Zipho looked at this over here and had some ideas about how some warning
output might trigger this spurious failure - I haven't had time to follow
up on that theory.
On 4 February 2016 at 14:26, Peter Briggs <peter.bri...@manchester.ac.uk>
> Hello again Peter
> I also see this when using planemo to run the tool tests both on
> trimmomatic and also on another of our tools i.e. one or more of the tests
> will be reported as 'failed' on the command line when the HTML report
> indicates that all tests executed successfully.
> Now I think about it, planemo itself must exit with status 0 in these
> cases as my tests on Travis-CI also report success, for example see:
> Scroll to the bottom of the log and the last test is reported as 'failed',
> however the Travis test overall passes. I hadn't really thought about it
> before since the planemo exit status seems to be correct (i.e. in cases
> where there are genuine tool test failures, it will return a non-zero
> status at the end which causes Travis to correctly report a failure).
> (Btw this referenced above used planemo 0.22.2 but I've seen it in older
> versions too.)
> I don't think I've ever seen planemo report a 'passed' test as 'failed',
> but generally I check the HTML to verify whether the failures are real or
> Best wishes
> On 22/01/16 11:40, Peter van Heusden wrote:
>> Hi there
>> When testing the latest trimmomatic tool (from
>> planemo test reports an error on the last test, but according to the
>> test report the test has succeeded (see attached HTML and JSON). For the
>> test setup you need to set some environment variables:
>> TRIMMOMATIC_DIR - the location of the trimmomatic jar
>> TRIMMOMATIC_JAR - the name of the jar file
>> TRIMMOMATIC_ADAPTERS_DIR - location of adapters
>> This is with planemo 0.22.2 and a fresh $HOME/.planemo.
>> Any ideas?
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> Peter Briggs peter.bri...@manchester.ac.uk
> Bioinformatics Core Facility University of Manchester
> B.1083 Michael Smith Bldg Tel: (0161) 2751482
> Please keep all replies on the list by using "reply all"
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