Common Workflow Language implementation for EBI Web Services

CWL implementation for consuming EMBL-EBI Bioinformatics Web Services tools' clients. These CWL files are generated from the EBI Job Dispatcher Web Services (XML) description with https://github.com/ebi-wp/webservice-cwl-generator

Contents

• cwls : cwl files for the EBI Web Service clients (using Python clients from webservice-clients)
• cwls-docker : cwl files for the EBI Web Service clients (using Python clients from webservice-clients Docker image)
• jsons : example json files for defining input values for parameters
• sequence : example sequence files for testing
• workflows : a set of workflows to highlight the use of the clients
• ymls : example yml files for defining input values for parameters

Getting Started

How to install cwltool

You will need cwl-runner (cwltool) to run CWL descriptions. Official instructions on how to install cwltool are provided in https://github.com/common-workflow-language/cwltool

How to install Docker (optional)

Docker installation instructions are provided in https://docs.docker.com/install/

Running CWL for EBI tools using local Python clients (does not require Docker)

You can find CWL definitions in cwls accompanied with predefined parameters defined in ymls. Running these CWL files expects webservice-clients directory to be found alongside the webservice-cwl directory.

Note: Before running cwltool, you need to defined your own values for the sequence (or asequence plus bsequence) parameters, including a required email address.

cwltool ./cwls/tcoffee.cwl ./ymls/tcoffee.yml

Running CWL for EBI tools (requires Docker)

You can find CWL definitions in cwls-docker accompanied with predefined parameters defined in ymls. Running these CWL files does not require webservice-clients to be found alongside the webservice-cwl directory, as the Docker image has got all the necessary clients pre-installed.

Note: Before running cwltool, you need to defined your own values for the sequence (or asequence plus bsequence) parameters, including a required email address.

cwltool ./cwls-docker/tcoffee.cwl ./ymls/tcoffee.yml

Chaining the tools into workflows

You can view examples of workflows chaining multiple tools together and example input ymls in the workflows folder.

Documentation

More documentation about EMBL-EBI Bioinformatics Web Services

Contact and Support

If you have any problems, suggestions or comments for our services please contact us via EBI Support.

License

The European Bioinformatics Institute - EMBL-EBI, is an Intergovernmental Organization which, as part of the European Molecular Biology Laboratory family, focuses on research and services in bioinformatics.

Apache License 2.0. See license for details.