Hi guys,

I have a new wrapper for samtools idxstats with a working
unit test via run_functional_tests.sh run locally or on TravisCI:
https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-November/017406.html

However, this tool's test is failing on the Test Tool Shed:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_idxstats/6564815949e0

Tool test results
Automated test environment
Time tested: ~ 11 hours ago
System: Linux 3.8.0-30-generic
Architecture: x86_64
Python version: 2.7.4
Galaxy revision: 11284:28469a503b56
Galaxy database version: 117
Tool shed revision:
Tool shed database version:
Tool shed mercurial version:
Tests that failed
Tool id: samtools_idxstats
Tool version: samtools_idxstats
Test: test_tool_000000
(functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/samtools_idxstats/samtools_idxstats/0.0.1)
Stderr:
Fatal error: Exit code 1 ()
Input BAI file not found: None
Traceback:
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 216, in test_tool
    self.do_it( td, shed_tool_id=shed_tool_id )
  File 
"/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
line 28, in do_it
    self.__verify_outputs( testdef, shed_tool_id, data_list )
  File 
"/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
line 134, in __verify_outputs
    self.__verify_output( output_tuple, shed_tool_id, elem,
maxseconds=maxseconds )
  File 
"/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
line 141, in __verify_output
    self.verify_dataset_correctness( outfile, hid=elem_hid,
attributes=attributes, shed_tool_id=shed_tool_id )
  File 
"/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py",
line 782, in verify_dataset_correctness
    self._assert_dataset_state( elem, 'ok' )
  File 
"/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py",
line 606, in _assert_dataset_state
    raise AssertionError( errmsg )
AssertionError: Expecting dataset state 'ok', but state is 'error'.
Dataset blurb: error

It appears that the upload has not generated the *.bai index and
assigned it to the variable input_bam.metadata.bam_index
(but this works via run_functional_tests.sh for me):

$ ls test-data/ex1.*
test-data/ex1.bam  test-data/ex1.idxstats.tabular

$ ./run_functional_tests.sh -id samtools_idxstats
...
Ran 1 test in 32.400s

OK
...
(all fine)

(Note that the bai file does not seem to be needed)

Tested with this revision, which works:

$ hg branch
default
$ hg log | head
changeset:   12309:1df960b4892a
tag:         tip
user:        John Chilton <jmchil...@gmail.com>
date:        Sun Nov 10 23:37:56 2013 -0600
summary:     PEP-8 cleanups of lib/galaxy/security/__init__.py.

Updated to current tip, also works:

$ hg branch
default
[galaxy@ppserver galaxy-central]$ hg log | head
changeset:   12321:e12a10e5418d
tag:         tip
user:        guerler
date:        Mon Nov 11 16:00:10 2013 -0500
summary:     UI: Fix tooltip placement for masthead icons

Are there anyone known differences on the Test Tool Shed
which could explain this failure?

Thanks,

Peter
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