Running PIA via the command line

To run PIA via the command line, you can either download the latest PIA release or pull the PIA Docker container. The Docker container has the Java execution of the JAR file as entrypoint, so the runtime arguments can directly be appendend e.g. for --help just run:

docker run --rm julianusz/pia:latest --help

To call PIA by the means of Java, you need to run the same command like

java -jar pia-X.Y.Z.jar --help

It might be necessary to increase the heap space for Java. To increase it to e.g. 8GB with the -Xmx parameter call PIA like

java -Xmx8G -jar pia-X.Y.Z.jar --help

Compiling files into a PIA intermediate file

The compilation is used to speed-up all following analyses by structuring and sorting the data. This step is needed only once per set of search engine results.

To run a compilation, call PIA with the mandatory parameters for outfile (after the -o) and infiles (all other arguments, shoudl point to search engine result files).

java -jar pia-X.Y.Z.jar --compile -o /path/for/pia-compilation.xml /data/in/search_result1.dat /data/in/search_result2.idXML [more search results]

For the Docker command, you need to mount the data input and output volumes (please refer to the Docker hub page).

Running an analysis with a parameter file

The command line allows you to execute an analysis via prior defined analysis in JSON format. Additionally to the json file, the prior compiled intermediate file must be given.

java -jar pia-X.Y.Z.jar pia-analysis.json pia-compilation.xml

Analysis in JSON format

To view an example JSON analysis file, you can simply execute:

java -jar pia-X.Y.Z.jar --example`