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edirect-software

EDirect

EDirect is a software package, developed by NCBI, which allows you to use the E-utilities API in a Unix environment. It helps you quickly and easily use the E-utilities API, and has built-in tools to extract specific data from XML files and create tables of data that can be more easily analyzed or visualized.

Information

Usage

See which versions of edirect are available:

$ module avail edirect

Load one version of edirect into your environment:

$ module load edirect/7.80

Installation

Notes from the sysadmin during installation:

$ cd /tmp
$ sudo mkdir -p /export/apps/edirect/7.80
$ sudo chown aorth /export/apps/edirect/7.80
$ wget ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/edirect.tar.gz
$ tar xf edirect.tar.gz -C /export/apps/edirect/7.80 --strip-components=1
$ cd /export/apps/edirect/7.80
$ export PATH=$PATH:/export/apps/edirect/7.80                                                                                                                                                              
$ sudo yum install perl-LWP-Protocol-https.noarch perl-Net-SSLeay.x86_64
$ ./setup.sh
$ sudo chown -R root:root /export/apps/edirect/7.80

EDirect has a really old fashioned installation process and doesn't even version their releases very obviously. Don't just blindly copy/paste the shell commands from the installation document, and make sure to check the release notes for information about versions.

edirect-software.txt · Last modified: 2018/01/30 12:45 by aorth