README.md

Common Workflow Language dependency manager

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

Setup

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:

pip install cwldep

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

Adding file dependencies

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

Changing the install target

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

Using archives

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

Using git upstream

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

Installing dependencies

This will install any dependencies listed in myfile.cwl

cwldep install myfile.cwl

Checking if upstream dependencies have changed

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

cwldep check myfile.cwl

Updating dependencies

This will install updated dependencies:

cwldep update myfile.cwl

Deleting unreferenced dependencies

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

cwldep clean myfile.cwl