Installation

conda

To most effectively use hubward, several command line programs are required to be on your PATH. The easiest, and recommended, way to install these is with the conda package manager, which comes with Anaconda Python. Anaconda comes with many scientific Python packages that are otherwise difficult to install, along with tools for building isolated environments. It’s a very convenient tool.

The following command will install hubward plus all optional dependencies into a new conda environment called hubward-test:

conda install -n hubward-test -c r -c bioconda hubward-all

This will install:

• bedtools

• UCSC utilities:

  • wigToBigWig
  • bedGraphToBigWig
  • bedToBigBed
  • bigBedToBed
  • fetchChromSizes
  • liftOver

• CrossMap

To use the new environment (which is isolated and independent from anything you may already have installed), use:

source activate hubward-test

Docker

The tests are run within a Docker container. Inspect the docker/Dockerfile to see how the system is set up, or run:

docker pull daler/hubward-test
./docker-test-wrapper.sh

to perform the test.