Installation

1. Pull an image from Docker Hub:

   docker pull rnacentral/r2dt
   

   Alternatively, build a Docker image locally (requires just):

   # Get the code
   git clone https://github.com/r2dt-bio/R2DT.git
   cd R2DT
   just build
   

   Or build a Singularity image:

   singularity build r2dt docker://rnacentral/r2dt
   

2. Enter an interactive terminal session:

   docker run -it -v `pwd`:/rna/r2dt/temp rnacentral/r2dt
   

   • -it - start an interactive session

   • make the current working directory available inside the container as /rna/r2dt/temp:

     -v `pwd`:/rna/r2dt/temp
     

   Any file placed in /rna/r2dt/temp within the container will be available on the host machine after the Docker container exits. The current directory is mounted inside the container so that all code and data changes are instantly reflected in the container.

Note

Starting with version 2.2, downloading a precomputed library is no longer necessary. For older versions, however, you must download the library manually and mount it inside the container using Docker’s -v option. For example:

curl -O -L https://github.com/r2dt-bio/R2DT/releases/download/v2.0/cms.tar.gz
tar -xzf cms.tar.gz
export R2DT_LIBRARY=<path to precomputed library>
docker run -it -v $R2DT_LIBRARY:/rna/r2dt/data/cms -v `pwd`:/rna/r2dt/temp rnacentral/r2dt

Setup a development environment

To set up a development container, you can use just by running the following commands:

# Display available commands
just

# Start the development container
just run

Alternatively, if you prefer not to use just, you can manually execute the commands listed in the justfile to achieve the same result.

Manual installation

If it is not possible to use containers, follow instructions in the base Dockerfile and main Dockerfile to install all the requirements manually.