Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/cwltool-1.0.20191225192155.dist-info/METADATA @ 0:26e78fe6e8c4 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author shellac
date Sat, 02 May 2020 07:14:21 -0400
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0
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1 Metadata-Version: 2.1
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2 Name: cwltool
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3 Version: 1.0.20191225192155
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4 Summary: Common workflow language reference implementation
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5 Home-page: https://github.com/common-workflow-language/cwltool
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6 Author: Common workflow language working group
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7 Author-email: common-workflow-language@googlegroups.com
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8 License: UNKNOWN
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9 Download-URL: https://github.com/common-workflow-language/cwltool
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10 Platform: UNKNOWN
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11 Classifier: Development Status :: 5 - Production/Stable
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12 Classifier: Environment :: Console
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13 Classifier: Intended Audience :: Developers
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14 Classifier: Intended Audience :: Science/Research
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15 Classifier: Intended Audience :: Healthcare Industry
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16 Classifier: License :: OSI Approved :: Apache Software License
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17 Classifier: Natural Language :: English
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18 Classifier: Operating System :: MacOS :: MacOS X
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19 Classifier: Operating System :: POSIX
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20 Classifier: Operating System :: POSIX :: Linux
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21 Classifier: Operating System :: OS Independent
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22 Classifier: Operating System :: Microsoft :: Windows
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23 Classifier: Operating System :: Microsoft :: Windows :: Windows 10
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24 Classifier: Operating System :: Microsoft :: Windows :: Windows 8.1
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25 Classifier: Programming Language :: Python :: 2
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26 Classifier: Programming Language :: Python :: 2.7
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27 Classifier: Programming Language :: Python :: 3
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28 Classifier: Programming Language :: Python :: 3.5
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29 Classifier: Programming Language :: Python :: 3.6
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30 Classifier: Programming Language :: Python :: 3.7
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31 Classifier: Programming Language :: Python :: 3.8
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32 Classifier: Topic :: Scientific/Engineering
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33 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
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34 Classifier: Topic :: Scientific/Engineering :: Astronomy
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35 Classifier: Topic :: Scientific/Engineering :: Atmospheric Science
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36 Classifier: Topic :: Scientific/Engineering :: Information Analysis
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37 Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
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38 Classifier: Topic :: System :: Distributed Computing
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39 Classifier: Topic :: Utilities
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40 Requires-Python: >=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, <4
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41 Description-Content-Type: text/x-rst
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42 Requires-Dist: setuptools
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43 Requires-Dist: requests (>=2.6.1)
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44 Requires-Dist: ruamel.yaml (<=0.16,>=0.12.4)
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45 Requires-Dist: rdflib (<4.3.0,>=4.2.2)
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46 Requires-Dist: shellescape (<3.5,>=3.4.1)
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47 Requires-Dist: schema-salad (<5,>=4.5)
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48 Requires-Dist: mypy-extensions
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49 Requires-Dist: six (>=1.9.0)
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50 Requires-Dist: psutil
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51 Requires-Dist: scandir
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52 Requires-Dist: prov (==1.5.1)
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53 Requires-Dist: bagit (>=1.6.4)
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54 Requires-Dist: typing-extensions
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55 Requires-Dist: coloredlogs
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56 Requires-Dist: future (>=0.16)
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57 Requires-Dist: pathlib2 (!=2.3.1)
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58 Requires-Dist: subprocess32 (>=3.5.0) ; os.name=="posix" and python_version<"3.5"
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59 Requires-Dist: typing (>=3.5.3) ; python_version<"3.6"
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60 Provides-Extra: deps
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61 Requires-Dist: galaxy-tool-util ; extra == 'deps'
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62 Provides-Extra: docs
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63 Requires-Dist: sphinx (>=2.2) ; extra == 'docs'
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64 Requires-Dist: sphinx-rtd-theme ; extra == 'docs'
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65
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66 ==================================================================
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67 Common Workflow Language tool description reference implementation
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68 ==================================================================
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69
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70 CWL conformance tests: |Conformance Status| |Linux Status| |Windows Status| |Coverage Status| |Downloads|
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71
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72 |CommandLineTool Support| |DockerRequirement Support| |EnvVarRequirement Support| |ExpressionTool Support|
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73 |InitialWorkDirRequirement Support| |InlineJavascriptRequirement Support| |MultipleInputRequirement Support| |Core Support|
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74 |ResourceRequirement Support| |ScatterRequirement Support| |SchemaDefRequirement Support| |ShellCommandequirement Support|
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75 |StepInputRequirement Support| |SubWorkflowRequirement Support| |Workflow Support|
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76
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77 .. |Conformance Status| image:: https://ci.commonwl.org/buildStatus/icon?job=cwltool-conformance
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78 :target: https://ci.commonwl.org/job/cwltool-conformance/
