Load Sample Cancer Study

Once you have initialized MySQL with the seed database, you are ready to import a sample cancer study. This is recommended, so that you can verify everything is working.

Download the Sample Study

To get started, download the sample study: brca-example-study.tar.gz.

Then, unpack and move the directory into your root cbio portal development directory. The directory should be called portal-study.

Import the Sample Study

This is done in a few steps:

First, load the meta-data for the sample study:

$PORTAL_HOME/core/src/main/scripts/cbioportalImporter.py --jvm-args "-cp $CATALINA_HOME/lib/mysql-connector-java-5.0.8-bin.jar:$PORTAL_HOME/core/target/core-1.0-SNAPSHOT.jar" --command import-study --meta-filename portal-study/meta_study.txt

Then, load copy number, mutation data and expression data:

$PORTAL_HOME/core/src/main/scripts/cbioportalImporter.py --jvm-args "-cp $CATALINA_HOME/lib/mysql-connector-java-5.0.8-bin.jar:$PORTAL_HOME/core/target/core-1.0-SNAPSHOT.jar" --command import-study-data --meta-filename portal-study/meta_CNA.txt --data-filename portal-study/data_CNA.txt

$PORTAL_HOME/core/src/main/scripts/cbioportalImporter.py --jvm-args "-cp $CATALINA_HOME/lib/mysql-connector-java-5.0.8-bin.jar:$PORTAL_HOME/core/target/core-1.0-SNAPSHOT.jar" --command import-study-data --meta-filename portal-study/meta_mutations_extended.txt --data-filename portal-study/data_mutations_extended.txt

$PORTAL_HOME/core/src/main/scripts/cbioportalImporter.py --jvm-args "-cp $CATALINA_HOME/lib/mysql-connector-java-5.0.8-bin.jar:$PORTAL_HOME/core/target/core-1.0-SNAPSHOT.jar" --command import-study-data --meta-filename portal-study/meta_expression_median.txt --data-filename portal-study/data_expression_median.txt

Lastly, load the case sets:

$PORTAL_HOME/core/src/main/scripts/cbioportalImporter.py --jvm-args "-cp $CATALINA_HOME/lib/mysql-connector-java-5.0.8-bin.jar:$PORTAL_HOME/core/target/core-1.0-SNAPSHOT.jar" --command import-patient-list --meta-filename portal-study/case_lists

Important

Please note that these data files are intentionally small, and do not contain all genes or all samples. Therefore, wen you deploy in the next step, and search for, e.g. BRCA1, you may not see any mutations. If you want to see mutations, try searching for: ACVR1B.