Labbook

Exercice 1

docker run -it ubuntu

root@ed76dc41b28c:/# figlet 'SIB courses are great!'

---

/ | _| ) _ _ _ _ _ _ _ _ _ _ _ _ | || \ / __/ | | | | '/ |/ \/ __| / ` | '/ \ ) | || |) | | (| () | || | | __ \ /_ \ | (| | | | / |_/|__/ __/ _,|| |/_||_/ _,|_| ___|

                  _   _

_ _ _ | || | / ` | '__/ \/ ` | __| | | (| | | | / (| | ||_| _, || _|_,|_() |___/

docker run \ -it \ --mount type=bind,source=/Users/pma/02_tmp/docker_share,target=/working_dir/ \ ubuntu-figlet

docker run \ -it \ -u "$(id -u):$(id -g)" \ --mount type=bind,source=/Users/pma/02_tmp/docker_share,target=/working_dir/ \ ubuntu-figlet

for the jupyter-lab docker

docker run \ -it \ --rm \ -p 8888:8888 \ --mount type=bind,source=/Users/pma/02_tmp/docker_share,target=/working_dir/ \ jupyter-lab

ssh -i key_pallard.pem pallard@18.192.227.69

singularity pull docker://grndstt/ubuntu-figlet:v2

Piepline

snakemake nextflow

both support docker, conda and singularity

conda + docker + snakemake

snakemake --containerize

https://snakemake.readthedocs.io/en/stable/snakefiles/deployment.html?highlight=conda#containerization-of-conda-based-workflows