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79
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80 .. |Linux Status| image:: https://img.shields.io/travis/common-workflow-language/cwltool/master.svg?label=Linux%20builds
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81 :target: https://travis-ci.org/common-workflow-language/cwltool
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82
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83 .. |Windows Status| image:: https://img.shields.io/appveyor/ci/mr-c/cwltool/master.svg?label=Windows%20builds
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84 :target: https://ci.appveyor.com/project/mr-c/cwltool
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85
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86 .. |Coverage Status| image:: https://img.shields.io/codecov/c/github/common-workflow-language/cwltool.svg
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87 :target: https://codecov.io/gh/common-workflow-language/cwltool
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88
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89 .. |Downloads| image:: https://pepy.tech/badge/cwltool/month
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90 :target: https://pepy.tech/project/cwltool
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91
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92 .. |CommandLineTool Support| image:: https://flat.badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/command_line_tool.json
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93 :target: https://ci.commonwl.org/job/cwltool-conformance/
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94
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95 .. |DockerRequirement Support| image:: https://flat.badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/docker.json
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96 :target: https://ci.commonwl.org/job/cwltool-conformance/
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97
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98 .. |EnvVarRequirement Support| image:: https://flat.badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/env_var.json
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99 :target: https://ci.commonwl.org/job/cwltool-conformance/
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100
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101 .. |ExpressionTool Support| image:: https://flat.badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/expression_tool.json
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102 :target: https://ci.commonwl.org/job/cwltool-conformance/
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103
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104 .. |InitialWorkDirRequirement Support| image:: https://flat.badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/initial_work_dir.json
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105 :target: https://ci.commonwl.org/job/cwltool-conformance/
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106
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107 .. |InlineJavascriptRequirement Support| image:: https://flat.badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/inline_javascript.json
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108 :target: https://ci.commonwl.org/job/cwltool-conformance/
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109
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110 .. |MultipleInputRequirement Support| image:: https://flat.badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/multiple_input.json
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111 :target: https://ci.commonwl.org/job/cwltool-conformance/
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112
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113 .. |Core Support| image:: https://flat.badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/required.json
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114 :target: https://ci.commonwl.org/job/cwltool-conformance/
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115
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116 .. |ResourceRequirement Support| image:: https://flat.badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/resource.json
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117 :target: https://ci.commonwl.org/job/cwltool-conformance/
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118
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119 .. |ScatterRequirement Support| image:: https://flat.badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/scatter.json
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120 :target: https://ci.commonwl.org/job/cwltool-conformance/
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121
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122 .. |SchemaDefRequirement Support| image:: https://flat.badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/schema_def.json
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123 :target: https://ci.commonwl.org/job/cwltool-conformance/
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124
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125 .. |ShellCommandequirement Support| image:: https://flat.badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/shell_command.json
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126 :target: https://ci.commonwl.org/job/cwltool-conformance/
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127
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128 .. |StepInputRequirement Support| image:: https://flat.badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/step_input.json
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129 :target: https://ci.commonwl.org/job/cwltool-conformance/
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130
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131 .. |SubWorkflowRequirement Support| image:: https://flat.badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/subworkflow.json
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132 :target: https://ci.commonwl.org/job/cwltool-conformance/
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133
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134 .. |Workflow Support| image:: https://flat.badgen.net/https/raw.githubusercontent.com/common-workflow-language/conformance/master/cwltool/cwl_v1.0/cwltool_latest/workflow.json
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135 :target: https://ci.commonwl.org/job/cwltool-conformance/
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136
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137
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138 This is the reference implementation of the Common Workflow Language. It is
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139 intended to be feature complete and provide comprehensive validation of CWL
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140 files as well as provide other tools related to working with CWL.
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141
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142 This is written and tested for
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143 `Python <https://www.python.org/>`_ ``2.7 and 3.x {x = 5, 6, 7, 8}``
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144
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145 The reference implementation consists of two packages. The ``cwltool`` package
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146 is the primary Python module containing the reference implementation in the
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147 ``cwltool`` module and console executable by the same name.
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148
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149 The ``cwlref-runner`` package is optional and provides an additional entry point
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150 under the alias ``cwl-runner``, which is the implementation-agnostic name for the
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151 default CWL interpreter installed on a host.
