Installation

Requirements

• Python >= 3.10

• MongoDB (for subcommands that query/insert data)

Which path to use

• Modern Linux / macOS (glibc >= 2.28, i.e. Ubuntu >= 18.04, RHEL/CentOS >= 8, Debian >= 10): plain pip install jasentool works — current pandas / numpy ship binary wheels for these platforms.

• Older Linux (glibc < 2.28): pip will not find matching binary wheels for current pandas / numpy on Python 3.12 and will fall back to source builds that require GCC >= 9.3. Use the conda from-source path below instead — conda-forge ships its own compatible binaries.

pip

pip install jasentool

From source

git clone https://github.com/SMD-Bioinformatics-Lund/jasentool.git
cd jasentool
pip install .

Development install

Install with optional dev dependencies (linting, formatting):

pip install ".[dev]"

conda

From PyPI

conda create -n jasentool python=3.11
conda activate jasentool
pip install jasentool

From source (recommended for older Linux)

git clone https://github.com/SMD-Bioinformatics-Lund/jasentool.git
cd jasentool
conda env create -f environment.yml
conda activate jasentool

environment.yml installs every binary-heavy dependency (pandas, numpy, matplotlib, biopython, pysam, cyvcf2, openpyxl) from conda-forge and then performs an editable (-e .) pip install of jasentool itself.

Verify installation

jasentool --help