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The Seven Bridges Platform is a simple solution for doing bioinformatics at industrial scale. But sometimes, everyone needs a little help.

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Seven Bridges Command Line Interface

Overview

Use the Seven Bridges Command Line Interface (SB CLI) to programmatically access and automate your interaction with the Platform via the API. The CLI is called by a simple command: sb.

The Seven Bridges Command Line Interface can be installed using an automated procedure or manually, as shown below.

Automated installation for Linux and macOS

Perform an automated installation with the following command:

curl https://igor.sbgenomics.com/downloads/sb/install.sh -sSf | sudo sh

During the installation, the script will:

  1. Download the SB binary.
  2. Install the SB binary.
  3. Enable bash completion for SB. Note that this only works with bash completion version 4, which should have been previously installed.
  4. Add man pages for SB.

During the procedure you will see information on whether each of the steps were successful or not. Upon completion, the script will inform you if SB has been successfully installed.

Manual installation for Linux, macOS, and FreeBSD

  1. Download the SB executable file for your environment:
    Linux

    macOS

    FreeBSD

  2. Change file permissions so you are able to run the executable (chmod +x sb).

  3. (Optional) Manually add bash completion for SB:
    a) for Linux
sb gen completion --type bash --completionfile /etc/bash_completion.d/sb.bash-completion
b) for macOS with Brew installed
sb gen completion --type bash --completionfile $(brew --prefix)/etc/bash_completion.d/sb.bash-completion
  1. (Optional) Add manual pages for SB:
sb gen man --dir `manpath | cut -d ':' -f 1`

Windows Installation

  1. Download the SB executable file for Windows:

Configure credentials

Prior to using the Seven Bridges Command Line Interface, you must enter your credentials to authenticate with the Platform. For this, you will need to know the following information:

  • API endpoint for the Seven Bridges Platform: https://api.sbgenomics.com
  • Your authentication token.

  • Launch the command line and enter the following:

sb configure
  1. Enter the API endpoint when prompted.
  2. Enter your authentication token.

Learn more about storing your credentials in a unified configuration file.

Specify your profiles

The Seven Bridges Command Line Interface allows you to use profiles for the credentials allowing you to access multiple user accounts. Each profile contains an endpoint and an auth token. The profiles are set up within the configuration file.

Use the following option to specify a profile:

--profile <profile_name>

Next step

Once you’ve installed and configured the Seven Bridges Command Line Interface as described above, check out our Seven Bridges Command Line Interface Reference to get started.

Seven Bridges Command Line Interface


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