Installation

1. Pull an image from Docker Hub:

   docker pull rnacentral/r2dt
   

   Alternatively, build a Docker image locally:

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

   Or build a Singularity image:

   singularity build r2dt docker://rnacentral/r2dt
   

2. Setup a precomputed data library (198 MB, last updated Aug 21, 2023):

   curl -O https://ftp.ebi.ac.uk/pub/databases/RNAcentral/r2dt/1.4/cms.tar.gz
   tar -xzf cms.tar.gz
   export R2DT_LIBRARY=<path to precomputed library>
   

3. Verify that the installation worked:

   docker run --entrypoint r2dt.py rnacentral/r2dt draw --help
   

   Or in Singularity:

   singularity exec r2dt r2dt.py draw --help
   

4. Enter an interactive terminal session:

   docker run -it -v $R2DT_LIBRARY:/rna/r2dt/data/cms -v `pwd`:/rna/r2dt/temp rnacentral/r2dt
   

   • -it - start an interactive session

   • -v $R2DT_LIBRARY:/rna/r2dt/data/cms - mount the precomputed data library folder as /rna/r2dt/data/cms inside the container. ⚠️ Note that <path_to_cms> should be a full path.

   • 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.

Setup a development environment

Set up a precomputed library as described above and run the container using just:

# see what commands are available
just

# run the container
just run

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.