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 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. 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 ___________________________________________________________ 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/
