edirect command not found

Introduction

When you run more command in linux terminal / console, you get the following error message

edirect: command not found

or when using sudo you get the following error message

sudo: edirect: command not found

Solutions to edirect: command not found

How To Fix edirect: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu edirect is provided by ncbi-entrez-direct package.

ncbi-entrez-direct is:

Entrez Direct (EDirect) is an advanced method for accessing NCBI’s set of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a terminal window or script. Functions take search terms from command-line arguments. Individual operations are combined to build multi-step queries. Record retrieval and formatting normally complete the process.

EDirect also provides an argument-driven function that simplifies the extraction of data from document summaries or other results that are returned in structured XML format. This can eliminate the need for writing custom software to answer ad hoc questions. Queries can move seamlessly between EDirect commands and UNIX utilities or scripts to perform actions that cannot be accomplished entirely within Entrez.

To fix this problem, we can install more using the command below.

sudo apt-get -y install ncbi-entrez-direct

This command might take some time to finish depending on your machine internet connection.

You can also use apt command to install ncbi-entrez-direct.

sudo apt -y install ncbi-entrez-direct

Or if you have aptitude installed you can use the following command.

sudo aptitude install ncbi-entrez-direct

Summary

In this tutorial we learn how to fix edirect command not found error in Ubuntu / Debian / Kali Linux or Raspbian distribution.