On Tue, Aug 9, 2016 at 6:33 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> Hello all,
>
> Recently I've been debugging various problems with my Galaxy tool TravisCI
> tests as part of moving to using "planemo test" rather than the fragile system
> I first created which mimicked a pre-ToolShed manual install:
>
> https://blastedbio.blogspot.co.uk/2013/09/using-travis-ci-for-testing-galaxy-tools.html
>
> Progress:
>
> https://travis-ci.org/peterjc/galaxy_mira - passing now :)
> https://travis-ci.org/peterjc/pico_galaxy - probably a loc file problem

I now understand why this was breaking and have a workaround,
filed as:

https://github.com/galaxyproject/planemo/issues/530

> https://travis-ci.org/peterjc/galaxy_blast - different loc file problem
>
> This email is about the problems testing the BLAST wrappers where I
> am using a BLAST database defined in test-data/*.loc files.
>
> (I wasted some time today trying moving/copying the loc files and
> databases to different places before I noticed the issue below)
>
> Problem lines quoted are from this run, galaxy master or dev branch:
> https://travis-ci.org/peterjc/galaxy_blast/builds/150072050
> as of this commit:
> https://github.com/peterjc/galaxy_blast/commit/03f81e7fb1e0562b46b8b2a2079c94f04c1f3adf
>
> Some of the command expect a single BLAST database from the
> test-data/*.loc files, and the test should do that, but we get:
>
> blastdbcmd ... -db path,path ...
> rpsblast ... -db path,path ...
> rpstblastn ... -db path,path ...
>
> Here we should get ... -db path (once only), not repeated with a
> comma, e.g.

I think I now understand how this happens, see:

https://github.com/galaxyproject/galaxy/pull/2644

Peter
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