Setup

System Requirements

Blast2GO Command Line is a Java application and can be run on Mac, Linux and Windows 64-bit systems. It is necessary to have Java 64-bit HotSpot version 11+ installed.

Download Adopt Open JRE here: https://adoptopenjdk.net/releases.html?variant=openjdk11&jvmVariant=hotspot

At least 2 GB of RAM is recommended. For the GO Mapping step, the Blast2GO database has to be imported into a MongoDB server, it occupies about 20 GB.

In general this program works offline, however, the CloudBlast and InterProScan depend on a working internet connection.

Product Activation

Blast2GO offers 2 types of product activation. Either bound to specific hardware or via a floating license. Floating licenses are served by an RLM license server in the same network and the setup instructions are provided upon request. This section describes how to activate the product on a specific hardware (either for evaluation or perpetual). You will need your Activation Key for these steps. The license can be obtained automatically from www.blast2go.com/cli-activation. To do so, a signature of the workstation has to be generated first. The command line parameter -createkeyfile will generate such a file named information.lic.
Note: On MS Windows all the following commands starting with ./blast2go cli.run must be replaced with blast2go cli.exe.
Steps to activate the Blast2GO Command Line:

  1. Generate the information.lic file with the following command:

    ./blast2go_cli.run -createkeyfile
  2. Go to www.blast2go.com/cli-activation to upload the information.lic, provide your Activation Key and your Email.
  3. The Blast2GO support team will create a license.lic file which has to be placed in the same folder as the blast2go cli executable.
  4. You can check the details of your license file with the option -showlicenseinfo

You can now continue with the GO Mapping database installation (See section 2.4) and have a look at the example use cases.

Create a Properties File

The Blast2GO Command Line needs a properties file, that contains all the information of the different parameters that can be changed for the analysis. The properties file is created with this command:

./blast2go_cli.run -createproperties cli.prop

Once this file has been created it is possible to edit it with a text editor. An editor with syntax highlighting is recommended since it allows us to better distinguish between comments and parameters.

Setting up a local Blast2GO Database

In order to set up a local GO Mapping database, please install MongoDB 3.4.X or higher, make sure that the server is running, and import one of the data-dumps provided by us.

Regarding MongoDB, please follow the official instructions for installation: https://docs.mongodb.com/manual/administration/install-on-linux

Make sure mongod is running, you should start mongod and check for error messages. On Ubuntu Linux, /data/db is not created automatically and starting mongod therefore fails. You can either create the folder or change the default database folder in mongo.conf (/etc/mongo.conf).

Blast2GO database dumps can be downloaded from:

https://resources.biobam.com/go_mapping_dumps/index.html

# set to the version you just downloaded
DB_VERSION=2019_10
wget -c https://resources.biobam.com/go_mapping_dumps/$DB_VERSION.gz
wget -c https://resources.biobam.com/go_mapping_dumps/$DB_VERSION.gz.md5
md5sum -c $DB_VERSION.gz.md5

Do not extract the database dump, instead import it as follows:

# set to your MongoDB server IP - 127.0.0.1 is an example for localhost
MONGODB_SERVER=127.0.0.1
mongorestore --host $MONGODB_SERVER --db go_db --collection $DB_VERSION --gzip --archive=$DB_VERSION.gz

Find the corresponding lines in the Blast2GO cli.prop file and modify them accordingly:

// ** GoMappingDirectParameters **
// Please specify your MongoDB connection URI:
// https://docs.mongodb.com/manual/reference/connection-string
GoMappingDirectParameters.mongoUri=mongodb://<MONGODB-SERVER-IP>/go_db

// This is the name of the MongoDB collection to be used.
GoMappingDirectParameters.collectionName=<MONGODB-VERSION>


Please consider the following for your mongod.conf:

  • disable journaling (we will only be reading from this database)
  • set wiredTiger as engine (default in newer MongoDB versions)
storage:
  # Where and how to store the database. You will need about 25 GB at least - database will not grow, unless you install another version on top.
  dbPath: /var/lib/mongodb
  journal:
    # journaling is not necessary
    enabled: false
  # Use this storage engine.
  engine: wiredTiger

net:
  # Change the IP address binding if necessary and take it into account for the MongoURI.
  port: 27017
  bindIp: <MONGODB-SERVER-IP>