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
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:
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.