antiSMASH CLI wrapper for CWL
First steps and small example of wrapping a command line tool in a Common Workflow Language (CWL) description.
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:
This code for demonstration purposes is provided under a CC-BY 4.0 license.
LICENSE for details.