| Previous changeset 80:f423a77bc669 (2020-11-17) Next changeset 82:60df9669d01c (2020-11-19) |
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Commit message:
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modified:
toolfactory/rgToolFactory2.py toolfactory/rgToolFactory2.xml |
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| diff -r f423a77bc669 -r 6395be766c2e toolfactory/rgToolFactory2.py --- a/toolfactory/rgToolFactory2.py Tue Nov 17 09:04:25 2020 +0000 +++ b/toolfactory/rgToolFactory2.py Wed Nov 18 21:47:51 2020 +0000 |
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| @@ -1,4 +1,3 @@ - # rgToolFactory.py # see https://github.com/fubar2/toolfactory # @@ -878,7 +877,19 @@ """planemo is a requirement so is available for testing and for generating test outputs if command or test overrides are supplied test outputs are sent to repdir for display - planemo test --engine docker_galaxy --database_type docker_postgres --galaxy_root /galaxy-central pyrevpos/pyrevpos.xml + planemo test --engine docker_galaxy --galaxy_root /galaxy-central pyrevpos/pyrevpos.xml + + Planemo runs: +python ./scripts/functional_tests.py -v --with-nosehtml --html-report-file +/export/galaxy-central/database/job_working_directory/000/17/working/TF_run_report_tempdir/tacrev_planemo_test_report.html +--with-xunit --xunit-file /tmp/tmpt90p7f9h/xunit.xml --with-structureddata +--structured-data-file +/export/galaxy-central/database/job_working_directory/000/17/working/tfout/tool_test_output.json functional.test_toolbox + + + for the planemo-biocontainer, + planemo test --conda_dependency_resolution --skip_venv --galaxy_root /galthrow/ rgToolFactory2.xml + """ xreal = "%s.xml" % self.tool_name tool_test_path = os.path.join(self.repdir,f"{self.tool_name}_planemo_test_report.html") @@ -891,8 +902,10 @@ cll = [ "planemo", "test", + "--conda_dependency_resolution", "--test_data", os.path.abspath(self.testdir), "--test_output", os.path.abspath(tool_test_path), + "--skip_venv", "--galaxy_root", self.args.galaxy_root, "--update_test_data", @@ -910,8 +923,10 @@ cll = [ "planemo", "test", + "--conda_dependency_resolution", "--test_data", os.path.abspath(self.testdir), "--test_output", os.path.abspath(tool_test_path), + "--skip_venv", "--galaxy_root", self.args.galaxy_root, os.path.abspath(xreal), |
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| diff -r f423a77bc669 -r 6395be766c2e toolfactory/rgToolFactory2.xml --- a/toolfactory/rgToolFactory2.xml Tue Nov 17 09:04:25 2020 +0000 +++ b/toolfactory/rgToolFactory2.xml Wed Nov 18 21:47:51 2020 +0000 |
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| @@ -132,9 +132,15 @@ </macros> <requirements> - <!--<requirement type="package" version="3.8.5" >python</requirement>--> - <requirement type="package" version="0.72.0" >planemo</requirement> - <requirement type="package" version="0.4.11" >galaxyxml</requirement> + <!-- + <requirement type="package" version="3.8.5" >python</requirement> + <requirement type="package" version="0.72.0">planemo</requirement> + --> + <container type="docker">quay.io/fubar2/planemo-biocontainer</container> + <requirement type="package" version="0.4.11">galaxyxml</requirement> + <requirement type="package" version="0.14.0">bioblend</requirement> + <requirement type="package" version="0.10.6">ephemeris</requirement> + </requirements> <command ><![CDATA[ |