genebio / get-sra

get-sra - SRA Toolkit Docker Implementation

README.md for the get-sra Docker Component

Overview

The get-sra Docker component is a streamlined tool for downloading sequence data from the NCBI's Sequence Read Archive (SRA), including dbGaP-protected data. It wraps the functionality of the SRA Toolkit into a Docker container for ease of use and reproducibility.

Features

• SRA Toolkit Integration: Direct access to SRA Toolkit features in a stable Docker environment.
• Supports dbGaP Access: Enables authorized users to download dbGaP-protected data.
• Efficient Data Retrieval: Optimized for downloading large datasets with minimal configuration.
• User-Friendly: Designed for ease of use with a clear command-line interface.

Prerequisites

• Docker installed on your machine.
• Access to the internet for downloading data from SRA.
• (Optional) dbGaP authorization keys for accessing protected data.

Installation

1. Clone the Repository:

   git clone [email protected]:Genebio/get-sra.git

2. Build the Docker Image: Navigate to the directory containing the Dockerfile and run:

   docker build -t get-sra:1.0.0 .

Usage

To use the get-sra tool, run the Docker container with the required parameters:

docker run --rm -it \
    -v [local-directory-path]:/data \
    get-sra:1.0.0 \
    --sra-id [SRA_ID] \
    --output-forward-fastq-gz /data/[forward-filename].fastq.gz \
    --output-reverse-fastq-gz /data/[reverse-filename].fastq.gz \
    --ngc-key-file /data/[keyfile.ngc]

Command-line Arguments

• --sra-id: The SRA ID of the file to download (Ex. SRR23085779)
• --ngc-key-file: (Optional) Path to the dbGaP access key file.
• --output-forward-fastq-gz: Path for the output forward strand FASTQ.GZ file.
• --output-reverse-fastq-gz: Path for the output reverse strand FASTQ.GZ file.
• --output-single-fastq-gz: Path for the output single-end FASTQ.GZ file.

Troubleshooting and Support

For issues and questions regarding the use of this tool, please refer to the issue tracker in the GitHub repository or contact [email protected].

Contribution

Contributions to this project are welcome. Please fork the repository and submit a pull request with your changes.