This sounds a lot like this; http://dev.list.galaxyproject.org/galaxy-cant-find-binaries-in-tp4662442p4662444.html.
When using the local job runner (as the test framework likely does), I believe samtools needs to be on Galaxy's path. I don't think it is enough to just have it available as a "tool dependency" (installed via tool shed or not). As workarounds Dave could either install the samtools OS package or place the tool shed install of this on Galaxy's path before starting? .Alternatively, I guess the underlying problem could be solved - though it is not entirely clear the best path forward on that, only that is a real problem. -John On Tue, Nov 12, 2013 at 6:07 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote: > 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 > ___________________________________________________________ > 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/
