Quick Start

Requirements

To run the PGAP pipeline you will need to be able to run Docker, and about 100GB of storage for the supplemental data, and Python, version 3.5 or higher.

Quick Start

Download the file using either

$ curl -OL https://github.com/ncbi/pgap/raw/prod/scripts/pgap.py

or

$ wget https://github.com/ncbi/pgap/raw/prod/scripts/pgap.py

depending upon which utility your system has installed. If one does not work, try the other.

Then try running the pipeline on the Mycoplasma genitalium genome provided with the installation:

$ chmod +x pgap.py
$ ./pgap.py --update # required files are downloaded and extracted
$ ./pgap.py -r -o mg37_results test_genomes/MG37/input.yaml # watch the progress reports and wait for some time.]

Output will be located in the mg37_resuts subdirectory.

Bring Your Own Data

To run this pipeline using your own genomes, you will need three input files, all in the same directory. Instructions for preparing your data are in the Input Files section.

1. A fasta file.
2. A YAML file containing metadata (usually called submol.yaml).
3. A YAML file the describes the pipeline inputs, including the above two files.

Useful options

To get a complete list of options, use the -h flag. However, here are some notable options.

Command	Description
-l, --list	List available versions.
-u, --update	Update to the latest PGAP version, including reference data.
-r, --report-usage-true	Set the report_usage flag in the YAML to true.
-n, --report-usage-false	Set the report_usage flag in the YAML to false.
-o path, --output path	Output directory to be created, which may include a full path.
-q, --quiet	Quiet mode, for scripts.
-d, --debug	Debug mode, useful for creating info that may be sent to the developers.