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update README
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berombau committed Sep 11, 2024
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## Installation

For the best polyglot experience on Linux, we recommend using [Pixi](https://pixi.sh/latest/) to manage your development environment. Environment creation support for Pixi on Windows and MacOS ARM is currently limited for R packages. Installation of the R dependencies in Pixi is more difficult, because Pixi does not support [post-link scripts](https://github.com/prefix-dev/pixi/issues/1573) and the bioconda channel for bioconductor packages does not yet support [osx-arm64](https://github.com/bioconda/bioconda-recipes/issues/33333).
For the best polyglot experience on most platforms, we recommend [renv](https://rstudio.github.io/renv/articles/renv.html) to manage the R and Python dependencies, see below for instructions.

Alternatively for Linux, you can use [Pixi](https://pixi.sh/latest/) to manage your development environment. Environment creation support for Pixi on Windows and MacOS ARM is currently limited for R packages. Installation of the R dependencies in Pixi is more difficult, because Pixi does not support [post-link scripts](https://github.com/prefix-dev/pixi/issues/1573) and the bioconda channel for bioconductor packages does not yet support [osx-arm64](https://github.com/bioconda/bioconda-recipes/issues/33333).

In a clean Linux shell without any active Python (`deactivate`) or Conda environments (`conda deactivate`), you can install all dependencies with the following command:

```bash
pixi install -a
```

For MacOS ARM and Windows, we recommend using Docker. For R users, we recommend `renv` to manage the R and Python dependencies.
For MacOS ARM and Windows, we recommend using Docker.

## Linux

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### Building the Docker image yourself

To edit and build the Docker image yourself, use can use the following command.:
To edit and build the Docker image yourself, use can use the following command.

```bash
docker build -t polygloty-docker .
docker run -it -v $(pwd)/usecase:/app/usecase -v $(pwd)/book:/app/book polygloty-docker pixi run pipeline
```

To publish it to Docker Hub, use the following command:
To publish it to Docker Hub, use the following command. It's a multi-architecture image that supports both ARM and AMD64, so make sure to assign enough memory (~32 GB) and disk resources (~100 GB) to Docker to build it.

```bash
docker login
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