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:21.1.0-0.15.0-4f26aeaf

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:21.1.0-0.15.0-4f26aeaf \
    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:21.1.0-0.15.0-4f26aeaf

Running with custom atomic weights

You are able to calculate average molecular mass from custom atomic weights by providing molar masses in the elements.txt.

docker run \
    --name=bmt \
    -p 8080:8080 \
    -e CHEMAXON_HOME=/usr/local/chemaxon \
    -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 \
    -v path/to/elements.txt:/usr/local/chemaxon/elements.txt \
    -d \
    hub.chemaxon.com/cxn-docker-release/chemaxon/biotoolkit:21.1.0-0.15.0-4f26aeaf

Running with Standardizer

Molecules can be passed through the customized list of standardization actions of Standardizer to derive the desired chemical form. Standardizer is a licensed Chemaxon product. To learn more about Standardizer click here

docker run \
    --name=bmt \
    -p 8080:8080 \
    -e CHEMAXON_HOME=/usr/local/chemaxon \
    -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 \
    -v path/to/standardizerConfiguration.xml:/data/bioreg-home/standardizerConfiguration.xml \
    -d \
    hub.chemaxon.com/cxn-docker-release/chemaxon/biotoolkit:21.1.0-0.15.0-4f26aeaf