instructions.md

docker setup

Easiest: go to supermicro, get rnaseq_docker.tar. Skip to the 'import' instructions, and then to the 'start docker container' part.

Notes on how image was made and how to use.

This is a quick hack together of things and my Docker foo could be... better. It is in no-way a good practice example.

build docker image

sudo docker build -t rnaseq --rm .

start docker container

Do this from the parent directory of the 'rnaseq-workshop' repository, so that the mounted folder contains the repository

sudo docker run -it --name rnalive --rm --mount type=bind,source="$(pwd)"/rnaseq-workshop,target=/home/zim-gast/rnaseq-workshop rnaseq:latest

Note difference to user instructions with --rm, so you don't end up with tons of copies of the same container, nor naming conflicts.

This should open a prompt in the container. Start with cd rnaseq-workshop, and hopefully after that things should run about the same as before. Except that Rstudio is not installed in this docker, but rather a second one.

clean up (e.g. if you've been making a lot of failed builds and want some HD space back)

sudo docker container prune
sudo docker image prune

export

first run the following to get the image ID from the tag / name

sudo docker image save rnaseq:latest > rnaseq_docker.tar

import

sudo docker image load -i rnaseq_docker.tar