User Tools

Site Tools



This shows you the differences between two versions of the page.

Link to this comparison view

edirect-software [2018/01/30 09:45] (current)
aorth created
Line 1: Line 1:
 +====== 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 =====
 +  * Latest Version: 7.80
 +  * Added: January, 2018
 +  * Link: https://​​edirect/​overview.html
 +  ​
 +===== Usage =====
 +See which versions of edirect are available:
 +<​code>​$ module avail edirect</​code>​
 +Load one version of edirect into your environment:​
 +<​code>​$ module load edirect/​7.80</​code>​
 +===== Installation ======
 +Notes from the sysadmin during installation:​
 +<​code>​$ cd /tmp
 +$ sudo mkdir -p /​export/​apps/​edirect/​7.80
 +$ sudo chown aorth /​export/​apps/​edirect/​7.80
 +$ wget ftp://​​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
 +$ ./
 +$ sudo chown -R root:root /​export/​apps/​edirect/​7.80</​code>​
 +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 [[https://​​books/​NBK179288/#​chapter6.Release_Notes|release notes]] for information about versions.
edirect-software.txt · Last modified: 2018/01/30 09:45 by aorth