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LDA-LncRNADiseaseAssociation

Build

There are two ways to build this project:

  • manually build using Maven
  • automated build using docker-compose

Maven Build

The Maven build will create the jar file into target/ folder.

mvn clean install

Docker Build

The Docker build will create the jar file into target/ folder.

docker-compose up

The docker script requires to setup the maven local repository, in order to avoid the download of the packages for each build. To this end, modify the line

    volumes:
    - ...
    - your_local_directory:/root/.m2 # TODO: change "your_local_directory" with the path to the local .m2 package repository
    command: ...

Generally, the .m2 folder is placed into C://Users/<You>/.m2 or /Users/<You>/.m2.

Execution

The execution of the jar via terminal is done with this command:

java -jar ./target/lda.jar <arguments>

There are several arguments that can be used. For more information use the argument -h. Using the -h argument will print the helper, ignoring the other arguments. If no arguments are specified, the helper will be shown automatically.

Example of execution with results save in specified output

An example of execution is:

java -jar ./target/lda.jar -f auc -m pvalue -o C:\\<user>\Documents\result_folder

will execute the software with model pValue and will save the results of predictions in the given folder. The output consists of a csv with header sorted alphabetically by couple lncRNA-disease.