Installation

Prerequisites

Required Software

1. Python 3.7+ with pandas
2. UCSC Command-line Tools:
   • gtfToGenePred - Convert GTF to genePred format
   • genePredToBed - Convert genePred to BED format
   • bedToBigBed - Convert BED to bigBed format
   • ixIxx - Create Trix search indexes

Installation Methods

Option A: Automatic Installation (Recommended)

# Clone the repository
git clone https://github.com/conesalab/SQANTI-browser.git
cd SQANTI-browser

# Install UCSC tools
bash install_ucsc_tools.sh

# Install Python dependencies
pip install -r requirements.txt

Option B: Manual Installation

1. Download UCSC Tools

Linux:

wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/gtfToGenePred
wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/genePredToBed
wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/bedToBigBed
wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/ixIxx

chmod +x gtfToGenePred genePredToBed bedToBigBed ixIxx
sudo mv gtfToGenePred genePredToBed bedToBigBed ixIxx /usr/local/bin/

macOS:

wget http://hgdownload.soe.ucsc.edu/admin/exe/macOSX.x86_64/gtfToGenePred
wget http://hgdownload.soe.ucsc.edu/admin/exe/macOSX.x86_64/genePredToBed
wget http://hgdownload.soe.ucsc.edu/admin/exe/macOSX.x86_64/bedToBigBed
wget http://hgdownload.soe.ucsc.edu/admin/exe/macOSX.x86_64/ixIxx

chmod +x gtfToGenePred genePredToBed bedToBigBed ixIxx
sudo mv gtfToGenePred genePredToBed bedToBigBed ixIxx /usr/local/bin/

2. Install Python Dependencies

pip install pandas

Option C: Conda Installation

conda install -c bioconda ucsc-gtftogenepred ucsc-genepredtobed ucsc-bedtobigbed ucsc-ixixx
pip install pandas

Verify Installation

Run the test script to verify everything is installed correctly:

python test_installation.py

Expected output:

Testing UCSC tools...
  ✓ gtfToGenePred - Found
  ✓ genePredToBed - Found
  ✓ bedToBigBed - Found
  ✓ ixIxx - Found
  All UCSC tools are available!

Testing Python dependencies...
  ✓ pandas - Available
  All Python dependencies are available!

🎉 All tests passed!

Troubleshooting

Tools not found in PATH

If tools are installed but not found, add them to your PATH:

export PATH="/path/to/ucsc/tools:$PATH"

Add this line to your ~/.bashrc or ~/.zshrc to make it permanent.

Permission denied

If you get permission errors when installing to /usr/local/bin/:

# Install to user directory instead
mkdir -p ~/bin
mv gtfToGenePred genePredToBed bedToBigBed ixIxx ~/bin/
export PATH="$HOME/bin:$PATH"