Mercurial > repos > shellac > guppy_basecaller
diff env/lib/python3.7/site-packages/cwltool/tests/test_dependencies.py @ 5:9b1c78e6ba9c draft default tip
"planemo upload commit 6c0a8142489327ece472c84e558c47da711a9142"
author | shellac |
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date | Mon, 01 Jun 2020 08:59:25 -0400 |
parents | 79f47841a781 |
children |
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--- a/env/lib/python3.7/site-packages/cwltool/tests/test_dependencies.py Thu May 14 16:47:39 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,46 +0,0 @@ -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