To get started with EDirect, you need three things:
- A Unix command line environment…
- With the Perl programming language installed, so you can execute…
- The EDirect installation package
Once you have installed EDirect, you can:
Unix is a simple operating system for issuing instructions to a computer. Before graphical user interfaces like Microsoft Windows or Mac OS X, any user who wanted to interact with a computer would have to type their instructions into a command line interface.
Although we now have other ways of interacting with a computer, using a command line interface (also called a “terminal emulator” or “terminal”) is still a powerful and flexible way of telling a computer what to do. If you are using a Mac or Linux computer, you already have a Unix command line environment ready to go! However, if you are using a Windows computer, you may need to install software to emulate this Unix environment.
One way you can get a Unix terminal in Windows is to install Cygwin. This open-source software lets you interact directly with your computer by typing instructions into a command line. Once you have installed EDirect, this software will also recognize EDirect commands which let you search, download, and re-format PubMed and other NLM data. If you do choose to use Cygwin, you will need to make sure you include the Perl programming language in your installation (see below).
In order to install the EDirect software, you will need to make sure that the Perl programming language is installed on your system. While you don’t necessarily need to know Perl in order to use EDirect, the EDirect installation process uses some Perl commands.
The Mac Terminal and many Linux distributions come with Perl pre-installed. If you are using Windows, you will need to make sure that the software you are using to emulate the Unix environment has Perl installed. If you are using Cygwin to emulate Unix, the Cygwin installer will offer you a large variety of tools that you can install with Cygwin, including programming languages like Perl and Python, and many different utilities.
When you install Cygwin, you can choose which languages and utilities to install on the “Select Packages” page of the installer. To make sure you have all necessary Perl packages, make sure that “Category” is selected in the “View” drop-down menu at the upper left, then find the “Perl” category in the list. In order to install all Perl packages, click on the circle-with-arrows icon (just to the right of the word “Perl”) until the label next to it switches from “Default” to “Install”. If you previously installed Cygwin without the required packages, you can re-run the installer to add additional packages to your installation.
To install EDirect, open your Unix terminal and execute the following commands. (The easiest way to do this is to copy the whole block and paste it directly into your terminal window.)
cd ~ perl -MNet::FTP -e \ '$ftp = new Net::FTP("ftp.ncbi.nlm.nih.gov", Passive => 1); $ftp->login; $ftp->binary; $ftp->get("/entrez/entrezdirect/edirect.tar.gz");' gunzip -c edirect.tar.gz | tar xf - rm edirect.tar.gz export PATH=$PATH:$HOME/edirect ./edirect/setup.sh
This installs the EDirect software and gets it ready to use. Depending on your system’s configuration, you may see the following message:
In order to complete the configuration process, please execute the following:
followed by a command that looks something like:
echo "export PATH=\$PATH:\$HOME/edirect" >> $HOME/.bash_profile
If you see this prompt, copy the command provided and paste it into your terminal.
Once the installation is complete, you will see the following message in your terminal window:
Entrez Direct has been successfully downloaded and installed.
You can confirm EDirect is installed correctly by using the testing script below.
To confirm that EDirect is installed and working properly, you can run your first EDirect script! Just type (or copy and paste) the following code into your terminal window, and press Enter.
echo "***********************" > installconfirm echo "esearch version:" >> installconfirm esearch -version >> installconfirm echo "xtract version:" >> installconfirm xtract -version >> installconfirm echo "EDirect install status:" >> installconfirm esearch -db pubmed -query "Babalobi OO[au] AND 2008[pdat]" | \ efetch -format xml | \ xtract -pattern Author -if Affiliation -contains Medicine \ -element Initials >> installconfirm echo "***********************" >> installconfirm cat installconfirm rm installconfirm
The result should be a message similar to the following:
*********************** esearch version: 7.00 xtract version: 7.00 EDirect install status: OK ***********************
If you see this output, you have installed EDirect successfully!
However, if your esearch or xtract version are earlier than the number stated above, you may need to update to the latest version of EDirect. If your output does not resemble the above sample (e.g. your esearch and xtract versions do not match, you get an additional “OO” following the “OK”, etc.), or you get an error message instead, please contact us for further assistance.
To update your EDirect installation to the latest version, you can simply re-install EDirect over your existing installation, using the same script you used for the initial installation. See EDirect Installation above.