snk 0.4.0

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snk

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Table of Contents

• Installation
• 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.

Basic Use

Install a pipeline as a CLI

snk install 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

Snk will dynamically generate config options for the CLI. For example if your config.yaml file has the option fasta: null you can set this option with --fasta.

rna-seq-star-deseq2 run --fasta example.fa

You can also configure the pipeline using a config file.

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

how it works

When installing a pipeline snk will

• create directory $PYTHON_BIN_DIR/../snk/pipelines/PIPELINE
• install the pipeline into this directory
• expose CLI at $PYTHON_BIN_DIR that point to pipeline directory in snk/pipelines/PIPELINE/bin
• As long as $PYTHON_BIN_DIR 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.