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152
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153 Install
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154 -------
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155
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156 Your operating system may offer cwltool directly. For [Debian](https://tracker.debian.org/pkg/cwltool "Debian cwltool package tracker") or [Ubuntu](https://launchpad.net/ubuntu/+source/cwltool "Ubuntu Launchpad overview for cwltool") try
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157
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158 .. code:: bash
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159
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160 apt-get install cwltool
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161
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162 Otherwise, to
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163 avoid conflicting versions of the same library,
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164 it is recommended to do the following:
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165
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166 .. code:: bash
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167
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168 virtualenv -p python2 venv # Create a virtual environment, can use `python3` as well
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169 source venv/bin/activate # Activate environment before installing `cwltool`
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170
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171 Installing the official package from PyPi (will install "cwltool" package as
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172 well)
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173
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174 .. code:: bash
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175
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176 pip install cwlref-runner
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177
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178 If installing alongside another CWL implementation then
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179
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180 .. code:: bash
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181
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182 pip install cwltool
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183
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184 Or you can install from source:
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185
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186 .. code:: bash
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187
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188 git clone https://github.com/common-workflow-language/cwltool.git # clone cwltool repo
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189 cd cwltool # Switch to source directory
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190 pip install . # Install `cwltool` from source
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191 cwltool --version # Check if the installation works correctly
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192
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193 Remember, if co-installing multiple CWL implementations then you need to
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194 maintain which implementation ``cwl-runner`` points to via a symbolic file
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195 system link or `another facility <https://wiki.debian.org/DebianAlternatives>`_.
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196
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197 =====
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198 Usage
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199 =====
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200
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201 Run on the command line
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202 -----------------------
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203
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204 Simple command::
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205
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206 cwl-runner [tool-or-workflow-description] [input-job-settings]
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207
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208 Or if you have multiple CWL implementations installed and you want to override
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209 the default cwl-runner use::
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210
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211 cwltool [tool-or-workflow-description] [input-job-settings]
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212
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213 You can set cwltool options in the environment with CWLTOOL_OPTIONS,
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214 these will be inserted at the beginning of the command line::
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215
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216 export CWLTOOL_OPTIONS="--debug"
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217
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218 Use with boot2docker
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219 --------------------
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220 boot2docker runs Docker inside a virtual machine and it only mounts ``Users``
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221 on it. The default behavior of CWL is to create temporary directories under e.g.
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222 ``/Var`` which is not accessible to Docker containers.
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223
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224 To run CWL successfully with boot2docker you need to set the ``--tmpdir-prefix``
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225 and ``--tmp-outdir-prefix`` to somewhere under ``/Users``::
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226
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227 $ cwl-runner --tmp-outdir-prefix=/Users/username/project --tmpdir-prefix=/Users/username/project wc-tool.cwl wc-job.json
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228
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229 Using user-space replacements for Docker
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230 ----------------------------------------
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231
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232 Some shared computing environments don't support Docker software containers for technical or policy reasons.
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233 As a work around, the CWL reference runner supports using alternative ``docker`` implementations on Linux
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234 with the ``--user-space-docker-cmd`` option.
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235
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236 One such "user space" friendly docker replacement is ``udocker`` https://github.com/indigo-dc/udocker and another
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237 is ``dx-docker`` https://wiki.dnanexus.com/Developer-Tutorials/Using-Docker-Images
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238
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239 udocker installation: https://github.com/indigo-dc/udocker/blob/master/doc/installation_manual.md#22-install-from-indigo-datacloud-repositories
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240
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241 dx-docker installation: start with the DNAnexus toolkit (see https://wiki.dnanexus.com/Downloads for instructions).
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242
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243 Run `cwltool` just as you normally would, but with the new option, e.g. from the conformance tests:
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244
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245 .. code:: bash
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246
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247 cwltool --user-space-docker-cmd=udocker https://raw.githubusercontent.com/common-workflow-language/common-workflow-language/master/v1.0/v1.0/test-cwl-out2.cwl https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/v1.0/empty.json
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248
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249 or
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250
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251 .. code:: bash
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252
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253 cwltool --user-space-docker-cmd=dx-docker https://raw.githubusercontent.com/common-workflow-language/common-workflow-language/master/v1.0/v1.0/test-cwl-out2.cwl https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/v1.0/empty.json
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254
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255 ``cwltool`` can use `Singularity <http://singularity.lbl.gov/>`_ version 2.6.1
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256 or later as a Docker container runtime.
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257 ``cwltool`` with Singularity will run software containers specified in
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258 ``DockerRequirement`` and therefore works with Docker images only, native
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259 Singularity images are not supported. To use Singularity as the Docker container
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260 runtime, provide ``--singularity`` command line option to ``cwltool``.
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261 With Singularity, ``cwltool`` can pass all CWL v1.0 conformance tests, except
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262 those involving Docker container ENTRYPOINTs.
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263
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264
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265 .. code:: bash
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266
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267 cwltool --singularity https://raw.githubusercontent.com/common-workflow-language/common-workflow-language/master/v1.0/v1.0/v1.0/cat3-tool-mediumcut.cwl https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/v1.0/cat-job.json
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268
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269 Running a tool or workflow from remote or local locations
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270 ---------------------------------------------------------
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271
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272 ``cwltool`` can run tool and workflow descriptions on both local and remote
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273 systems via its support for HTTP[S] URLs.
