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BASys2 Docker

About

This archive contains the Docker backend pipeline for use with the BASys2-app-docker-single Docker image. It is a Perl script that automates the process of analyzing bacterial genomes, including gene prediction, annotation, and functional analysis.

The script is designed to be run from the command line and takes several input parameters, including the type of input data, job ID or accession number, and annotation type. The script uses various bioinformatics tools and databases to perform the analysis and generate output files.

Setup

1. Download the BASys2 Docker Repository from, unzip the file.
2. Download the Docker image from Docker Hub here or by using the following command:

   docker pull wishartlab/basys2-app-docker-single:latest

3. Download the BASys2 Database, unzip the file, and place the contents in the ./basys2-app/DB folder of the repository.
4. Download the BASys2 Sub-Programs, unzip the file, and place the contents in the ./basys2-app/sub_programs folder of the repository.
5. Make sure the ./basys2-app/sub_programs folder is executable by running the following command:

   chmod +x ./basys2-app/sub_programs/*

6. Make sure the basys2.pl script is executable by running the following command:

   chmod +x ./basys2-app/scripts/basys2.pl

Usage

1. To use the BASys2 Docker, you will use docker compose to run two containers: one for the BASys2 pipeline and one for the database. The docker-compose.yml file in the repository contains the configuration for these containers. From the root directory of the repository, run the following command to start the containers:

   docker-compose up -d

2. The pipeline is designed to be run from the command line within the Docker container. You can enter the BASys2 docker container via this command:

   docker exec -ti basys2-app-docker-single-main-1 bash

3. You can now run your analysis using the BASys2 pipeline, using the following command to run it:

   perl /basys2-app/scripts/basys2.pl {input type} {filename or accession}

   • Input type may be GenBank accession number -g, raw FASTA sequence -s, metagenomic contig -c, or FASTQ read files -q.For raw FASTA sequence and metagenomic contig inputs, you must ensure that the input file is present within ./basys2-app/JOBS/{job_name} directory. For example, ./basys2-app/JOBS/{job_name}/{job_name}.fasta.
   • For FASTQ read file inputs, two input files must be present within ./basys2-app/JOBS folders under the desired job name, and their name must be provided as the basys2.pl script parameter. For example:

     perl basys2.pl -q -1=read1.fq -2=read2.fq {job_name}

   • If GenBank accession is specified, the BASys2 script will automatically create the corresponding folder in ./basys2-app/JOBS directory and start running the BASys2 pipeline.

Requirements

The BASys2 Docker requires the following software to be installed on your system:

1. Latest Docker (tested on Docker version 28.0.4, build b8034c0). Docker Installation Guide
2. BASys2 Repository, Sub-programs and Database (download below).

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