In this talk, I showed you how to take a Python script and turn it into a stand-alone command-line tool, ready for distribution via the Python Package Index (PyPI).
đź’ˇ You can download a
.zipfile of the “before” and “after” code examples demoed here.
Packaging your script up as a package is a good thing to do for a few reasons:
- More people can use your scripts - not just within Nextflow
- This is useful for development, for stand-alone testing
- It’s useful for people using other workflow managers
- It helps when users are testing a method / debugging with small sample sizes
- It allows scripts to be released under different licenses to the pipeline itself
- Software packaging, that is providing container images with all requirements, is handled automatically
- Even if it’s a small script that you think no-one will ever use outside of your pipeline, it’s easy to do and you don’t lose anything 🙂
Once released in PyPI, releases via Bioconda are simple (see Bytesize 40: Software packaging). Once in Bioconda, software will be available for Conda users, but also Docker + Singularity, via the BioContainers project.