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274
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275 Input job files and Workflow steps (via the `run` directive) can reference CWL
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276 documents using absolute or relative local filesytem paths. If a relative path
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277 is referenced and that document isn't found in the current directory then the
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278 following locations will be searched:
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279 http://www.commonwl.org/v1.0/CommandLineTool.html#Discovering_CWL_documents_on_a_local_filesystem
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280
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281 You can also use `cwldep <https://github.com/common-workflow-language/cwldep>`
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282 to manage dependencies on external tools and workflows.
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283
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284 Overriding workflow requirements at load time
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285 ---------------------------------------------
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286
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287 Sometimes a workflow needs additional requirements to run in a particular
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288 environment or with a particular dataset. To avoid the need to modify the
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289 underlying workflow, cwltool supports requirement "overrides".
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290
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291 The format of the "overrides" object is a mapping of item identifier (workflow,
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292 workflow step, or command line tool) to the process requirements that should be applied.
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293
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294 .. code:: yaml
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295
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296 cwltool:overrides:
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297 echo.cwl:
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298 requirements:
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299 EnvVarRequirement:
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300 envDef:
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301 MESSAGE: override_value
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302
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303 Overrides can be specified either on the command line, or as part of the job
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304 input document. Workflow steps are identified using the name of the workflow
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305 file followed by the step name as a document fragment identifier "#id".
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306 Override identifiers are relative to the toplevel workflow document.
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307
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308 .. code:: bash
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309
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310 cwltool --overrides overrides.yml my-tool.cwl my-job.yml
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311
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312 .. code:: yaml
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313
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314 input_parameter1: value1
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315 input_parameter2: value2
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316 cwltool:overrides:
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317 workflow.cwl#step1:
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318 requirements:
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319 EnvVarRequirement:
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320 envDef:
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321 MESSAGE: override_value
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322
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323 .. code:: bash
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324
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325 cwltool my-tool.cwl my-job-with-overrides.yml
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326
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327
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328 Combining parts of a workflow into a single document
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329 ----------------------------------------------------
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330
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331 Use ``--pack`` to combine a workflow made up of multiple files into a
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332 single compound document. This operation takes all the CWL files
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333 referenced by a workflow and builds a new CWL document with all
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334 Process objects (CommandLineTool and Workflow) in a list in the
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335 ``$graph`` field. Cross references (such as ``run:`` and ``source:``
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336 fields) are updated to internal references within the new packed
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337 document. The top level workflow is named ``#main``.
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338
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339 .. code:: bash
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340
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341 cwltool --pack my-wf.cwl > my-packed-wf.cwl
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342
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343
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344 Running only part of a workflow
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345 -------------------------------
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346
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347 You can run a partial workflow with the ``--target`` (``-t``) option. This
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348 takes the name of an output parameter, workflow step, or input
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349 parameter in the top level workflow. You may provide multiple
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350 targets.
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351
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352 .. code:: bash
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353
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354 cwltool --target step3 my-wf.cwl
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355
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356 If a target is an output parameter, it will only run only the steps
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357 that contribute to that output. If a target is a workflow step, it
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358 will run the workflow starting from that step. If a target is an
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359 input parameter, it will only run only the steps that are connected to
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360 that input.
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361
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362 Use ``--print-targets`` to get a listing of the targets of a workflow.
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363 To see exactly which steps will run, use ``--print-subgraph`` with
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364 ``--target`` to get a printout of the workflow subgraph for the
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365 selected targets.
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366
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367 .. code:: bash
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368
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369 cwltool --print-targets my-wf.cwl
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370
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371 cwltool --target step3 --print-subgraph my-wf.cwl > my-wf-starting-from-step3.cwl
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372
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373
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374 Visualizing a CWL document
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375 --------------------------
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376
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377 The ``--print-dot`` option will print a file suitable for Graphviz ``dot`` program. Here is a bash onliner to generate a Scalable Vector Graphic (SVG) file:
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378
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379 .. code:: bash
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380
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381 cwltool --print-dot my-wf.cwl | dot -Tsvg > my-wf.svg
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382
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383 Modeling a CWL document as RDF
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384 ------------------------------
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385
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386 CWL documents can be expressed as RDF triple graphs.
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387
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388 .. code:: bash
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389
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390 cwltool --print-rdf --rdf-serializer=turtle mywf.cwl
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391
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392
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393 Leveraging SoftwareRequirements (Beta)
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394 --------------------------------------
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395
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396 CWL tools may be decorated with ``SoftwareRequirement`` hints that cwltool
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397 may in turn use to resolve to packages in various package managers or
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398 dependency management systems such as `Environment Modules
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399 <http://modules.sourceforge.net/>`__.
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400
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401 Utilizing ``SoftwareRequirement`` hints using cwltool requires an optional
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402 dependency, for this reason be sure to use specify the ``deps`` modifier when
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403 installing cwltool. For instance::
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404
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405 $ pip install 'cwltool[deps]'
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406
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407 Installing cwltool in this fashion enables several new command line options.
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408 The most general of these options is ``--beta-dependency-resolvers-configuration``.
