Hey Peter, Thanks for continuing to apply pressure on these issues. I have pushed some logging into Galaxy's development branch (https://github.com/galaxyproject/galaxy/commit/8cb06d7fc2913b4d83ca01b50d76e...) that should make that error more informative. I don't know when that will get pushed out to bitbucket and the shed retested - but once those two things happen we will hopefully have a better idea what the problem is (probably some subtle deployment problem - some incompatible version of samtools on the path? samtools on Galaxy's path but not the test script's path?). -John On Mon, Mar 23, 2015 at 6:06 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Tue, Mar 3, 2015 at 9:55 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Tue, Jan 27, 2015 at 2:23 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Hi all,
I have a query about a failing tool test on the Tool Shed, where it seems Galaxy is trying to convert both the expected BAM output and the tool's BAM output into SAM for comparison - but this fails.
https://toolshed.g2.bx.psu.edu/view/peterjc/samtools_depad
2015-01-27 02:13:51 ... Converting local (test-data) bam to sam failed
(and same error on the second test)
https://toolshed.g2.bx.psu.edu/view/peterjc/samtools_depad is still failing, although now with a more concise traceback:
Test runs 2015-01-29 02:26:31 Automated test environment Tests that failed Tool id: samtools_depad Tool version: samtools_depad Test: test_tool_000000 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/samtools_depad/samtools_depad/0.0.1) Stderr: Traceback: Traceback (most recent call last): ... Converting local (test-data) bam to sam failed
The same occurs on the Test Tool Shed (with a very slightly updated version of this tool), although with a more concise traceback:
https://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_depad
2015-01-25 08:21:59 ... Tool id: samtools_depad Tool version: samtools_depad Test: test_tool_000000 (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/samtools_depad/samtools_depad/0.0.2) Stderr: Traceback: ... Converting local (test-data) bam to sam failed
https://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_depad also still failing,
Test runs 2015-01-25 08:21:59 ... Converting local (test-data) bam to sam failed
Still failing on the Test Tool Shed, bug filed on Trello, https://trello.com/c/TL0IdLlG/2570-toolshed-converting-local-test-data-bam-t...
Tests currently stalled on the main Tool Shed, reported here: http://dev.list.galaxyproject.org/Tests-not-being-run-on-toolsheds-tc4666816... https://lists.galaxyproject.org/pipermail/galaxy-dev/2015-March/021708.html
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