comparison tests/test_shm_csr.py @ 5:495a521cf9f2 draft

"planemo upload commit 40d62ec3d2fea3c3bac605c976941e1f3b7e2cd4"

4:c8f02bce10d0

CONTROL_NWK377_PB_IGHC_MID1_40nt_2 = TEST_DATA_DIR / "CONTROL_NWK377_PB_IGHC_MID1_40nt_2.txz"


@pytest.fixture(scope="module")
def shm_csr_result():
    temp_dir = Path(tempfile.mkdtemp())
    tool_dir = temp_dir / "shm_csr"
    shutil.copytree(GIT_ROOT, tool_dir)
    working_dir = temp_dir / "working"
    working_dir.mkdir(parents=True)

        filter_unique_count,
        class_filter,
        empty_region_filter,
        fast
    ]
    with open(temp_dir / "stderr", "wt") as stderr_file:
        with open(temp_dir / "stdout", "wt") as stdout_file:
            subprocess.run(cmd, cwd=working_dir, stdout=stdout_file,
                           stderr=stderr_file, check=True)
    yield Path(out_files_path)
    #shutil.rmtree(temp_dir)

5:495a521cf9f2

CONTROL_NWK377_PB_IGHC_MID1_40nt_2 = TEST_DATA_DIR / "CONTROL_NWK377_PB_IGHC_MID1_40nt_2.txz"


@pytest.fixture(scope="module")
def shm_csr_result():
    docker_container = "quay.io/rhpvorderman/mulled-v2-f7d31c9d7424063a492fc0e5ecbf89bc757c0107:2b50bdd4d8c1fefc6ec24b0753fad0dcecec843b-0"
    temp_dir = Path(tempfile.mkdtemp())
    tool_dir = temp_dir / "shm_csr"
    shutil.copytree(GIT_ROOT, tool_dir)
    working_dir = temp_dir / "working"
    working_dir.mkdir(parents=True)

        filter_unique_count,
        class_filter,
        empty_region_filter,
        fast
    ]
    docker_cmd = ["docker", "run", "-v", f"{temp_dir}:{temp_dir}",
                  "-v", f"{input}:{input}",
                  "-w", str(working_dir),
                  docker_container] + cmd
    with open(temp_dir / "stderr", "wt") as stderr_file:
        with open(temp_dir / "stdout", "wt") as stdout_file:
            subprocess.run(docker_cmd, cwd=working_dir, stdout=stdout_file,
                           stderr=stderr_file, check=True)
    yield Path(out_files_path)
    #shutil.rmtree(temp_dir)