Installing cwltool to execute cwl YAML

cwltool

Installation of cwltool

Create a new virtual environment

• This can be done using conda or virtualenv

virtualenv ~/my_virtual_env
#Or use
conda new --name my_virtual_env python=2.7

Source the virtual environment

source ~/my_virtual_env/bin/activate
#Now when you do
echo $PATH
#you should see
~/my_virtual_env/bin
#listed as an entry

Install toil

pip install toil'[cwl]'==3.15.0

Install the python tool you made (optional, only needed if trying to test with setup.py)

python setup.py install && python setup.py clean

This will install the example python script into your virtualenvironment’s /bin folder This makes it so it can be referenced from your terminal, as well as from the cwl files

So now, whenever you want to run a command, that python file will be found (because all commands are just files found in the $PATH variable)

Try to run your file

cwltool example_cwl_tool_that_calls_python_script.cwl inputs.yaml
#Because the tool's
baseCommand
#param has the python script listed inside, the runner will find it and run it.

With cwltoil

cwltoil sometool.cwl inputs.yaml --outdir /place_for_outputs

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