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ACTIN-Database

ACTIN-Database allows loading the outputs of other ACTIN modules into a mysql database.

Before this application can be used, a schema has to be set up on a mysql server (v5.7.21 to v8.0.18 are supported) from the database schema defined in generate_database.sql. See readme for help on additional steps and what is required to be able to compile this module.

Clinical Data Loader

The clinical data loader loads up clinical data from ACTIN-Clinical as follows:

java -cp actin.jar com.hartwig.actin.database.clinical.ClinicalLoaderApplication \
    -clinical_directory /path/to/clinical_json_files \
    -db_user user -db_pass pass -db_url url

Molecular Data Loader

The molecular data loader loads up molecular data from ACTIN-Molecular as follows:

java -cp actin.jar com.hartwig.actin.database.molecular.MolecularLoaderApplication \
    -molecular_json /path/to/molecular_json \
    -db_user user -db_pass pass -db_url url

Treatment Data Loader

The treatment data loader loads up treatment data from ACTIN-Treatment as follows:

java -cp actin.jar com.hartwig.actin.database.treatment.TreatmentLoaderApplication \
    -treatment_database_directory /path/to/treatment_database_dir \
    -db_user user -db_pass pass -db_url url

Treatment Match Data Loader

The treatment match data loader loads up treatment match results from ACTIN-Algo as follows:

java -cp actin.jar com.hartwig.actin.database.algo.TreatmentMatchLoaderApplication \
    -treatment_match_json /path/to/treatment_match_json \
    -db_user user -db_pass pass -db_url url

Version History and Download Links

  • Upcoming (first release)