diff env/lib/python3.9/site-packages/cwltool/tests/test_dependencies.py @ 0:4f3585e2f14b draft default tip

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"

--- /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
[e-mail](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
+
+
[e-mail](onWindows(), reason="bioconda currently not working on MS Windows")
[e-mail](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
+
+
[e-mail](
+    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