Installation

READ ME FIRST Note that the recommended method of using PGAP is provided in the Quick Start section. This page is provided as a reference for those who wish to integrate this pipeline into their current CWL platform.

Required files

There are three items need to run the PGAP pipeline, all of which should be the same version. The following instructions uses [version] as a placeholder for the version string, which has the format YYYY-MM-DD.build####.

• Docker image
  • The all inclusive PGAP docker image is based on pgap-utils. You should use pgap-utils for your custom installation.
  • The latest version may be found on dockerhub.
  • To install the image for most docker installations: docker pull ncbi/pgap-utils:[version]
• Supplemental reference data
  • Stored on AWS S3
  • May be downloaded from https://s3.amazonaws.com/pgap/input-[version].tgz
  • When extracted, will contain a single directory named input-[version] and an additional softlink to that directory called input.
  • This directory should be given as the supplemental_data input parameter for the pipeline.
• CWL code
  • The CWL software is available from GitHub at https://github.com/ncbi/pgap. Download the source code package for the latest release, which is located at https://github.com/ncbi/pgap/releases, and extract the code.

Running the pipeline on a test genome

Example genomes and input files may be found in https://s3.amazonaws.com/pgap-data/test_genomes-[version].tgz. See Input Files section to prepare your own genomes.