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/6564815949e...

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 jmchilton@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