Mercurial > repos > shellac > guppy_basecaller

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

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"planemo upload commit 6c0a8142489327ece472c84e558c47da711a9142"
author shellac
date Mon, 01 Jun 2020 08:59:25 -0400
parents 79f47841a781
children
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4:79f47841a781 5:9b1c78e6ba9c
1 import pytest
2
3 import pytest
4
5 from cwltool.utils import onWindows
6
7 from .util import get_data, get_main_output, needs_docker
8
9
10 try:
11 from galaxy.tools import deps
12 except ImportError:
13 deps = None
14
15 @needs_docker
16 @pytest.mark.skipif(not deps, reason="galaxy-lib is not installed")
17 def test_biocontainers():
18 wflow = get_data("tests/seqtk_seq.cwl")
19 job = get_data("tests/seqtk_seq_job.json")
20 error_code, _, _ = get_main_output(
21 ["--beta-use-biocontainers", wflow, job])
22
23 assert error_code == 0
24
25 @pytest.mark.skipif(onWindows(), reason="bioconda currently not working on MS Windows")
26 @pytest.mark.skipif(not deps, reason="galaxy-lib is not installed")
27 def test_bioconda():
28 wflow = get_data("tests/seqtk_seq.cwl")
29 job = get_data("tests/seqtk_seq_job.json")
30 error_code, _, stderr = get_main_output(
31 ["--beta-conda-dependencies", "--debug", wflow, job])
32
33 assert error_code == 0, stderr
34
35 import os
36 from distutils import spawn
37 @pytest.mark.skipif(not spawn.find_executable("modulecmd"), reason="modulecmd not installed")
38 def test_modules():
39 wflow = get_data("tests/random_lines.cwl")
40 job = get_data("tests/random_lines_job.json")
41 os.environ["MODULEPATH"] = os.path.join(os.getcwd(), 'tests/test_deps_env/modulefiles')
42 error_code, _, stderr = get_main_output(
43 ["--beta-dependency-resolvers-configuration",
44 "tests/test_deps_env_modules_resolvers_conf.yml", "--debug", wflow, job])
45
46 assert error_code == 0, stderr