@@ -11,7 +11,7 @@ A specific project's translation script can be executed either in an app like ma
This is a quick tour on how to build and run the Docker container through different scenarios. This is not a lecture on containerisation in general, nor Linux/ Unix, shell scripting or programming. But if you encounter a specific problem, feel free to ping the [MA team](https://modelarchive.org/contact).
This section describes three use cases of the Docker container (including a build-how to per use case) but starts with a short primer of what is common to all scenarios described here.
This section describes four use cases of the Docker container (including a build-how to per use case) but starts with a short primer of what is common to all scenarios described here.
### Prerequisites
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@@ -30,25 +30,51 @@ Since the Docker container will run as a dedicated, non-root user, it is advisab
$whoami
localuser
$id
uid=12345(localuser) ...
uid=(localuser) ...
$
```
Look for the `uid` in the output of `id`. In the example above, `12345` is the ID of user `localuser`, currently logged in and executing the commands.
Look for the `uid` in the output of `id`. In the example above, `1234` is the ID of user `localuser`, currently logged in and executing the commands.
One last thing that is needed for the example runs of the Docker container is data. For simplicity, we assume that a directory `/home/user/models` exists on the local computer executing a converter, full of modelling data.
### Run a fixed converter from within the Docker container (app-like)
This use case comes closest to having a Docker container that works like a [ModelCIF](https://mmcif.wwpdb.org/dictionaries/mmcif_ma.dic/Index/) converter app, that you can
- hand over to others
- send to a compute cluster
- turn into a [Singularity](https://sylabs.io/singularity/) image
and it works out of the box.
The idea is to copy a translation script from one of the [projects](projects/) into the Docker image along with all the software needed to run it. That enables you to start the script as a command with [`docker run`](https://docs.docker.com/engine/reference/run/).
The whole build of the Docker image, including installing necessary software and copying the translation script, is covered by our [Dockerfile](./Dockerfile). You just need to specify the translation script by [build time argument](https://docs.docker.com/engine/reference/commandline/build/#set-build-time-variables---build-arg)`CONVERTERSCRIPT` during [`docker build`](https://docs.docker.com/engine/reference/commandline/build/). By default, the translation script is renamed to `convert2modelcif` to be called as a command. This can be overwritten using build time argument `CONVERTERCMD`. There is also an alias `2cif` to the converter command, which is immutable.
The following command will build a Docker image named `converter` (with tag `latest`). The translation script will be copied from [`USDA-ASFVG/translate2modelcif.py`](projects/USDA-ASFVG/translate2modelcif.py) and made available as `convert2modelcif` in the Docker image/ `docker run`. By `MMCIF_USER_ID`, we use UID `1234` for the internal user of the Docker image, so mounted files have the right owner inside and outside of the Docker container (assuming the example user from above). Pay attention to the alternative Dockerfile location specified by `-f docker/Dockerfile`, as we are calling `docker build` from the [projects](projects/) subdirectory to get the right build context:
```terminal
$# DOCKER_BUILDKIT=1 is only needed for older versions of Docker.
