On Tue, Mar 3, 2015 at 9:55 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote: > On Tue, Jan 27, 2015 at 2:23 PM, Peter Cock <p.j.a.c...@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-to-sam-failed Tests currently stalled on the main Tool Shed, reported here: http://dev.list.galaxyproject.org/Tests-not-being-run-on-toolsheds-tc4666816.html https://lists.galaxyproject.org/pipermail/galaxy-dev/2015-March/021708.html 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
