Adding repositories containing bioinformatics tools in Red Hat-derived distributions

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Go back to parent page Introduction to Linux for bioinformatics

Adding EPEL to your software sources

EPEL stands for Extra Packages for Enterprise Linux and contains some bioinformatics tools. To install, EPEL provides an RPM to download, which will set up the EPEL repository. Once plugged in, use the Package Manager to install bioinformatics packages.

First, find out whether your distribution is based on Red Hat Enterprise Linux 5 or 6. Open a terminal and type 
uname -a
The result shows you the version of RHEL (indicated in yellow below).

Unameonrhel6.png

Choose the correct version on from the EPEL website and download the corresponding RPM.

Double-click on the .rpm file to install the RPM with the Package Installer

Unameonrhel6 2.png

Alternatively, install the .rpm file with 
# yum install epel-release-6-8.noarch.rpm

Once installation is done, you can start installing software by using the Package Manager.

Unameonrhel6 3.png


Adding AgResearch repo to your software sources

The AgResearch repo

From their page: "This agr-free repository is the result of packaging bioinformatics software together with any required dependencies over an extended period of time. It is now freely available as a resource for the bioinformatics community."

Download the public key of AgResearch

A public key is used to verify the source of a file. In this case, we want to check whether a package comes from AgResearch. Therefore, we first need to install their public key.

Download it from here and put the file into the folder /etc/pki/rpm-gpg. You can do this for example (with the right permissions) with: 

cd /etc/pki/rpm-gpg; wget http://rpm.agresearch.co.nz/RPM-GPG-KEY-agresearch

Add the repo file

Download the repository description file of the AgResearch repository and put it in /etc/yum.repos.d. 

cd  /etc/yum.repos.d ; wget http://rpm.agresearch.co.nz/agr-free.repo

Install yum plugin priorities

Install a plugin for yum, which is the default cli package manager in RedHat. 

yum install -y yum-plugin-priorities

Give priorities to the repositories

agr-free is designed to be used with other repo's, such as EPEL. If you give higher priority to certain repo's, their packages will be preferentially installed over other repo's (e.g. versions can differ between repo's). This will avoid conflicts. AgResearch recommend to set the priorities as mentioned on their website http://rpm.agresearch.co.nz/.

Install bioinformatics packages using yum

yum install MUMmer


Go back to parent page Introduction to Linux for bioinformatics
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