Mercurial > repos > shellac > guppy_basecaller
diff env/lib/python3.7/site-packages/cwltool/tests/test_dependencies.py @ 2:6af9afd405e9 draft
"planemo upload commit 0a63dd5f4d38a1f6944587f52a8cd79874177fc1"
author | shellac |
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date | Thu, 14 May 2020 14:56:58 -0400 |
parents | 26e78fe6e8c4 |
children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/env/lib/python3.7/site-packages/cwltool/tests/test_dependencies.py Thu May 14 14:56:58 2020 -0400 @@ -0,0 +1,46 @@ +import pytest + +import pytest + +from cwltool.utils import onWindows + +from .util import get_data, get_main_output, needs_docker + + +try: + from galaxy.tools import deps +except ImportError: + deps = None + +@needs_docker +@pytest.mark.skipif(not deps, reason="galaxy-lib is not installed") +def test_biocontainers(): + 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(): + 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 + +import os +from distutils import spawn +@pytest.mark.skipif(not spawn.find_executable("modulecmd"), reason="modulecmd not installed") +def test_modules(): + 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