ova image: trouble initiating planemo bwa template

[martenson]

ubuntu@packer-virtualbox-iso-1466017992:~/Desktop/tools$ ls
2.fasta  2.fastq  bwa  seqtk_seq.xml  test-data  tool_test_output.html  tool_test_output.json
ubuntu@packer-virtualbox-iso-1466017992:~/Desktop/tools$ rm -rf bwa
ubuntu@packer-virtualbox-iso-1466017992:~/Desktop/tools$ planemo project_init --template bwa bwa
wget -q -O - 'https://codeload.github.com/galaxyproject/planemo/tar.gz/master' | tar  -C /tmp/tmprco1fp -zxf - --strip-components=2
ls '/tmp/tmprco1fp'
appliance.rst         database           Makefile             planemo.shed2tap.rst      slideshow_template.html        test_lint.py      tool_builder.py           _writing_from_help_command.rst
bioblend.py       demo           modules.rst          planemo.shed.rst          standards              test_normalize.py     tool_dependencies_good_1.xml  writing_how_do_i.rst
bootstrap_history.py  developing.rst         network_util.py          planemo.test.rst          _static                test_planemo.py       tool_dependencies_good_2.xml  _writing_intro.rst
build_slideshow.py    docker.py          new_version.py       planemo.xml.rst           templates.py               test_profile_commands.py  tool_factory_2            _writing_lint_intro.rst
bwa           engine             notebooks            pre-commit-lint           test                   test_run.py       tool_lint.py              _writing_parameters.rst
categories.py         exit_codes.py      options.py           pre-commit-lint-and-test      test_build_and_lint.py         test_shed_create.py   tools.py              _writing_publish_intro.rst
cli.py            galaxy             organization.rst         presentations         test_cmd_serve.py          test_shed_diff.py     travis_test.sh            writing.rst
commands          galaxy_changelog.html  other_docs.rst       print_version_for_release.py  test_cmd_shed_serve.py         test_shed_diff_xml.py     update_extern.sh          _writing_scripts.rst
commands.rst          galaxy_changelog.md    package_bwa_0_7_7        publishing.rst            test_cmd_test.py           test_shed_download.py     update_planemo_recipe.bash    writing_standalone.rst
commands_to_rst.py    github_util.py         package_samtools_0.1.16  README                test_command_io.py         test_shed_expansion.py    update_report_assets.sh       _writing_suites.rst
commit_version.py     git.py             package_seqtk_1_0_r75    readme.rst            test_config_init.py        test_shed_init.py     Vagrantfile               _writing_test_and_serve_appliance.rst
conda.py          glob.py            planemo.commands.rst     reports               test_conformance_cwl.bash      test_shed_lint.py     virtualenv.py             _writing_test_and_serve.rst
conda_testing         history.rst        planemo.cwl.rst          repository_dependencies_shed.xml  test_database_commands.py      test_shed_operations.py   writing               _writing_testing.rst
conduct.rst       images             planemo.database.rst     repository_dependencies.xml   test_dependency_script.py      test_shed.py      writing_advanced.rst          _writing_using_seqtk.rst
config.py         index.rst          planemo.engine.rst       runnable.py           test_engines.py            test_shed_test.py     writing_appliance.rst         xml
configuration.rst     __init__.py        planemo_ext.rst          scripts               test_galaxy_config.py          test_shed_upload.py   _writing_clusters.rst         xml_bad_1.xml
conf.py           installation.rst       planemo.galaxy.rst       setup.py              test_galaxy_serve.py           test_test_checker.py  _writing_collections.rst      xml_good_1.xml
contributing.rst      io.py          planemo.galaxy.test.rst  shed              test_galaxy_test.py        test_test_report.py   _writing_conclusion.rst       xml_good_2.xml
cwl           linters            planemo.linters.rst      shed2tap              test_galaxy_workflow_utils.py  test_utils.py         writing_cwl_appliance.rst     xsd_command.xsd
cwl_draft3_spec       lint.py            planemo_logo.png         shed_app.py           test_git.py            test_validation.py    _writing_cwl_intro.rst        xsd_schema_1.xsd
cwl-runner        lint_sphinx_output.py  planemo.reports.rst      shed_app_test_utils.py        test_init_and_test.py          test_wheel.bash       writing_cwl.rst
data              make.bat           planemo.rst          shed_lint.py          test_io.py             test_xml_diff.py      writing_cwl_standalone.rst
mv '/tmp/tmprco1fp/bwa'/* '/opt/galaxy/tools/bwa'
mv '/tmp/tmprco1fp/bwa'/.* '/opt/galaxy/tools/bwa'
mv: cannot move '/tmp/tmprco1fp/bwa/.' to '/opt/galaxy/tools/bwa/.': Device or resource busy
mv: cannot move '/tmp/tmprco1fp/bwa/..' to '/opt/galaxy/tools/bwa/..': Device or resource busy

[martenson]

$ ls /opt/galaxy/tools/bwa
bwa-mem.xml  test-data
$ ls /opt/galaxy/tools/bwa/test-data/
bwa-aln-test1.bam  bwa-mem-fastq1.fq  bwa-mem-fastq2.fq  bwa-mem-mt-genome.fa

[jmchilton]

Yeah - I get the same thing locally but that is all the relevant files I think. It is unfortunate UX - but I don't think this requires a fix prior to the GCC.

[martenson]

It looks to work fine though, the indices can be built.

[jmchilton]

This using clever reflected shell commands thing is fun - but I think it is becoming a real maintenance headache. @erasche long ago said we should abandon that approach and I'm starting to think he might be correct.

[jmchilton]

Moving the issue here - https://github.com/galaxyproject/planemo-machine/issues/77 - thanks a million.