Docker

To not miss a post like this, sign up for my newsletter to learn computational biology and bioinformatics. I have been writing blog posts for over 10 years. I was using blogspot and in 2018, I switched to blogdown and I love it. My blogdown website divingintogeneticsandgenomics.com was using Hugo v0.42 and blogdown v1.0. It has been many years and now I have a macbook pro with an M3 chip. I could not install the old versions of the R packages to serve the site.

Sign up for my newsletter to not miss a post like this https://divingintogeneticsandgenomics.ck.page/newsletter Start here Docker is a great tool to ensure reproducibility of your computing work. I was using the bioconductor image on google cloud, but the image does not have the gsutil command. You can install once in the container, but once you exit the container, the gsutil command will be gone. You will need to modify the docker image if you want to keep using it.

Create a google VM Follow the process using the console https://cloud.google.com/compute/docs/instances/create-start-instance#console_1 Install docker Follow https://docs.docker.com/engine/install/debian/ Note this example for the debian build. If you created your VM using ubuntu as the boot disk, you should follow the ubuntu section https://docs.docker.com/engine/install/ubuntu/. In the GCP VM: sudo apt-get update sudo apt-get install \ ca-certificates \ curl \ gnupg \ lsb-release sudo mkdir -p /etc/apt/keyrings curl -fsSL https://download.docker.com/linux/debian/gpg | sudo gpg –dearmor -o /etc/apt/keyrings/docker.

Background Please read the following before go ahead: what is docker? what is Rocker? what is singularity? from Harvard Research computing website: Odyssey has singularity installed. Why Singularity? There are some important differences between Docker and Singularity: Docker and Singularity have their own container formats. Docker containers may be imported to run via Singularity. Docker containers need root privileges for full functionality which is not suitable for a shared HPC environment.