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.
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:
Generate the information.lic file with the following command:
- Go to www.blast2go.com/cli-activation to upload the information.lic, provide your Activation Key and your Email.
- The Blast2GO support team will create a license.lic file which has to be placed in the same folder as the blast2go cli executable.
- 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:
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:
Do not extract the database dump, instead import it as follows:
Find the corresponding lines in the Blast2GO cli.prop file and modify them accordingly:
- For more details on how to configure your mongo URI go to https://docs.mongodb.com/manual/reference/connection-string
- The configuration has been tested with mongod v3.4.6, it should work with any higher version as well.
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)