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