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[DEPRECATED]

Toil-Scripts is now deprecated and no longer being maintained. It may be run and used at the user's discretion. Dependencies are locked at: toil-lib==1.2.0a1.dev126, and toil==3.5.0a1.dev277 . Other versions may work, but are not guaranteed to run.

It's intended that new workflows will reside at: https://github.com/BD2KGenomics/toil-workflows

University of California, Santa Cruz Genomics Institute

Repository of Toil-based Genomic Pipelines

To install these pipelines, 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
  • GATK exome variant pipeline: toil-exome

Source code and installation instructions for the CGL RNA-seq pipeline have moved to: https://github.com/BD2KGenomics/toil-rnaseq

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 the Toil team at: [email protected] If you find any errors or corrections please feel free to make a pull request. Feedback of any kind is appreciated.