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409 This option allows one to specify a dependency resolver's configuration file.
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410 This file may be specified as either XML or YAML and very simply describes various
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411 plugins to enable to "resolve" ``SoftwareRequirement`` dependencies.
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412
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413 To discuss some of these plugins and how to configure them, first consider the
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414 following ``hint`` definition for an example CWL tool.
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415
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416 .. code:: yaml
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417
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418 SoftwareRequirement:
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419 packages:
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420 - package: seqtk
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421 version:
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422 - r93
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423
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424 Now imagine deploying cwltool on a cluster with Software Modules installed
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425 and that a ``seqtk`` module is available at version ``r93``. This means cluster
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426 users likely won't have the binary ``seqtk`` on their ``PATH`` by default, but after
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427 sourcing this module with the command ``modulecmd sh load seqtk/r93`` ``seqtk`` is
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428 available on the ``PATH``. A simple dependency resolvers configuration file, called
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429 ``dependency-resolvers-conf.yml`` for instance, that would enable cwltool to source
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430 the correct module environment before executing the above tool would simply be:
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431
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432 .. code:: yaml
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433
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434 - type: modules
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435
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436 The outer list indicates that one plugin is being enabled, the plugin parameters are
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437 defined as a dictionary for this one list item. There is only one required parameter
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438 for the plugin above, this is ``type`` and defines the plugin type. This parameter
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439 is required for all plugins. The available plugins and the parameters
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440 available for each are documented (incompletely) `here
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441 <https://docs.galaxyproject.org/en/latest/admin/dependency_resolvers.html>`__.
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442 Unfortunately, this documentation is in the context of Galaxy tool
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443 ``requirement`` s instead of CWL ``SoftwareRequirement`` s, but the concepts map fairly directly.
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444
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445 cwltool is distributed with an example of such seqtk tool and sample corresponding
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446 job. It could executed from the cwltool root using a dependency resolvers
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447 configuration file such as the above one using the command::
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448
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449 cwltool --beta-dependency-resolvers-configuration /path/to/dependency-resolvers-conf.yml \
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450 tests/seqtk_seq.cwl \
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451 tests/seqtk_seq_job.json
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452
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453 This example demonstrates both that cwltool can leverage
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454 existing software installations and also handle workflows with dependencies
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455 on different versions of the same software and libraries. However the above
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456 example does require an existing module setup so it is impossible to test this example
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457 "out of the box" with cwltool. For a more isolated test that demonstrates all
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458 the same concepts - the resolver plugin type ``galaxy_packages`` can be used.
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459
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460 "Galaxy packages" are a lighter weight alternative to Environment Modules that are
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461 really just defined by a way to lay out directories into packages and versions
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462 to find little scripts that are sourced to modify the environment. They have
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463 been used for years in Galaxy community to adapt Galaxy tools to cluster
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464 environments but require neither knowledge of Galaxy nor any special tools to
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465 setup. These should work just fine for CWL tools.
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466
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467 The cwltool source code repository's test directory is setup with a very simple
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468 directory that defines a set of "Galaxy packages" (but really just defines one
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469 package named ``random-lines``). The directory layout is simply::
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470
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471 tests/test_deps_env/
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472 random-lines/
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473 1.0/
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474 env.sh
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475
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476 If the ``galaxy_packages`` plugin is enabled and pointed at the
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477 ``tests/test_deps_env`` directory in cwltool's root and a ``SoftwareRequirement``
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478 such as the following is encountered.
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479
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480 .. code:: yaml
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481
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482 hints:
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483 SoftwareRequirement:
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484 packages:
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485 - package: 'random-lines'
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486 version:
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487 - '1.0'
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488
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489 Then cwltool will simply find that ``env.sh`` file and source it before executing
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490 the corresponding tool. That ``env.sh`` script is only responsible for modifying
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491 the job's ``PATH`` to add the required binaries.
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492
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493 This is a full example that works since resolving "Galaxy packages" has no
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494 external requirements. Try it out by executing the following command from cwltool's
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495 root directory::
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496
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497 cwltool --beta-dependency-resolvers-configuration tests/test_deps_env_resolvers_conf.yml \
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498 tests/random_lines.cwl \
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499 tests/random_lines_job.json
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500
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501 The resolvers configuration file in the above example was simply:
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502
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503 .. code:: yaml
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504
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505 - type: galaxy_packages
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506 base_path: ./tests/test_deps_env
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507
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508 It is possible that the ``SoftwareRequirement`` s in a given CWL tool will not
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509 match the module names for a given cluster. Such requirements can be re-mapped
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510 to specific deployed packages and/or versions using another file specified using
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511 the resolver plugin parameter `mapping_files`. We will
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512 demonstrate this using `galaxy_packages` but the concepts apply equally well
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513 to Environment Modules or Conda packages (described below) for instance.
