Hello Dave
Thanks for addressing the specific issue of the tests failing to run.
Re my initial problem vis-a-vis a tool with tests that worked locally
but failed on the toolsheds, this appears to be a result of the two
environments using differing versions of perl. This caused the ordering
of data in the output files to differ from the reference output in the
tests on the toolshed.
As the tool wraps a third-party program, I've addressed this by
explicitly specifying the version of perl that it uses (at least it
seems to have worked for my latest version on the test toolshed - I will
update the main toolshed next).
The repositories in question are:
https://toolshed.g2.bx.psu.edu/view/pjbriggs/pal_finder
https://testtoolshed.g2.bx.psu.edu/view/pjbriggs/pal_finder
I see a separate problem with a different tool which I'll investigate
next and report if I can't understand the toolshed test failure.
Thanks again for your help,
Best wishes
Peter
On 18/03/15 13:46, Dave Bouvier wrote:
Gentlemen,
The issue with the nightly testing was due to a stalled test run
blocking subsequent tests. I've cleared out that blockage and a manual
test run appears to have completed successfully, as should future
automated test runs. As always, feel free to let us know if you
encounter any additional inexplicable behavior.
--Dave B.
On 03/18/2015 07:00 AM, Peter Cock wrote:
On Wed, Mar 18, 2015 at 10:13 AM, Peter Briggs
<peter.bri...@manchester.ac.uk> wrote:
Hello Peter C.
Thanks for your comments and advice Ironically after I sent that
email the
tests for the next tool I looked at in the toolshed had been run in
the past
couple of days.
That's good. I can also confirm that the Test Tool Shed example I
gave was tested overnight, although it looks like a novel failure:
https://testtoolshed.g2.bx.psu.edu/view/peterjc/sample_seqs
I'm interested because I've got a couple of tools that seem to work okay
when I run the tests locally, but are reported as failing on the
toolshed,
and I wanted to see if I'd addressed the issue for one of them by
updating
the tool dependencies.
I suggest asking on this mailing list, posting the shareable Tool Shed
URL
and a copy of the error message. Hopefully it will be a simple issue
(forgetting a test file is my most common mistake), or it may be
that another tool author has seen the same error (which can happen
due to problems in Galaxy itself).
(As an aside I'd also assumed that passing tests is one of the
conditions
for the tool to be marked as "verified", but maybe that's not the case?)
I think there is still a human involved, but passing tests is expected
for a "verified" tool.
However as you say, more testing locally seems to be a good way to go -
thanks for your suggestions. I looked at planemo briefly a while ago
and it
looked good. The other issue I've had with testing is actually
testing tool
installation (i.e. tool_dependencies.xml) - I recall that planemo didn't
deal with that side of things, so I had to set up the environment for
the
tests manually.
There is some work on tool_dependencies.xml ongoing within planemo,
John Chilton would be the person to ask (CC'd directly).
Thanks again for your advice and the links, I will investigate trying
to set
up a local solution (including some CI testing!).
This is something where using planemo ought to be very useful - for
now I still do my local testing with a test Galaxy instance via:
$ ./run_tests.sh -id my_tool_id
Peter
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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
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