On Tue, Aug 9, 2016 at 6:33 PM, Peter Cock <[email protected]> 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 ___________________________________________________________ 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/