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514
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515 So consider the resolvers configuration file
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516 (`tests/test_deps_env_resolvers_conf_rewrite.yml`):
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517
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518 .. code:: yaml
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519
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520 - type: galaxy_packages
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521 base_path: ./tests/test_deps_env
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522 mapping_files: ./tests/test_deps_mapping.yml
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523
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524 And the corresponding mapping configuraiton file (`tests/test_deps_mapping.yml`):
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525
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526 .. code:: yaml
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diff changeset
527
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528 - from:
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529 name: randomLines
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530 version: 1.0.0-rc1
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diff changeset
531 to:
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532 name: random-lines
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533 version: '1.0'
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diff changeset
534
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diff changeset
535 This is saying if cwltool encounters a requirement of ``randomLines`` at version
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
536 ``1.0.0-rc1`` in a tool, to rewrite to our specific plugin as ``random-lines`` at
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
537 version ``1.0``. cwltool has such a test tool called ``random_lines_mapping.cwl``
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diff changeset
538 that contains such a source ``SoftwareRequirement``. To try out this example with
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
539 mapping, execute the following command from the cwltool root directory::
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parents:
diff changeset
540
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541 cwltool --beta-dependency-resolvers-configuration tests/test_deps_env_resolvers_conf_rewrite.yml \
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
542 tests/random_lines_mapping.cwl \
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diff changeset
543 tests/random_lines_job.json
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diff changeset
544
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diff changeset
545 The previous examples demonstrated leveraging existing infrastructure to
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diff changeset
546 provide requirements for CWL tools. If instead a real package manager is used
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diff changeset
547 cwltool has the opportunity to install requirements as needed. While initial
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diff changeset
548 support for Homebrew/Linuxbrew plugins is available, the most developed such
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diff changeset
549 plugin is for the `Conda <https://conda.io/docs/#>`__ package manager. Conda has the nice properties
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diff changeset
550 of allowing multiple versions of a package to be installed simultaneously,
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diff changeset
551 not requiring evaluated permissions to install Conda itself or packages using
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parents:
diff changeset
552 Conda, and being cross platform. For these reasons, cwltool may run as a normal
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553 user, install its own Conda environment and manage multiple versions of Conda packages
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diff changeset
554 on both Linux and Mac OS X.
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diff changeset
555
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556 The Conda plugin can be endlessly configured, but a sensible set of defaults
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parents:
diff changeset
557 that has proven a powerful stack for dependency management within the Galaxy tool
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558 development ecosystem can be enabled by simply passing cwltool the
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diff changeset
559 ``--beta-conda-dependencies`` flag.
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diff changeset
560
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561 With this we can use the seqtk example above without Docker and without
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diff changeset
562 any externally managed services - cwltool should install everything it needs
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563 and create an environment for the tool. Try it out with the follwing command::
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diff changeset
564
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diff changeset
565 cwltool --beta-conda-dependencies tests/seqtk_seq.cwl tests/seqtk_seq_job.json
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diff changeset
566
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diff changeset
567 The CWL specification allows URIs to be attached to ``SoftwareRequirement`` s
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parents:
diff changeset
568 that allow disambiguation of package names. If the mapping files described above
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569 allow deployers to adapt tools to their infrastructure, this mechanism allows
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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570 tools to adapt their requirements to multiple package managers. To demonstrate
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diff changeset
571 this within the context of the seqtk, we can simply break the package name we
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parents:
diff changeset
572 use and then specify a specific Conda package as follows:
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parents:
diff changeset
573
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
574 .. code:: yaml
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diff changeset
575
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
576 hints:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
577 SoftwareRequirement:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
578 packages:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
579 - package: seqtk_seq
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parents:
diff changeset
580 version:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
581 - '1.2'
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parents:
diff changeset
582 specs:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
583 - https://anaconda.org/bioconda/seqtk
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
584 - https://packages.debian.org/sid/seqtk
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parents:
diff changeset
585
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parents:
diff changeset
586 The example can be executed using the command::
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587
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588 cwltool --beta-conda-dependencies tests/seqtk_seq_wrong_name.cwl tests/seqtk_seq_job.json
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diff changeset
589
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590 The plugin framework for managing resolution of these software requirements
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591 as maintained as part of `galaxy-tool-util <https://github.com/galaxyproject/galaxy/tree/dev/packages/tool_util>`__ - a small,
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parents:
diff changeset
592 portable subset of the Galaxy project. More information on configuration and implementation can be found
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parents:
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593 at the following links:
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594
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
595 - `Dependency Resolvers in Galaxy <https://docs.galaxyproject.org/en/latest/admin/dependency_resolvers.html>`__
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parents:
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596 - `Conda for [Galaxy] Tool Dependencies <https://docs.galaxyproject.org/en/latest/admin/conda_faq.html>`__
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597 - `Mapping Files - Implementation <https://github.com/galaxyproject/galaxy/commit/495802d229967771df5b64a2f79b88a0eaf00edb>`__
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598 - `Specifications - Implementation <https://github.com/galaxyproject/galaxy/commit/81d71d2e740ee07754785306e4448f8425f890bc>`__
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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599 - `Initial cwltool Integration Pull Request <https://github.com/common-workflow-language/cwltool/pull/214>`__
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diff changeset
600
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parents:
diff changeset
601 Use with GA4GH Tool Registry API
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602 --------------------------------
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603
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diff changeset
604 Cwltool can launch tools directly from `GA4GH Tool Registry API`_ endpoints.
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parents:
diff changeset
605
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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606 By default, cwltool searches https://dockstore.org/ . Use ``--add-tool-registry`` to add other registries to the search path.
