Running the Biomolecule Toolkit Container

The examples for running the Biomolecule Toolkit container are shown here.

Running with MySQL on localhost:3306 having database with name bioreg, with local license file

docker run \
--name=bmt \
-p 8080:8080 \
-v /path/to/license_dir:/data/bioreg-home \
-e CHEMAXON_LICENSE_URL=/data/bioreg-home/license.cxl \
-d \
hub.chemaxon.com/cxn-docker-release/chemaxon/biotoolkit:20.16.0-0.13.1-4f26aeaf 

Running with MySQL on remote host with license file on a file server

docker run \
--name=bmt \
-p 8080:8080 \
-e CHEMAXON_LICENSE_URL=http://my.license.server/bmt/license.cxl \
-e DB_URL=jdbc:mysql://my.remote.mysql.host:3306/bmt_db_name?autoReconnect=true&useUnicode=yes&characterEncoding=UTF-8 \
-e DB_USERNAME=bmt_db_user \
-e DB_PASSWORD=bmt_db_user_password \
-d \
hub.chemaxon.com/cxn-docker-release/chemaxon/biotoolkit:20.16.0-0.13.1-4f26aeaf

Running with Oracle on remote host with license file on a file server

Oracle JDBC drivers are no longer shipping with Biomolecule Toolkit. It is the responsibility of the customer to obtain the Oracle JDBC driver and add it to the BMT classpath as shown in the examples below.

The following package versions are tested with BMT:

  • com.oracle.database.jdbc:ojdbc8:19.7.0.0

  • com.oracle.database.nls:orai18n:19.7.0.0

docker run \
--name=bmt \
-p 8080:8080 \
-e CHEMAXON_LICENSE_URL=http://my.license.server/bmt/license.cxl \
-e DB_URL=jdbc:oracle:thin:@my.remote.oracle.host:myOraclePort:myOracleInstanceName \
-e DB_DRIVERCLASSNAME=oracle.jdbc.OracleDriver \
-e DB_TYPE=ORACLE \
-e DB_USERNAME=bmt_db_user \
-e DB_PASSWORD=bmt_db_user_password \
-v path/to/Oracle/packages/ojdbc8-19.7.0.0.jar:/usr/local/ojdbc.jar \
-v path/to/Oracle/packages/orai18n-19.7.0.0.jar:/usr/local/orai18n.jar \
-d \
hub.chemaxon.com/cxn-docker-release/chemaxon/biotoolkit:20.16.0-0.13.1-4f26aeaf \
java -cp /usr/local/bioreg-app.jar:/usr/local/ojdbc.jar:/usr/local/orai18n.jar org.springframework.boot.loader.JarLauncher

Running with HTTPS

docker run \
--name=biotoolkit \
-p 8443:8443 \
-v /path/to/license_dir:/data/bioreg-home \
-e CHEMAXON_LICENSE_URL=/data/bioreg-home/license.cxl \
-e spring_profiles_active=enforce-https \
-v /path/to/keystore_dir:/data/keystore_dir \
-e SERVER_SSL_KEYSTORE=/data/keystore_dir/.keystore \
-e SERVER_SSL_KEYSTOREPASSWORD=my_ssl_keystore_password \
-d \
hub.chemaxon.com/cxn-docker-release/chemaxon/biotoolkit:20.16.0-0.13.1-4f26aeaf