On Tue, Aug 9, 2016 at 6:33 PM, Peter Cock p.j.a.cock@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...
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/03f81e7fb1e0562b46b8b2a2079c9...
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