Importer Tool

• Introduction
• Import Cancer Type

Introduction

The page describes how to import data into the cBioPortal using Python scripts found in our scripts directory. The follow assumptions have been made:

1. The cBioPortal software has been correctly built from source.
2. The MySQL JDBC driver file is present on your filesystem.
3. The data to import is in the proper File Format.
4. The PORTAL_HOME environment variable has been properly defined as described on the Software Configuration wiki page.

Import Cancer Type

The following command is used to import cancer type data:

#!shell $PORTAL_HOME/core/src/main/scripts/cbioportalImporter.py --jvm-args "-cp /path-to-jdbc-driver/mysql-connector-java-5.1.16.jar:$PORTAL_HOME/core/target/core-1.0-SNAPSHOT.jar" --command import-cancer-type --meta-filename ~/path-to-cancer-type-file/cancer_type.txt