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        "author": "Common workflow language working group",
        "author_email": "common-workflow-language@googlegroups.com",
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        "description": "==================================================================\nCommon workflow language tool description reference implementation\n==================================================================\n\nCWL Conformance test: |Build Status|\n\nThis is the reference implementation of the Common Workflow Language.  It is\nintended to be feature complete and provide comprehensive validation of CWL\nfiles as well as provide other tools related to working with CWL.\n\nThis is written and tested for Python 2.7.\n\nThe reference implementation consists of two packages.  The \"cwltool\" package\nis the primary Python module containing the reference implementation in the\n\"cwltool\" module and console executable by the same name.\n\nThe \"cwlref-runner\" package is optional and provides an additional entry point\nunder the alias \"cwl-runner\", which is the implementation-agnostic name for the\ndefault CWL interpreter installed on a host.\n\nInstall\n-------\n\nInstalling the official package from PyPi (will install \"cwltool\" package as\nwell)::\n\n  pip install cwlref-runner\n\nIf installling alongside another CWL implementation then::\n\n  pip instal cwltool\n\nTo install from source::\n\n  git clone https://github.com/common-workflow-language/cwltool.git\n  cd cwltool && python setup.py install\n  cd cwlref-runner && python setup.py install  # co-installing? skip this\n\nRemember, if co-installing multiple CWL implementations then you need to\nmaintain which implementation ``cwl-runner`` points to via a symbolic file\nsystem link or [another facility](https://wiki.debian.org/DebianAlternatives).\n\nRun on the command line\n-----------------------\n\nSimple command::\n\n  cwl-runner [tool-or-workflow-description] [input-job-settings]\n\nOr if you have multiple CWL implementations installed and you want to override\nthe default cwl-runner use::\n\n  cwltool [tool-or-workflow-description] [input-job-settings]\n\nImport as a module\n----------------\n\nAdd::\n\n  import cwltool\n\nto your script.\n\nUse with boot2docker\n--------------------\nboot2docker is running docker inside a virtual machine and it only mounts ``Users``\non it. The default behavoir of CWL is to create temporary directories under e.g.\n``/Var`` which is not accessible to Docker containers.\n\nTo run CWL successfully with boot2docker you need to set the ``--tmpdir-prefix``\nand ``--tmp-outdir-prefix`` to somewhere under ``/Users``::\n\n    $ cwl-runner --tmp-outdir-prefix=/Users/username/project --tmpdir-prefix=/Users/username/project wc-tool.cwl wc-job.json\n\n.. |Build Status| image:: https://ci.commonwl.org/buildStatus/icon?job=cwltool-conformance\n   :target: https://ci.commonwl.org/job/cwltool-conformance/\n\nTool or workflow loading from remote or local locations\n-------------------------------------------------------\n\n``cwltool`` can run tool and workflow descriptions on both local and remote\nsystems via its support for HTTP[S] URLs.\n\nInput job files and Workflow steps (via the `run` directive) can reference CWL\ndocuments using absolute or relative local filesytem paths. If a relative path\nis referenced and that document isn't found in the current directory then the\nfollowing locations will be searched:\nhttp://www.commonwl.org/v1.0/CommandLineTool.html#Discovering_CWL_documents_on_a_local_filesystem",
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        "license": "Apache 2.0",
        "maintainer": null,
        "maintainer_email": null,
        "name": "cwltool-ucsc",
        "package_url": "https://pypi.org/project/cwltool-ucsc/",
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        "summary": "Common workflow language reference implementation patched for UCSC-CGL",
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