Docker image for running leafcutter and dasper

Contents

This repository contains the instructions to create the auto_splice docker image. This docker image contains:

1. A working installation of leafcutter and dasper. This includes the leafcutter dependencies regtools and samtools in the directory /tools/.
2. An ".exons" file created by applying the leafcutter script gtf_to_exons.R to the Ensembl v104 GTF. This is stored in the directory /data/gtf/.
3. An "auto_dasper.R" script for running dasper stored in the directory /home/rstudio/auto_splice.

Check version of leafcutter and dasper installed

# you may need to replace "docker" with "sudo docker"
docker run dzhang32/auto_splice:1.0 Rscript -e "packageVersion('leafcutter')"
docker run dzhang32/auto_splice:1.0 Rscript -e "packageVersion('dasper')"

Running auto_dasper.R

docker run dzhang32/auto_splice:1.0 Rscript /home/rstudio/auto_splice/auto_dasper.R --help

Start R Studio server instance on this docker image

In order to run leafcutter or dasper, you may want to start an RStudio server instance on this docker image. This docker image inherits from rocker and has RStudio Server pre-installed. My guide on how to set-up RStudio server within a rocker-based image on a remote server can be found here. Additionally, you may find the Bioconductor docker help page useful too.