Installation

Installation

Dependency

• gcc 4.8+ or clang 3.4+ and cmake 3.2+ is needed
• Only python3 is supported
• CIRI-long requires pysam lib, which need executable binary and header of zlib, bzip2, xz, please refer to documentation of pysam for installation instructions
• all python dependencies are listed in requirements.txt
• samtools version 1.9 or higher
• python binding of minimap2

Install CIRI-long from source code

Installation under virtualenv is highly recommended. You can simply clone the whole repository, then use make to start a complete installation

git clone https://github.com/bioinfo-biols/CIRI-long.git CIRI-long
cd CIRI-long

# Create virtual environment
python3 -m venv venv

# Activate virtualenv
source ./venv/bin/activate

# Install CIRI-long
make

# Test for installation
make test

The package should take less than 1 min to install on a normal computer.

Install CIRI-long using pip

pip install CIRI-long