snk 0.0.2

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snk

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Table of Contents

• Installation
• [About][#about]
• License

Installation

pip install snk

About

Snk is a SnakeMake pipeline management system. Snk allows you to install SnakeMake pipelines as Command Line Interfaces (CLIs). Using a pipeline as a CLI increases it's interoperability and allows complex pipelines to be used as modular components in a larger system.

https://excalidraw.com/#room=4cb5ad1ed651d8a96369,xM0iaXAGVFNiNJOuILncPg

Basic Use

Install a pipeline as a CLI

snk install https://github.com/snakemake-workflows/rna-seq-star-deseq2

Inspect the CLI

rna-seq-star-deseq2 --help

View the dag

rna-seq-star-deseq2 dag --pdf 

Run the pipeline

rna-seq-star-deseq2 run

Configure

rna-seq-star-deseq2 config # print the config 
rna-seq-star-deseq2 config > config.yml # save the config 
rna-seq-star-deseq2 run --config config.yml # run with config 

how it works

When installing a pipeline snk will

• create directory ~/.local/snk/pipelines/PIPELINE
• install the pipeline into this directory
• expose CLI at ~/.local/bin that point to pipeline directory in ~/.local/snk/pipelines/PIPELINE/bin
• As long as ~/.local/bin/ is on your PATH, you can now invoke the pipeline globally

hey what about snakedeploy??

yes

License

snk is distributed under the terms of the MIT license.