I wrote a nice self-containing python in the cwl. How can I include python’s pip requirements: “pip install” before running the script?
I want to keep everything in one script, see below.
Thank you for your help.
cwlVersion: v1.0 class: CommandLineTool baseCommand: ["python", "convert.py"] inputs: in_file: type: File out_file: type: string requirements: InitialWorkDirRequirement: listing: - entryname: convert.py entry: |- import numpy as np data = np.loadtxt('$(inputs.in_file.path)') with open('$(inputs.out_file)','w') as fOut: fOut.write("Sum is: "+str(np.sum(data))) outputs: outfile: type: File outputBinding: glob: $(inputs.out_file)