PyMOL is a great program that runs natively on all 3 major platforms. However, I wanted to use a docker image that allegedly can run PyMOL (albeit an older version 1.8.2.) The reason might not …
Docker
Dockerization – details needed
Reproducible research Docker is a great tool to provide methods for reproducible research that should allow other researchers to reproduce any advanced calculations that you, as a researcher have done, most likely in association with …
Survival command line
The built-in Terminal in MacOS and Linux and in Windows with added software provides access to the core of the computer. They are simply a software version (an emulation) of what used to be a hardware …
Docker saves the day – Roadmaps – rivem
Edit: April 8, 2025 Images were updated to remove the error that presented the roadmap in a mirror image. Docker saves the day! Here is a great example of how Docker can help save a …
Docker notes – Shell Access to Running Container
In some instances we start a container, but it will default to immediately running a program within and prevent immediate shell access. This is possible since Docker version1.3 Assuming that the container is already running …
Docker notes – Bypass entrypoint
When activated by docker run some docker container immediately start a software within. This can be useful for the author of the image, but for others it may cause issues. Here is one example amongst many, …
Docker notes – Remove stopped containers
As I am creating the docker tutorials “for biologists” I find that having some notes here could be useful. This is therefore a bit like a Frequently Asked Questions (FAQ) that I answer to myself …
Preparing Docker tutorials for biologists
Docker Containers I don’t remember how exactly I discovered Docker containers a bit over a year ago, but it seemed a very good system and I immediately saw the potential, then I thought that it …