This sounds a lot like this; http://dev.list.galaxyproject.org/galaxy-cant-find-binaries-in-tp4662442p466.... 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.cock@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/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 ___________________________________________________________ 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/