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parents:
diff changeset
607
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
608 For example ::
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
609
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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610 cwltool quay.io/collaboratory/dockstore-tool-bamstats:develop test.json
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611
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612 and (defaults to latest when a version is not specified) ::
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613
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614 cwltool quay.io/collaboratory/dockstore-tool-bamstats test.json
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615
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616 For this example, grab the test.json (and input file) from https://github.com/CancerCollaboratory/dockstore-tool-bamstats ::
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617
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618 wget https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fbriandoconnor%2Fdockstore-tool-bamstats/versions/develop/PLAIN-CWL/descriptor/test.json
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619 wget https://github.com/CancerCollaboratory/dockstore-tool-bamstats/raw/develop/rna.SRR948778.bam
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620
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621
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622 .. _`GA4GH Tool Registry API`: https://github.com/ga4gh/tool-registry-schemas
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623
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624 ===========
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625 Development
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626 ===========
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627
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628 Running tests locally
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629 ---------------------
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630
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631 - Running basic tests ``(/tests)``:
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632
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633 To run the basic tests after installing `cwltool` execute the following:
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634
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635 .. code:: bash
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636
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637 pip install -rtest-requirements.txt
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638 py.test --ignore cwltool/schemas/ --pyarg cwltool
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639
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640 To run various tests in all supported Python environments we use `tox <https://github.com/common-workflow-language/cwltool/tree/master/tox.ini>`_. To run the test suite in all supported Python environments
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641 first downloading the complete code repository (see the ``git clone`` instructions above) and then run
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642 the following in the terminal:
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643 ``pip install tox; tox``
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644
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645 List of all environment can be seen using:
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646 ``tox --listenvs``
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647 and running a specfic test env using:
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648 ``tox -e <env name>``
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649 and additionally run a specific test using this format:
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650 ``tox -e py36-unit -- tests/test_examples.py::TestParamMatching``
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651
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652 - Running the entire suite of CWL conformance tests:
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653
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654 The GitHub repository for the CWL specifications contains a script that tests a CWL
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655 implementation against a wide array of valid CWL files using the `cwltest <https://github.com/common-workflow-language/cwltest>`_
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656 program
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657
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658 Instructions for running these tests can be found in the Common Workflow Language Specification repository at https://github.com/common-workflow-language/common-workflow-language/blob/master/CONFORMANCE_TESTS.md
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659
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660 Import as a module
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661 ------------------
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662
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663 Add
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664
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665 .. code:: python
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666
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667 import cwltool
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668
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669 to your script.
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670
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671 The easiest way to use cwltool to run a tool or workflow from Python is to use a Factory
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672
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673 .. code:: python
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674
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675 import cwltool.factory
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676 fac = cwltool.factory.Factory()
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677
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678 echo = fac.make("echo.cwl")
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679 result = echo(inp="foo")
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680
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681 # result["out"] == "foo"
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682
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683
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684 CWL Tool Control Flow
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685 ---------------------
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686
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687 Technical outline of how cwltool works internally, for maintainers.
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688
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689 #. Use CWL ``load_tool()`` to load document.
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690
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691 #. Fetches the document from file or URL
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692 #. Applies preprocessing (syntax/identifier expansion and normalization)
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693 #. Validates the document based on cwlVersion
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694 #. If necessary, updates the document to latest spec
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695 #. Constructs a Process object using ``make_tool()``` callback. This yields a
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696 CommandLineTool, Workflow, or ExpressionTool. For workflows, this
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697 recursively constructs each workflow step.
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698 #. To construct custom types for CommandLineTool, Workflow, or
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699 ExpressionTool, provide a custom ``make_tool()``
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700
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701 #. Iterate on the ``job()`` method of the Process object to get back runnable jobs.
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702
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703 #. ``job()`` is a generator method (uses the Python iterator protocol)
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704 #. Each time the ``job()`` method is invoked in an iteration, it returns one
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705 of: a runnable item (an object with a ``run()`` method), ``None`` (indicating
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706 there is currently no work ready to run) or end of iteration (indicating
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707 the process is complete.)
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708 #. Invoke the runnable item by calling ``run()``. This runs the tool and gets output.
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709 #. Output of a process is reported by an output callback.
