Docker/README.md

In TRON-Bioinformatics/splice2neo: Aberrant splice junction analysis with associated mutations

Container support

We provide a Singularity and a Docker image that contains all software pre-installed for running the splice2neo analysis. However, singularity is our preferred method for running splice2neo as it allows unprivileged users to run the application in a container.

Singularity

To use the the singularity image, you have to first build it from the definition file. Please make sure you have fakeroot permissions or ask your sysadmin to build the image.

singularity build --fakeroot splice2neo.sif splice2neo.def

To run the analysis, bind your input directory into the container. The container ships the HG19 version of BSgenome.

Script usage

singularity exec -e -B `pwd` -B /path/to/your/inputs splice2neo.sif Rscript splice2neo.R

Interactive usage

singularity shell -B `pwd` -B /path/to/your/inputs splice2neo.sif

Within the container you can now open a R-Session and execute the commands.

Docker / podman

We use podman to build and manage our Docker images. Podman is API compatible with Docker and provides unprivileged execution of images.

podman build -t tronbioinformatics/splice2neo:"${TAG}" .

TRON-Bioinformatics/splice2neo documentation built on Nov. 9, 2024, 5:28 p.m.