03 Running Guidescan in Docker

This repository contains a Docker Compose configuration for running the Guidescan application, which consists of various interconnected services. Docker Compose makes it easy to set up and manage these services as a single unit, providing a consistent and isolated environment for running the application.

Prerequisites

• Docker

Preparation

Clone this repository

git clone https://github.com/pritykinlab/guidescanpy.git

Navigate to the docker folder

cd path-to-guidescanpy/docker

Configuration

The .env file in this folder contains variables that are substituted in docker-compose.yml and made available to the running container. At a minimum, the following POSTGRES variables are needed to make things work.

POSTGRES_USER
POSTGRES_PASSWORD
POSTGRES_DB

The following Docker volumes need to be created/made available to the docker process. If not present, these are created automatically.

guidescan_data

This is the volume where the data files for guidescan live. The typical folder structure in this volume (once the guidescan_snakemake service is run, see Generating guidescan data for details), looks as follows:

	├── databases
	│   ├── cas9
	│   │   ├── sacCer3.bam
	│   │   ├── sacCer3.bam.bai	
	│   │   ├── sacCer3.bam.sorted
	│   │   ├── sacCer3.bam.sorted.bai
	│   │   └── sacCer3.sam
	│   └── cpf1
	│       ├── sacCer3.bam
	│       ├── sacCer3.bam.bai	
	│       ├── sacCer3.bam.sorted
	│       ├── sacCer3.bam.sorted.bai
	│       └── sacCer3.sam
	├── indices
	│   ├── sacCer3.index.forward
	│   ├── sacCer3.index.gs
	│   └── sacCer3.index.reverse
	├── job_status
	│   ├── add_sacCer3.txt
	│   └── init_db.txt
	├── kmers
	│   ├── cas9
	│   │   └── sacCer3.csv
	│   └── cpf1
	│       └── sacCer3.csv
	└── raw
	    ├── sacCer3_chr2acc
	    ├── sacCer3.fna
	    ├── sacCer3.fna.forward.dna
	    ├── sacCer3.fna.reverse.dna
	    └── sacCer3.gtf.gz

guidescan_postgres_data

This is the volume where the contents of the relational Postgres database for guidescan live.

Generating guidescan data

Run docker-compose up --build --abort-on-container-exit guidescan_snakemake. If this part fails, you can generate data manually by these steps.

Running Guidescan

Run docker-compose up --build guidescan_app.