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710 #. ``job()`` may be iterated over multiple times. It will yield all the work
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711 that is currently ready to run and then yield None.
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712
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713 #. ``Workflow`` objects create a corresponding ``WorkflowJob`` and ``WorkflowJobStep`` objects to hold the workflow state for the duration of the job invocation.
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714
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715 #. The WorkflowJob iterates over each WorkflowJobStep and determines if the
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716 inputs the step are ready.
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717 #. When a step is ready, it constructs an input object for that step and
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718 iterates on the ``job()`` method of the workflow job step.
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719 #. Each runnable item is yielded back up to top level run loop
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720 #. When a step job completes and receives an output callback, the
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721 job outputs are assigned to the output of the workflow step.
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722 #. When all steps are complete, the intermediate files are moved to a final
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723 workflow output, intermediate directories are deleted, and the output
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724 callback for the workflow is called.
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725
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726 #. ``CommandLineTool`` job() objects yield a single runnable object.
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727
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728 #. The CommandLineTool ``job()`` method calls ``make_job_runner()`` to create a
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729 ``CommandLineJob`` object
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730 #. The job method configures the CommandLineJob object by setting public
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731 attributes
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732 #. The job method iterates over file and directories inputs to the
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733 CommandLineTool and creates a "path map".
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734 #. Files are mapped from their "resolved" location to a "target" path where
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735 they will appear at tool invocation (for example, a location inside a
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736 Docker container.) The target paths are used on the command line.
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737 #. Files are staged to targets paths using either Docker volume binds (when
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738 using containers) or symlinks (if not). This staging step enables files
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739 to be logically rearranged or renamed independent of their source layout.
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740 #. The ``run()`` method of CommandLineJob executes the command line tool or
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741 Docker container, waits for it to complete, collects output, and makes
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742 the output callback.
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743
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744
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745 Extension points
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746 ----------------
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747
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748 The following functions can be passed to main() to override or augment
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diff changeset
749 the listed behaviors.
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750
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751 executor
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752 ::
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753
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754 executor(tool, job_order_object, runtimeContext, logger)
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755 (Process, Dict[Text, Any], RuntimeContext) -> Tuple[Dict[Text, Any], Text]
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756
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757 An implementation of the toplevel workflow execution loop, should
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758 synchronously run a process object to completion and return the
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759 output object.
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760
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761 versionfunc
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762 ::
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763
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764 ()
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765 () -> Text
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766
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767 Return version string.
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768
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769 logger_handler
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770 ::
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771
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772 logger_handler
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773 logging.Handler
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774
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775 Handler object for logging.
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776
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777 The following functions can be set in LoadingContext to override or
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778 augment the listed behaviors.
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779
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780 fetcher_constructor
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781 ::
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782
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783 fetcher_constructor(cache, session)
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784 (Dict[unicode, unicode], requests.sessions.Session) -> Fetcher
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785
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786 Construct a Fetcher object with the supplied cache and HTTP session.
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diff changeset
787
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788 resolver
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789 ::
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790
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791 resolver(document_loader, document)
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diff changeset
792 (Loader, Union[Text, dict[Text, Any]]) -> Text
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793
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794 Resolve a relative document identifier to an absolute one which can be fetched.
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795
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796 The following functions can be set in RuntimeContext to override or
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797 augment the listed behaviors.
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diff changeset
798
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diff changeset
799 construct_tool_object
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800 ::
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801
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802 construct_tool_object(toolpath_object, loadingContext)
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803 (MutableMapping[Text, Any], LoadingContext) -> Process
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diff changeset
804
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diff changeset
805 Hook to construct a Process object (eg CommandLineTool) object from a document.
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diff changeset
806
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diff changeset
807 select_resources
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808 ::
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809
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diff changeset
810 selectResources(request)
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811 (Dict[str, int], RuntimeContext) -> Dict[Text, int]
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812
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diff changeset
813 Take a resource request and turn it into a concrete resource assignment.
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diff changeset
814
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diff changeset
815 make_fs_access
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816 ::
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817
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818 make_fs_access(basedir)
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diff changeset
819 (Text) -> StdFsAccess
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diff changeset
820
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821 Return a file system access object.
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822
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823 In addition, when providing custom subclasses of Process objects, you can override the following methods:
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824
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825 CommandLineTool.make_job_runner
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826 ::
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827
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828 make_job_runner(RuntimeContext)
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diff changeset
829 (RuntimeContext) -> Type[JobBase]
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830
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831 Create and return a job runner object (this implements concrete execution of a command line tool).
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832
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833 Workflow.make_workflow_step
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834 ::
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835
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836 make_workflow_step(toolpath_object, pos, loadingContext, parentworkflowProv)
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837 (Dict[Text, Any], int, LoadingContext, Optional[ProvenanceProfile]) -> WorkflowStep
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838
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839 Create and return a workflow step object.
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840
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841