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Installation
There are three ways of installing reper on your system: Docker, Singularity and a manual installation. The preferred ways are Docker and Singularity since all dependencies are automatically dealt with.
In order to run reper, you need a config file. An example is included in the github repository.
git clone https://github.com/nterhoeven/reper.git
Then you can either download the existing container from Dockerhub
docker pull nterhoeven/reper
or build a Docker container yourself
cd reper
docker build .
It is helpful to create an alias for the reper docker command:
alias reper="docker run --user=$(id -u):$(id -g) -it --rm -v $(pwd):/data nterhoeven/reper"
reper can then be run with
reper <command>
First, clone in the github repository.
git clone https://github.com/nterhoeven/reper.git
You can now build the Singularity container with
cd reper
sudo singularity build --writable reper-singularity.img Singularity
or you can use the pre-build docker container with singularity
singularity pull docker://nterhoeven/reper
It is helpful to create an alias for the reper singularity command
alias reper="singularity exec <path/to/the/.img/file> reper"
reper can then be run with
reper <command>
First you should make sure to have all dependencies installed. Then you can clone the github repository
git clone https://github.com/nterhoeven/reper.git
As second step, you have to tell reper where the dependencies can be found. Therefore
you have to edit the second section of the reper.conf file. You can do this manually or (if everything is accessible via $PATH) use the update_exe_path.sh script:
./update_exe_path.sh reper.conf