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update readme
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JoshuaHess12 committed Apr 20, 2021
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Expand Up @@ -15,8 +15,9 @@ All steps can be run using YAML files in conjunction with the function 'RunHDIpr
All image processing can be run with dependecies installed via Docker, the command_hdi_prep.py code, and entering the path to a .yaml file that contains processing steps as follows:
1. Install [Docker](https://www.docker.com) on your machine.
2. Check that Docker is installed with `docker images`
3. Place your data in the Docker container and enter shell with `docker run -it -v /path/to/data:/data joshuahess/hdi-prep:v1.0.1 bash`
4. Run the pipeline with your new data using the following command:
3. Pull the hdi-prep docker container `docker pull joshuahess/hdi-prep:latest` where latest is the version number.
4. Mount your data in the Docker container and enter shell with `docker run -it -v /path/to/data:/data joshuahess/hdi-prep:latest bash`
5. Run the pipeline with your new data using the following command:
```bash
python app/command_hdi_prep.py --path_to_yaml /data/yourfile.yaml --out_dir /data
```
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