ycya88/ncbi_edirect
This repository provides Docker images for the NCBI EDirect command-line applications.
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:
Default tags include latest
and specific EDirect version tags.
To pull the latest image:
docker pull ycya88/ncbi_edirect:latest
To start an interactive terminal session:
docker exec -it $(docker run -itd ycya88/ncbi_edirect:latest /bin/bash) /bin/bash
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"
To verify the installation:
docker run --rm -it ycya88/ncbi_edirect:latest /bin/bash -c "./installconfirm"
docker pull ycya88/ncbi_edirect