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://fcara...@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" <g...@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+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' 
>>> ___________________________________________________________
>>> Please keep all replies on the list by using "reply all"
>>> in your mail client.  To manage your subscriptions to this
>>> and other Galaxy lists, please use the interface at:
>>> 
>>>   http://lists.bx.psu.edu/
>> 
>> 
> 
> 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.

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Reply via email to