Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/cwltool/schemas/v1.2.0-dev5/index.md @ 0:4f3585e2f14b draft default tip
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author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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1 # Common Workflow Language Specifications, v1.2.0-dev5 |
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2 |
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3 The CWL specifications are divided up into several documents. |
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4 |
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5 The [User Guide](http://www.commonwl.org/user_guide/) provides a gentle |
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6 introduction to writing CWL command line tools and workflows. Currently it is for CWL v1.0 only. |
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7 |
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8 The [Command Line Tool Description Specification](CommandLineTool.html) |
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9 specifies the document schema and execution semantics for wrapping and |
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10 executing command line tools. |
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11 |
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12 The [Workflow Description Specification](Workflow.html) specifies the document |
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13 schema and execution semantics for composing workflows from components such as |
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14 command line tools and other workflows. |
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15 |
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16 The |
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17 [Semantic Annotations for Linked Avro Data (SALAD) Specification](SchemaSalad.html) |
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18 specifies the preprocessing steps that must be applied when loading CWL |
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19 documents and the schema language used to write the above specifications. |
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20 |
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21 Also available are inheritance graphs (as SVG images) for the [Schema Salad object model](salad.svg) and the [CWL object model](cwl.svg). |
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22 |
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23 # Running the CWL conformance tests |
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24 |
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25 Install a CWL runner of your choice. The reference runner can be installed as |
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26 the default runner by doing: |
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27 ``` |
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28 pip install cwlref-runner |
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29 ``` |
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30 |
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31 Install the CWL test parser: |
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32 ``` |
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33 pip install cwltest |
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34 ``` |
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35 You may need to activate a virtualenv first, or do a local install by adding `--user` after `install` above. |
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36 |
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37 From within a copy of [this repository](https://github.com/common-workflow-language/cwl-v1.2) (e.g. cwl-v1.2) execute the main test script |
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38 ``` |
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39 ./run_test.sh |
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40 ``` |
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41 |
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42 If the CWL runner isn't installed as `cwl-runner` then you can specify the name for the runner: |
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43 ``` |
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44 ./run_test.sh RUNNER=cwltool |
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45 ``` |
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46 |
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47 You can also specify additional options that are specific for the particular CWL runner you are using. |
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48 For example, with CWL reference runner you can turn on parallel execution mode: |
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49 ``` |
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50 ./run_test.sh RUNNER=cwltool EXTRA=--parallel |
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51 ``` |
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52 |
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53 This can be combined with launching more than one CWL conformance test at once with `-j`: |
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54 ``` |
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55 ./run_test.sh -j4 RUNNER=cwltool EXTRA=--parallel |
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56 ``` |
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57 |
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58 You can list all the tests |
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59 ``` |
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60 ./run_test.sh -l |
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61 ``` |
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62 |
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63 You can run a particular test |
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64 ``` |
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65 ./run_test.sh -n23 |
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66 ``` |
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67 |
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68 |
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69 If you are running tests using the CWL reference runner "cwltool" for an unreleased version of the CWL standards use the `--enable-dev` flag: |
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70 ``` |
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71 ./run_test.sh RUNNER=cwltool EXTRA=--enable-dev |
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72 ``` |
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73 |
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74 |
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75 For details of options you can pass to the test script, do: |
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76 ``` |
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77 ./run_test.sh --help |
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78 ``` |