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 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.
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 "/home/travis/build/peterjc/galaxy_blast/test-data/four_human_proteins.fasta,/home/travis/build/peterjc/galaxy_blast/galaxy-dev/test-data/four_human_proteins.fasta" -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 arguments):
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 "/home/travis/build/peterjc/galaxy_blast/test-data/three_human_mRNA.fasta /home/travis/build/peterjc/galaxy_blast/galaxy-dev/test-data/three_human_mRNA.fasta" -task megablast -evalue 0.001 -out "/tmp/tmp9NURC9/files/000/dataset_76.dat" -outfmt 6 -num_threads "${GALAXY_SLOTS:-8}"]
But when a single database is given we get a repeated path:
blastn ... -db "path path"
galaxy.jobs.command_factory INFO 2016-08-05 14:58:22,901 Built script [/tmp/tmp9NURC9/job_working_directory/000/78/tool_script.sh] for tool command[blastn -version > /tmp/tmp9NURC9/tmp/GALAXY_VERSION_STRING_78 2>&1; blastn -query "/tmp/tmp9NURC9/files/000/dataset_77.dat" -db "/home/travis/build/peterjc/galaxy_blast/test-data/rhodopsin_nucs.fasta /home/travis/build/peterjc/galaxy_blast/galaxy-dev/test-data/rhodopsin_nucs.fasta" -task megablast -evalue 0.001 -out "/tmp/tmp9NURC9/files/000/dataset_78.dat" -outfmt 6 -num_threads "${GALAXY_SLOTS:-8}"]
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).
Peter