Run recipe - cTAKES USD

Use this when the person running the batch only needs the commands.

The plain command already uses the STAR pipeline. Leave the pipeline flag out for the normal run.

Install once

git clone https://codeberg.org/editnori/Ctakes_USD.git
cd Ctakes_USD

bash scripts/setup.sh
bash scripts/flight_check.sh

If Java is missing

bash scripts/get_java.sh
export CTAKES_JAVA_HOME="$PWD/.ctakes_deps/java/current"
bash scripts/flight_check.sh

Run the export CTAKES_JAVA_HOME=... line again in a new terminal before running cTAKES.

Run one batch

mkdir -p input/batch1
cp /path/to/site/notes/*.txt input/batch1/

bash scripts/run_pipeline.sh -i input/batch1 -o outputs/batch1

Check the output

outputs/batch1/annotations.sqlite
outputs/batch1/run_manifest.json
outputs/batch1/run_pipeline.log

Run more than one batch

input/
  batch1/
  batch2/
  batch3/

bash scripts/run_input.sh --input-root input --output-root outputs/site_run --foreground

bash scripts/run_pipeline.sh -i input/batch1 -o outputs/batch1_standard --writers standard