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This repository contains a collection of genomic pipelines developed by the UCSC Computational Genomics Lab.

To install these pipelines, just type: pip install toil-scripts

Entrypoints are supplied to pipelines that work with the current stable release of Toil:

• Fastq to BAM alignment: toil-bwa
• CGL RNA-seq Pipeline (hg38): toil-rnaseq
• UNC best practices RNA-seq pipeline (hg19): toil-rnaseq-unc
• SplAdder alternative splicing pipeline: toil-spladder
• GATK exome variant pipeline: toil-exome

Each pipeline has its own README that provides instructions on how to get up and running. The general dependencies for these pipelines are:

1. Toil
2. Docker

Our group utilizes genomics tools encapsulated within Docker containers for portability. Each of these pipelines can be run locally on your laptop, on a baremetal cluster, or on a cloud provider.

If there are any questions please contact John Vivian ([email protected]). If you find any errors or corrections please feel free to make a pull request. Feedback of any kind is appreciated.