Mercurial > repos > shellac > sam_consensus_v3
comparison env/lib/python3.9/site-packages/cwltool/tests/test_dependencies.py @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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-1:000000000000 | 0:4f3585e2f14b |
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1 import os | |
2 from distutils import spawn | |
3 | |
4 import pytest | |
5 | |
6 from cwltool.utils import onWindows | |
7 | |
8 from .util import get_data, get_main_output, needs_docker | |
9 | |
10 try: | |
11 from galaxy.tools import deps # type: ignore | |
12 except ImportError: | |
13 deps = None | |
14 | |
15 | |
16 @needs_docker | |
17 @pytest.mark.skipif(not deps, reason="galaxy-lib is not installed") | |
18 def test_biocontainers() -> None: | |
19 wflow = get_data("tests/seqtk_seq.cwl") | |
20 job = get_data("tests/seqtk_seq_job.json") | |
21 error_code, _, _ = get_main_output(["--beta-use-biocontainers", wflow, job]) | |
22 | |
23 assert error_code == 0 | |
24 | |
25 | |
26 @pytest.mark.skipif(onWindows(), reason="bioconda currently not working on MS Windows") | |
27 @pytest.mark.skipif(not deps, reason="galaxy-lib is not installed") | |
28 def test_bioconda() -> None: | |
29 wflow = get_data("tests/seqtk_seq.cwl") | |
30 job = get_data("tests/seqtk_seq_job.json") | |
31 error_code, _, stderr = get_main_output( | |
32 ["--beta-conda-dependencies", "--debug", wflow, job] | |
33 ) | |
34 | |
35 assert error_code == 0, stderr | |
36 | |
37 | |
38 @pytest.mark.skipif( | |
39 not spawn.find_executable("modulecmd"), reason="modulecmd not installed" | |
40 ) | |
41 def test_modules() -> None: | |
42 wflow = get_data("tests/random_lines.cwl") | |
43 job = get_data("tests/random_lines_job.json") | |
44 os.environ["MODULEPATH"] = os.path.join( | |
45 os.getcwd(), "tests/test_deps_env/modulefiles" | |
46 ) | |
47 error_code, _, stderr = get_main_output( | |
48 [ | |
49 "--beta-dependency-resolvers-configuration", | |
50 "tests/test_deps_env_modules_resolvers_conf.yml", | |
51 "--debug", | |
52 wflow, | |
53 job, | |
54 ] | |
55 ) | |
56 | |
57 assert error_code == 0, stderr |