NCBI EDirect Docker Images

This repository provides Docker images for the NCBI EDirect command-line applications.

Overview

The EDirect tools offer a suite of command-line applications for accessing and querying NCBI databases. This Docker image simplifies the setup and usage of these tools.

GitHub Repository:ycya88/ncbi_edirect⁠

The Docker image defaults to:

• Base Image: Ubuntu
• Mode: User

Default tags include latest and specific EDirect version tags.

Quick Start

Update to the Latest Image

To pull the latest image:

docker pull ycya88/ncbi_edirect:latest

Interactive Terminal

To start an interactive terminal session:

docker exec -it $(docker run -itd ycya88/ncbi_edirect:latest /bin/bash) /bin/bash

Example Usage

Fetch a Nucleotide Sequence in FASTA Format

To fetch a nucleotide sequence by ID:

docker run --rm -it ycya88/ncbi_edirect:latest /bin/bash -c "efetch -db nucleotide -id u00001 -format fasta"

To search and fetch a nucleotide sequence:

docker run --rm -it ycya88/ncbi_edirect:latest /bin/bash -c "esearch -db nucleotide -query u00001 | efetch -format fasta"

Check Installation

To verify the installation:

docker run --rm -it ycya88/ncbi_edirect:latest /bin/bash -c "./installconfirm"

Reference

https://github.com/ncbi/docker⁠