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BWASPR Installation and Setup

Installation as a Singularity container

All the BWASPR dependencies are encapsulated in a Singularity container available from our Singularity Hub.

Assuming git and singularity are installed on your system, you can get the BWASPR code from GitHub and the container from our Singularity Hub as follows:

git clone https://github.com/BrendelGroup/BWASPR.git
cd BWASPR/demo
singularity pull http://BrendelGroup.org/bwaspr.sif
singularity exec -e -B `pwd` bwaspr.sif ./xdoit sample OUT-sample

Here the last command (singularity exec) will execute the Rscript.BWASPR workflow described in the demo directory, using all the required R packages already loaded in the Singularity container.

Optional: System-wide Installation

BWASPR use via the Singularity container is highly recommended, with no known drawbacks. However, if desired, you can of course install all the required R packages individually on your computer system. The Singularity definition file in this repository should serve as a guide to perform such an installation. The bwaspr.sif container was built on the current long-term supported Ubuntu 20.04 distribution 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.

Finally

proceed to the demo/README document, and we'll tell you how to execute sample workflows (or, equally easy, your very own data analyses).