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docker: html anchors
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falkmielke committed Feb 11, 2025
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Expand Up @@ -193,7 +193,7 @@ You can access it via a browser, going to <localhost:8787>, with the username `r
You can shut down the container with the keyboard shortcut `[ctrl]+[C]` (probably `[ctrl]+[Z] [Return]` on Windows).


## <a href="sec-mounting"></a> File Access
## <a name="#sec-mounting"></a> File Access

The downside of this is that your container is isolated (well... at least to a certain degree).

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Feel free to systematically and scientifically repeat the tests on your own machine.


## <a href="sec-permanence"></a> Container Permanence: The `--rm` Option
## <a name="#sec-permanence"></a> Container Permanence: The `--rm` Option

As briefly touched above, `docker run` comes with the `--rm` option.
This basically enables two separate workflows, i.e. usage paradigms.
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Ideally, you want to implement **version control and virtual environments within the container**, to be a "full stack open science developer".


## <a href="sec-rootless"></a> "Because Roots Are Important"[^6]: Rootless Mode
## <a name="#sec-rootless"></a> "Because Roots Are Important"[^6]: Rootless Mode

One of the main criticism about Docker is the necessity to run in a privileged user environment, which is indeed a security issue.
This may refer to the system process requiring elevated privileges, or users in the `docker` system group [effectively having superuser privileges](https://github.com/moby/moby/issues/9976).
Expand Down Expand Up @@ -613,7 +613,7 @@ This way of handling private repositories [seems to be good practice](https://st
The next best alternative would be mounting the `~/.ssh` folder from the host to the container via `-v`.


# <a href="sec-commands"></a> Useful Commands
# <a name="#sec-commands"></a> Useful Commands

We have briefly seen `docker --version`, `docker build`, `docker run`, and there are certainly more settings and tweaks on these commands to learn about.

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You can define an entrypoint in the Dockerfile (i.e. set a default), or overwrite it on each `run`.


# <a href="sec-podman"></a> Podman
# <a name="#sec-podman"></a> Podman

## Purpose

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