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  1. Home
  2. Tag: Docker

Docker

Understanding Python installation mess

Posted on November 22, 2022

Summary Useful ramblings about the difficulties to understand Python installation on macOS. In this Tutorial-like post we’ll see: – Where is Python installed, and which version – Upgrading to a new Python.org version, without replacement …

Posted in bash, bioinformatics, Computing, Docker, PythonTagged Docker, export, installation, jupyter, jupyter lab, jupyter notebook, macos, markdown, notebook, path, pip, python

bioinformatics tutorials

Posted on June 26, 2020

  June 26, 2020. I have added a new entry under the “Tutorials” menu for “bioinformatics” to provide a place for tutorials that are more than just about one subject. “bioinformatics is the science of …

Posted in Announcements, bash, bioinformatics, Docker, sequence analysis, VirologyTagged alium, bioinformatics, coronavirus, COVID19, Docker, pistil, SARS, SARS-CoV-2, sequence analysis, spike protein

Docker PyMOL

Posted on March 3, 2020

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 …

Posted in Docker, Molecular Graphics, PyMOL, X11Tagged DISPLAY, Docker, PyMOL, python, X11

Docker notes – Shell Access to Running Container

Posted on November 1, 2019

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 …

Posted in DockerTagged --it, bash, Docker, exec, rm, run, ssh

Docker notes – Bypass entrypoint

Posted on October 31, 2019

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, …

Posted in DockerTagged --it, bash, bioinformatics, Docker, docker file, entry point, ENTRYPOINT, rm, run

Docker notes – Remove stopped containers

Posted on October 24, 2019

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 …

Posted in DockerTagged Container, Docker, FAQ, remove, rm, run, stop

Preparing Docker tutorials for biologists

Posted on October 24, 2019

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 …

Posted in DockerTagged Container, Docker, FreeBSD, Kubernetes, Linux, LinuX Containers, LXC, Solaris, Unix, virtualization

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