Hi Peter,

2014-07-31 10:57 GMT+02:00 Peter Cock <p.j.a.c...@googlemail.com>:

> Hi Dave,
>
> You are right that on closer inspection I've mixed tool_dependencies.xml
> and repository_dependencies.xml *again*. Evidentially my mental model
> does not match Greg's here:
>
> (*) I need to define a tool installation recipe for something not in the
> Tool Shed --> write an install script called tool_dependencies.xml
>
> (*) I need to depend on a Python package by pointing at another repository
> in the Tool Shed --> repository_dependencies.xml
>

I might be wrong, but I think that also goes to tool_dependencies.xml


> (*) I need to depend on a datatype package by pointing at another
> repository
> in the Tool Shed --> repository_dependencies.xml
>
> (*) I need to depend on a binary package by pointing at another repository
> in the Tool Shed --> repository_dependencies.xml ? No. You need
> tool_dependencies.xml for this too
>


As far as I understood, everything that is referenced in the tool.xml under
the requirement section, needs to be in a tool_dependencies.xml file. Any
other dependency are from the repository (data_types, data_manager,
workflows ...).

Ciao,
Bjoern



> But that aside, the test framework error here is completely unhelpful.
>
> Why is there no error message about missing a dependency?
> Was there an error from running my tool which was not shown?
>
> Thanks,
>
> Peter
>
> On Wed, Jul 30, 2014 at 6:07 PM, Dave Bouvier <d...@bx.psu.edu> wrote:
> > Peter,
> >
> > I believe part of the problem is that the install and test framework is
> > unable to resolve the dependency on blast+ 2.2.29 because it is defined
> as a
> > repository dependency, not a tool dependency. I would recommend replacing
> > the repository dependency in the blast_rbh repository with a tool
> dependency
> > definition that references package_blast_plus_2_2_29.
> >
> > --Dave B.
> >
> > On 07/30/2014 05:27 AM, Peter Cock wrote:
> >>
> >> Hi all,
> >>
> >> I'm not sure when this started (having hardly looked at my Tool Shed
> >> test results since GCC2014), but I think this is a fairly recent problem
> >> with my BLAST RBH tests failing (which has held me back from posting
> >> this to the main Tool Shed).
> >>
> >> This could be some silly mistake in my tar-ball, but usually missing
> >> test files and the like get an explicit error. The tests are passing
> >> on my GitHub/TravisCI setup (using Twill and the API backend):
> >> e.g. https://travis-ci.org/peterjc/galaxy_blast/builds/30592097
> >>
> >> Here is the current error (the same for the last few Test Tool Shed
> >> runs), https://testtoolshed.g2.bx.psu.edu/view/peterjc/blast_rbh
> >>
> >> Traceback (most recent call last):
> >>    File
> >>
> "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
> >> line 108, in test_tool
> >>      self.do_it( td )
> >>    File
> >>
> "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
> >> line 35, in do_it
> >>      self._verify_outputs( testdef, test_history, shed_tool_id,
> >> data_list, galaxy_interactor )
> >>    File
> >>
> "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
> >> line 69, in _verify_outputs
> >>      galaxy_interactor.verify_output( history, output_data,
> >> output_testdef=output_testdef, shed_tool_id=shed_tool_id,
> >> maxseconds=maxseconds )
> >>    File
> >>
> "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py",
> >> line 53, in verify_output
> >>      self.wait_for_history( history_id, maxseconds )
> >>    File
> >>
> "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py",
> >> line 107, in wait_for_history
> >>      self.twill_test_case.wait_for( lambda: not self.__history_ready(
> >> history_id ), maxseconds=maxseconds)
> >>    File
> >>
> "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py",
> >> line 2453, in wait_for
> >>      result = func()
> >>    File
> >>
> "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py",
> >> line 107, in <lambda>
> >>      self.twill_test_case.wait_for( lambda: not self.__history_ready(
> >> history_id ), maxseconds=maxseconds)
> >>    File
> >>
> "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py",
> >> line 257, in __history_ready
> >>      return self._state_ready( state, error_msg="History in error
> state."
> >> )
> >>    File
> >>
> "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py",
> >> line 316, in _state_ready
> >>      raise Exception( error_msg )
> >> Exception: History in error state.
> >>
> >> Is a more detailed log available which might help debug this?
> >>
> >> Thanks,
> >>
> >> Peter
> >>
> >> As an aside, this looks like the Test Tool Shed is still using the
> >> Twill backend for the functional tests?
> >> ___________________________________________________________
> >> 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/
> >>
> >> To search Galaxy mailing lists use the unified search at:
> >>    http://galaxyproject.org/search/mailinglists/
> >>
> >
> ___________________________________________________________
> 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/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
>
___________________________________________________________
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/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Reply via email to