view env/lib/python3.7/site-packages/cwltool/tests/test_dependencies.py @ 0:26e78fe6e8c4 draft

"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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