diff env/lib/python3.7/site-packages/cwltool/tests/test_dependencies.py @ 2:6af9afd405e9 draft

"planemo upload commit 0a63dd5f4d38a1f6944587f52a8cd79874177fc1"
author shellac
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