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AEGeAn Installation and Setup

Installation as a singularity container https://www.singularity-hub.org/static/img/hosted-singularity--hub-%23e32929.svg

All the AEGeAn dependencies are encapsulated in a Singularity. Assuming git and singularity are installed on your system, you can get the AEGeAn code from GitHub and the container from our Singularity Hub as follows:

git clone https://github.com/BrendelGroup/AEGeAn.git
cd AEGeAn
wget https://BrendelGroup.org/SingularityHub/aegean.sif
alias rws="singularity exec -e -B ~/AEGeAn ~/AEGeAn/aegean.sif"
rws fidibus -h

Here the last command (singularity exec) will execute the fidibus script and display its help message.

For a gentle introduction to singularity, see our group handbook article.

Optional: System-wide Installation

AEGeAn use via the singularity container is highly recommended, with no known drawbacks. However, if desired, you can of course install all the required third party software and our fidibus Python package individually on your computer system. The singularity recipe file in this repository should serve as a guide to perform such an installation. The aegean.simg container was built on the current Fedora 39 release and thus the instructions apply to that particular Linux version. For different Linux distributions, you will have to install the equivalent packages using your distribution's package manager.