diff env/lib/python3.7/site-packages/cwltool/tests/test_dependencies.py @ 5:9b1c78e6ba9c draft default tip

"planemo upload commit 6c0a8142489327ece472c84e558c47da711a9142"
author shellac
date Mon, 01 Jun 2020 08:59:25 -0400
parents 79f47841a781
children
line wrap: on
line diff
--- 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