First try wrapping antiSMASH in a Common Workflow Language description
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README.md
antismash-job.json
antismash.cwl

README.md

antiSMASH CLI wrapper for CWL

First steps and small example of wrapping a command line tool in a Common Workflow Language (CWL) description.

Running

To run this yourself, you'll need Docker and a CWL implementation. For starters, the reference implementation will work. Run pip install cwltool cwl-runner to install it, use a virtual environment if you like. Also, the antiSMASH docker container is rather large, so having a decent internet connection will help.

To grab the example file, run

wget -O nisin.gbk "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&rettype=gbwithparts&id=HM219853"

Then, you can run antismash with the provided job file like this:

./antismash.cwl antismash-job.json

License

This code for demonstration purposes is provided under a CC-BY 4.0 license. See LICENSE for details.