recipe entrez-direct

Entrez Direct (EDirect) is an advanced method for accessing the NCBI's set 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.

Homepage:

https://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/versions/22.4.20240717/README

License:

PUBLIC DOMAIN

Recipe:

/entrez-direct/meta.yaml

package entrez-direct

(downloads) docker_entrez-direct

versions:
22.4-0,  22.1-0,  21.6-0,  16.2-1,  16.2-0,  15.6-1,  15.6-0,  13.9-2,  13.9-1, 

22.4-0,  22.1-0,  21.6-0,  16.2-1,  16.2-0,  15.6-1,  15.6-0,  13.9-2,  13.9-1,  13.9-0,  13.8-0,  13.3-0,  11.0-2,  11.0-1,  11.0-0,  10.2-0,  10.0-0,  7.70-2,  7.70-1,  7.70-0,  7.00-1,  7.00-0,  5.80-0,  4.00-1,  4.00-0

depends wget:

requirements:

additional platforms:
linux-aarch64,  osx-arm64

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install entrez-direct

and update with::

   mamba update entrez-direct

To create a new environment, run:

mamba create --name myenvname entrez-direct

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/entrez-direct:<tag>

(see `entrez-direct/tags`_ for valid values for ``<tag>``)

Download stats

Link to this page

Render an install-with-bioconda badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/entrez-direct/README.html)