file-setup/README.md

# File setup

This software implements a parallelized pipeline to setup image files. It is used for nopaque's File setup service but you can also use it standalone, for that purpose a convenient wrapper script is provided.

## Software used in this pipeline implementation
- Official Debian Docker image (buster-slim) and programs from its free repositories: https://hub.docker.com/_/debian


## Use this image

1. Create input and output directories for the pipeline.
``` bash
mkdir -p /<my_data_location>/input /<my_data_location>/output
```

2. Place your images files inside a directory in `/<my_data_location>/input`.

3. Start the pipeline process. Check the pipeline help (`file-setup --help`) for more details.
```
# Option one: Use the wrapper script
## Install the wrapper script (only on first run). Get it from https://gitlab.ub.uni-bielefeld.de/sfb1288inf/file-setup/-/raw/1.0.0/wrapper/file-setup, make it executeable and add it to your ${PATH}
cd /<my_data_location>
file-setup -i input -o output

# Option two: Classic Docker style
docker run \
    --rm \
    -it \
    -u $(id -u $USER):$(id -g $USER) \
    -v /<my_data_location>/input:/input \
    -v /<my_data_location>/output:/output \
    gitlab.ub.uni-bielefeld.de:4567/sfb1288inf/file-setup:1.0.0 \
        -i /input \
        -o /output
```

4. Check your results in the `/<my_data_location>/output` directory.