the above tag with something like the following:
<?xml version="1.0"?> <tool_dependency> <package name="bedtools" version="2.17.0"> <install version="1.0"> <actions> <action type="download_by_url" target_filename="bedtools-2.17.0.tar.gz">http://bedtools.googlecode.com/files/BEDTools.v2.17.0.tar.gz</action> <action type="shell_command">make clean</action> <action type="shell_command">make all</action> <action type="move_directory_files"> <source_directory>bin</source_directory> <destination_directory>$INSTALL_DIR/bin</destination_directory> </action> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> </action> </actions> </install> <readme> GCC version 4.1 or greater is recommended. 3.x versions will typically not compile BEDTools </readme> </package> </tool_dependency>
Greg Von Kuster
On Dec 3, 2012, at 9:21 PM, Franco Caramia wrote:
Hi Greg,
Our Galaxy version is galaxy-dist 7712:e6444e7a1685 . The tool is “contra” from this repo: http://fcaramia@toolshed.g2.bx.psu.edu/repos/fcaramia/contra I own the repo and uploaded the tool_dependencies file Then the following steps:
Installing the tool from toolshed: Success Installing tool dependencies: Failed Deleting tool: Success Re-installing tool: Failed
Thanks,
Franco
On 4/12/12 12:40 AM, "Greg Von Kuster" greg@bx.psu.edu wrote:
Hello Franco,
It's impossible to help you with this issue and the issues you sent in your previous messages unless you provide more information. What version of Galaxy are you running? From what tool shed are you installing repositories. What repository are you installing? What are the precise steps you took to produce the behavior?
Keep in mind that the Galaxy test tool shed tracks the galaxy-central repository on bitbucket while the Galaxy main tool shed tracks the galaxy-dist repository on bitbucket.
Greg Von Kuster
On Dec 2, 2012, at 11:36 PM, Franco Caramia wrote:
URL: http://bioinf-galaxy/admin_toolshed/browse_repositories?operation=activate+o... 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('/'):
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