Mercurial > repos > shellac > sam_consensus_v3
view env/lib/python3.9/site-packages/cwltool/tests/test_dependencies.py @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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import os from distutils import spawn import pytest from cwltool.utils import onWindows from .util import get_data, get_main_output, needs_docker try: from galaxy.tools import deps # type: ignore except ImportError: deps = None @needs_docker @pytest.mark.skipif(not deps, reason="galaxy-lib is not installed") def test_biocontainers() -> None: wflow = get_data("tests/seqtk_seq.cwl") job = get_data("tests/seqtk_seq_job.json") error_code, _, _ = get_main_output(["--beta-use-biocontainers", wflow, job]) assert error_code == 0 @pytest.mark.skipif(onWindows(), reason="bioconda currently not working on MS Windows") @pytest.mark.skipif(not deps, reason="galaxy-lib is not installed") def test_bioconda() -> None: wflow = get_data("tests/seqtk_seq.cwl") job = get_data("tests/seqtk_seq_job.json") error_code, _, stderr = get_main_output( ["--beta-conda-dependencies", "--debug", wflow, job] ) assert error_code == 0, stderr @pytest.mark.skipif( not spawn.find_executable("modulecmd"), reason="modulecmd not installed" ) def test_modules() -> None: wflow = get_data("tests/random_lines.cwl") job = get_data("tests/random_lines_job.json") os.environ["MODULEPATH"] = os.path.join( os.getcwd(), "tests/test_deps_env/modulefiles" ) error_code, _, stderr = get_main_output( [ "--beta-dependency-resolvers-configuration", "tests/test_deps_env_modules_resolvers_conf.yml", "--debug", wflow, job, ] ) assert error_code == 0, stderr