troubleshooting - ampinzonv/BB3 GitHub Wiki

Common Errors and Solutions

1. Permission Error:

   • Problem: Error: You do not have write permissions for /path/to/directory.
   • Solution: Run the script with sudo or choose a directory where you have write permissions.

2. Missing Dependencies:

   • Problem: Error: Required command 'blastn' not found.
   • Solution: Install the BLAST+ tools:

     # On Ubuntu/Debian
     sudo apt-get install ncbi-blast+
     
     # On macOS with Homebrew
     brew install blast
     

3. Error Loading BioBASH:

   • Problem: bb_* commands not available after installation.
   • Solution: Verify that the correct lines are in your configuration file and that you've loaded it with source.

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OS-Specific Adjustments

For macOS:

• If you use Zsh as your default shell, modify ~/.zshrc instead of ~/.bash_profile.
• For zcat, you may need to install GNU coreutils with Homebrew:

  brew install coreutils
  

For Linux:

• On some distributions, you may need to explicitly install ncbi-blast+.
• Ensure you have sufficient permissions to write to bin.

Additional Notes

• BioBASH is designed to work with common biological files such as FASTA, FASTQ, and BLAST results.
• The installation directory contains individual scripts for different functionalities.
• All functions have built-in documentation accessible when invoking the function without any argument.
• The $BIOBASH_HOME variable is crucial for proper operation - do not modify it manually.