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.

R2DT looks for the Traveler utils folder (providing infernal2mapping.py, enrich_json.py, and json2svg.py) in the following locations:

1. the R2DT_TRAVELER_UTILS environment variable,

2. /rna/traveler/utils (the location used in the Docker image),

3. the utils folder of the Traveler installation containing the traveler executable found in PATH.

If the folder cannot be found, R2DT prints a warning and falls back to traveler --all, which computes its own template mapping. The layouts may differ from the standard traveler --draw output and the enriched JSON/SVG files are not generated, so when installing manually make sure the Traveler utils folder is available, for example:

export R2DT_TRAVELER_UTILS=/path/to/traveler/utils

Minimal installation for drawing with known templates

Running r2dt.py draw --force_template <model_id> (including custom templates in local_data) requires only a subset of the R2DT dependencies:

• Traveler (including its utils folder, see above)

• Infernal (also provides the esl-* Easel programs)

• Bio-Easel (provides esl-alidepair.pl and the Perl modules used by the jiffy scripts)

• jiffy-infernal-hmmer-scripts (provides ali-pfam-lowercase-rf-gap-columns.pl and ali-pfam-sindi2dot-bracket.pl)

• the Python packages from requirements.txt

tRNAscan-SE, Ribovore, RNAView, RNArtist, R-scape, and RNAstructure are not used by this code path. Note that template selection (running draw without --force_template) and template-free mode require the full installation.