Public Repository

Last pushed: 6 months ago
Short Description
RNAscClust Docker Image
Full Description

RNAscClust Docker Image
This Docker Image is an easy distributable installation of the tool RNAscClust for clustering RNA alignments, that can be used for running the provided benchmarks or other sets of alignments.

One of the main goals is to provide a very quick and hassle-free access to run the RNAscClust pipeline. The pipeline inside the docker container can run in parallel multi-core mode. However for large datasets it is recommended to have a install installation of the pipeline source package, preferably under a system with SGE grid computing computer cluster system.

Docker acquisition and usage recipe

The prerequisite of using the provided Docker image is a Docker client installed with the necessary user permissions for running a docker image.

  docker pull mmiladi/rnascclust:latest
  docker run -it -h dockersgeserver mmiladi/rnascclust:latest

The docker container will startup with providing examples on how to run the pipeline and evaluations.

Reproducing results and figures in the manuscript

Executing the following series of commands allows full reproducibility of the results and figures shown in the paper:

  #Inside the host system:
  mkdir cluster_evaluation
  docker pull mmiladi/rnascclust:latest
  docker run -it -v `pwd`/cluster_evaluation:/cluster_evaluation -h dockersgeserver mmiladi/rnascclust:latest
  # Inside the docker image:
  bash /rnascclust/bin/clustering/run_clustering_docker.sh
Docker Pull Command
Owner
mmiladi

Comments (0)