Web Service Clients CWL Generator

cwlgenerator.py allows auto-generation of Common Workflow Language (CWL) definitions for Sample CLI Clients for EMBL-EBI's Job Dispatcher Web Service Bioinformatics Tools.

CWL generated with this program are uploaded to the webservice-cwl repository. These CWL require the actual clients or the webservice-clients Docker image from webservice-clients in order to run the clients.

How to use it

Download the source code or clone the repository:

git clone https://github.com/ebi-jdispatcher/webservice-cwl-generator.git

Specially if you have no root access to your machine, you might need to use virtualenv. Prepare a virtual environment where all the Python dependencies will be installed. This project has been developed and tested with Python 3.6.5.

virtualenv -p `which python` env
source ./env/bin/activate
# deactivate

A full list of Python dependencies is provided in requirements.txt. Install dependencies with:

pip install --upgrade -r requirements.txt

Now run the program to generate python clients for all supported EBI tools, they will be placed in the dist folder. All available clients are listed in clients.ini.

Generating CWL for the clients

Run the following commands to generate CWL using Python or Perl clients for all the Bioinformatics tools provided.

# based on python clients
python cwlgenerator.py python

# based on perl clients
python cwlgenerator.py perl

Alternatively, use --client <client_name> to get only a selected client.

python cwlgenerator.py python --client clustalo,ncbiblast

CWL can also run the clients with Docker by using the Docker image provided in the webservice-clients repository. We can generate CWL with Docker dependency by passing the --docker flag.

python cwlgenerator.py python --client clustalo,ncbiblast --docker

Running the generated CWL with cwltool

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

Example using CWL with a Python client and Docker

An example test for Clustal Omega using the Python client:

cwltool dist/clustalo.cwl --email <[email protected]> --sequence sp:wap_rat,sp:wap_mouse,sp:wap_pig

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.