Installing Biobash - ampinzonv/BB3 GitHub Wiki

Step 1: Download BioBASH

The best way to get BioBash on your system is downloading the latest release and unpacking.

Alternatively you can Clone the GitHub repository:

git clone https://github.com/ampinzonv/BB3.git

After unpacking you can move to the BB3 directory:

cd BB3

Step 2: Run the Installation Script

bash biobash_install.sh

Step 3: Installation Process

Follow on screen messages. It is quite easy.

Installation Verification

To verify that BioBASH has been installed correctly:

  1. Restart your Terminal or load the configuration:

    source ~/.bashrc  # or ~/.bash_profile on macOS

  2. Test a BioBASH Function:

    bb_fastq_stats

    This should display the bb_fastq_stats function's help message.

Displaying all BioBash functions

All biobash programs begin with "bb_" followed by a descriptive name. So Just typ "bb_" (without quotes) in your terminal and hit twice the TAB key. You will see all available BioBash function as depicted below:

Detailed installation explanation

Before installing BioBASH will check you have the following components installed:

  • Operating System: Linux or macOS
  • Bash: Version 4.0 or higher
  • Dependencies:
    • blastn (part of the BLAST+ package)
    • zcat
    • awk
    • sed
    • grep

Then it will follow these steps:

  1. Environment Verification:

    • Checks that it's running in Bash.
    • Verifies all dependencies are installed.
    • Reads the current BioBASH version from the version file.

  2. Confirmation and Directory Selection:

    • Displays the BioBASH version to be installed.
    • Requests confirmation before proceeding.
    • Proposes a default installation directory (/usr/local/bin).
    • Allows you to specify an alternative directory.

  3. Permission Verification:

    • Checks if the user has write permissions in the chosen directory.
    • Creates the installation directory if it doesn't exist.

  4. File Installation:

    • Copies the main BioBASH files to the installation directory.
    • The files include:
      • biobash_core.sh: Core functions.
      • file.sh: File processing functions.
      • blast.sh: BLAST functions.
      • plot_ascii.sh: ASCII visualization functions.
      • utility.sh: Various utilities.
      • load_biobash.sh: Script to load BioBASH.
      • test_biobash_core.sh: Unit tests.
      • biobash_uninstall.sh: Uninstallation script.

  5. Bash Configuration File Update:

    • Modifies the .bashrc (Linux) or .bash_profile (macOS) file.
    • Adds the necessary lines to load BioBASH automatically: 
      # BioBASH integration
export BIOBASH_HOME="/installation/path/biobash-X.Y"
source $BIOBASH_HOME/load_biobash.sh

  6. Completion:

    • Reports successful installation.
    • Provides instructions for loading BioBASH in the current session.