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EDirect

Description

edirect website

Entrez Direct (EDirect) provides access to the NCBI's suite of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window. 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.

Environment Modules

Run module spider edirect to find out what environment modules are available for this application.

Environment Variables

  • HPC_EDIRECT_DIR - installation directory
  • HPC_EDIRECT_BIN - executable directory

Additional Usage Information

To be able to make many requests to NCBI API you need to have an API key. Log into your NCBI account and copy the text of the API key generated from your NCBI Account Settings into the ~/.ncbi/api_key file on HiPerGator to be able to exceed the NCBI free request limit.

See NCBI Insights: API Keys for reference on getting a key.

Categories

biology, phylogenetics