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Showing content from https://github.com/common-workflow-language/cwldep below:

common-workflow-language/cwldep: Common Workflow Language dependency manager

This tool helps you to import tools and workflows from other sources for use in your own workflow.

It is highly recommended to setup virtual environment before installing cwldep:

virtualenv -p python2 venv   # Create a virtual environment, can use `python3` as well
source venv/bin/activate     # Activate environment before installing `cwldep`

Install from PyPi:

Install from source:

git clone https://github.com/common-workflow-language/cwldep.git # clone cwldep repo
cd cwldep         # Switch to source directory
python setup.py install
cwldep -h  # Check if the installation works correctly

cwldep add myfile.cwl https://raw.githubusercontent.com/common-workflow-language/workflows/master/tools/samtools-faidx.cwl

This will download the CWL file and its dependencies to raw.githubusercontent.com/common-workflow-language/workflows/master/tools

Include it in your workflow as a relative file reference:

steps:
  step1:
    in: ...
    out: ...
    run: raw.githubusercontent.com/common-workflow-language/workflows/master/tools/samtools-faidx.cwl

cwldep add --install-to samtools myfile.cwl https://raw.githubusercontent.com/common-workflow-language/workflows/master/tools/samtools-faidx.cwl

You can also import archives (.tar.gz, .tar.bz2, and .zip):

cwldep add myfile.cwl https://github.com/common-workflow-language/workflows/archive/draft2.tar.gz

This will download and extract to the local directory github.com/common-workflow-language/workflows/archive

You can also import git repositories:

cwldep add myfile.cwl https://github.com/common-workflow-language/workflows

This will clone into the local directory github.com/common-workflow-language/workflows

cwldep add --set-version=draft-2 myfile.cwl https://github.com/common-workflow-language/workflows

This will install any dependencies listed in myfile.cwl

cwldep install myfile.cwl

This will report if the upstream dependencies listed in myfile.cwl have changed

This will install updated dependencies:

This will delete any dependencies listed in the ".dep.lock" file that are not referenced by myfile.cwl.

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