Mercurial > repos > shellac > sam_consensus_v3
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/env/lib/python3.9/site-packages/cwltool/tests/test_dependencies.py Mon Mar 22 18:12:50 2021 +0000 @@ -0,0 +1,57 @@ +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