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://travis-ci.org/peterjc/galaxy_mira - passing now :)
https://travis-ci.org/peterjc/pico_galaxy - probably a loc file problem
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:
as of this commit:

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.

galaxy.jobs.command_factory INFO 2016-08-05 14:55:08,543 Built script
[/tmp/tmp9NURC9/job_working_directory/000/58/tool_script.sh] for tool
command[blastdbcmd -version >
/tmp/tmp9NURC9/tmp/GALAXY_VERSION_STRING_58 2>&1; blastdbcmd -dbtype
prot -db 
-info -out "/tmp/tmp9NURC9/files/000/dataset_58.dat"]

For other tools you can select multiple databases as input, and
the blastn tests try that, e.g. a working test gave this (where the
space is deliberate as that's how the NCBI handle multiple DB

blastn ... -db "path1 path2"

galaxy.jobs.command_factory INFO 2016-08-05 14:58:01,783 Built script
[/tmp/tmp9NURC9/job_working_directory/000/76/tool_script.sh] for tool
command[blastn -version > /tmp/tmp9NURC9/tmp/GALAXY_VERSION_STRING_76
2>&1; blastn -query "/tmp/tmp9NURC9/files/000/dataset_75.dat" -db
-task megablast -evalue 0.001 -out
"/tmp/tmp9NURC9/files/000/dataset_76.dat" -outfmt 6 -num_threads

But when a single database is given we get a repeated path:

blastn ... -db "path path"

galaxy.jobs.command_factory INFO 2016-08-05 14:58:22,901 Built script
[/tmp/tmp9NURC9/job_working_directory/000/78/tool_script.sh] for tool
command[blastn -version > /tmp/tmp9NURC9/tmp/GALAXY_VERSION_STRING_78
2>&1; blastn -query "/tmp/tmp9NURC9/files/000/dataset_77.dat" -db
-task megablast -evalue 0.001 -out
"/tmp/tmp9NURC9/files/000/dataset_78.dat" -outfmt 6 -num_threads

Any thoughts on where this is breaking? In planemo?

These tests are working locally via "planemo test" (older
version of planemo, older version of Galaxy, Python 2.6).

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