Bioinformatics Example Repository

This repository contains example tools and pipelines discussed on my blog.

Detailed user documentation is available on the project website including tool usage, pipeline usage, and documentation of metrics produced.

Posts

Below we list posts that reference example tools, pipelines, and metrics contained in this repository:

• Sample Demultiplexing an Illumina Sequencing Run

Building

Cloning the Repository

To clone the repository: git clone https://github.com/nh13/bfx-examples.git

Running the build

bfx-examples is built using sbt.

Use sbt assembly to build an executable jar for tools in tools/target/scala-2.12/ and for pipelines in pipelines/target/scala-2.12/. Tests may be run with sbt test. Java SE 8 is required.

Command line

• Use java -jar tools/target/scala-2.12/bfx-examples-tools.jar to see the tools supported.
• Use java -jar tools/target/scala-2.12/bfx-examples-tools.jar <command> to see the help message for a particular tool.
• Use java -jar pipelines/target/scala-2.12/bfx-examples-pipelines.jar to see the pipelines supported.
• Use java -jar pipelines/target/scala-2.12/bfx-examples-pipelines.jar <command> to see the help message for a particular pipeline.

Configuring pipelines

Please see the example bfx-examples-pipelines configuration for customizing dagr for your environment.