agr-free RPMs

A bioinformatics software repository for CentOS/RHEL 6 x86_64

Welcome to the AgResearch RPM repository for bioinformatics software. This is not our own software, it is simply free software we have packaged as RPM for ease of installation on CentOS 6, or other RHEL 6 clones. Historically, some bioinformatics software has been difficult to install. Packages may have many dependencies. This repository is the result of packaging such software together with any required dependencies over an extended period of time, and it is now freely available as a resource for the bioinformatics community.

See the list of agr-free packages for details of exactly what is here. Only the x86_64 architecture is supported.

How to use agr-free

Save the agr-free.repo config file as /etc/yum.repos.d/agr-free.repo. You will need to install the AgResearch RPM GPG public key into /etc/pki/rpm-gpg/RPM-GPG-KEY-agresearch, so that package signatures can be verified. (Downloading individual RPMs from the repository is possible, but not recommended.)

This repository is designed to be used with those listed below, using the yum priorities plugin to avoid conflicts. The priorities we use at AgResearch are shown in the table. You need to think carefully about the priorities you choose. In particular our agr-free.repo config file sets the priority of agr-free to 1, which may not be what you want (but is what we use and have tested here). Packages from agr-free may depend on packages from any of these repositories. Other RPM repositories such as RPMForge are unlikely to be compatible. See also Available Repositories for CentOS.

Yum repositories with their priorities as used at AgResearch
Repository Priority Remark
agr-free 1 Bioinformatics and supporting packages
CentOS 6 base/updates 5 Core OS packages and updates (any RHEL 6 clone should be OK)
EPEL 6 10 Extra packages for Enterprise Linux

Mirroring agr-free

In case you want to mirror agr-free locally, the whole repository is available for rsync. This is best done as a scheduled task, e.g. once a week. Please pick a random time to avoid overloading our server at 'obvious' update times like midnight.

rsync -rlt --delete .


All feedback is welcome, whether you've found that something is broken, or you just want to say how useful this repository has been for your work. Contact details on the right.


Reasonable care has been taken in packaging this software, and it is all in use internally within AgResearch. However, please note as follows.

There is no warranty for the software, to the extent permitted by applicable law. Except when otherwise stated in writing the copyright holders and/or other parties provide the software "as is" without warranty of any kind, either expressed or implied, including, but not limited to, the implied warranties of merchantability and fitness for a particular purpose. The entire risk as to the quality and performance of the software is with you. Should the software prove defective, you assume the cost of all necessary servicing, repair or correction.

In no event unless required by applicable law or agreed to in writing will any copyright holder, or any other party who may modify and/or redistribute the software as permitted above, be liable to you for damages, including any general, special, incidental or consequential damages arising out of the use or inability to use the software (including but not limited to loss of data or data being rendered inaccurate or losses sustained by you or third parties or a failure of the software to operate with any other software), even if such holder or other party has been advised of the possibility of such damages.

Hey, it's all free. What did you expect? :)


simon (dot) guest (at)