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        "description": "# Common Workflow Language dependency manager\n\nThis tool helps you to import tools and workflows from other sources for use in your own workflow.\n\n# Setup\nIt is highly recommended to setup virtual environment before installing `cwldep`:\n\n```\nvirtualenv -p python2 venv   # Create a virtual environment, can use `python3` as well\nsource venv/bin/activate     # Activate environment before installing `cwldep`\n```\n\nInstall from source:\n```\ngit clone https://github.com/common-workflow-language/cwldep.git # clone cwldep repo\ncd cwldep         # Switch to source directory\npython setup.py install\ncwldep -h  # Check if the installation works correctly\n```\n\n# Adding file dependencies\n\n```\ncwldep add myfile.cwl https://raw.githubusercontent.com/common-workflow-language/workflows/master/tools/samtools-faidx.cwl\n```\n\nThis will download the CWL file *and its dependencies* to `raw.githubusercontent.com/common-workflow-language/workflows/master/tools`\n\nInclude it in your workflow as a relative file reference:\n\n```\nsteps:\n  step1:\n    in: ...\n    out: ...\n    run: raw.githubusercontent.com/common-workflow-language/workflows/master/tools/samtools-faidx.cwl\n```\n\n# Changing the install target\n\n```\ncwldep add --install-to samtools myfile.cwl https://raw.githubusercontent.com/common-workflow-language/workflows/master/tools/samtools-faidx.cwl\n```\n\n# Using archives\n\nYou can also import archives (.tar.gz, .tar.bz2, and .zip):\n\n```\ncwldep add myfile.cwl https://github.com/common-workflow-language/workflows/archive/draft2.tar.gz\n```\n\nThis will download and extract to the local directory `github.com/common-workflow-language/workflows/archive`\n\n# Using git upstream\n\nYou can also import git repositories:\n\n```\ncwldep add myfile.cwl https://github.com/common-workflow-language/workflows\n```\n\nThis will clone into the local directory `github.com/common-workflow-language/workflows`\n\n```\ncwldep add --set-version=draft-2 myfile.cwl https://github.com/common-workflow-language/workflows\n```\n\n# Installing dependencies\n\nThis will install any dependencies listed in `myfile.cwl`\n\n```\ncwldep install myfile.cwl\n```\n\n# Checking if upstream dependencies have changed\n\nThis will report if the upstream dependencies listed in `myfile.cwl` have changed\n\n```\ncwldep check myfile.cwl\n```\n\n# Updating dependencies\n\nThis will install updated dependencies:\n\n```\ncwldep update myfile.cwl\n```\n\n# Deleting unreferenced dependencies\n\nThis will delete any dependencies listed in the \".dep.lock\" file that are not referenced by `myfile.cwl`.\n\n```\ncwldep clean myfile.cwl\n```\n\n\n",
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