Installation

Installation

Requirements

• Python ≥ 3.8
• That's it — nanoTimeSort has no third-party dependencies (pure standard library).

From PyPI (recommended)

pip install nanotimesort

From Bioconda

conda install -c conda-forge -c bioconda nanotimesort

⏳ The bioconda recipe is currently under review (bioconda/bioconda-recipes#70005). Until it is merged, use the PyPI install above.

From GitHub

pip install git+https://github.com/duceppemo/nanoTimeSort.git

or clone first:

git clone https://github.com/duceppemo/nanoTimeSort.git
cd nanoTimeSort
pip install .

Both install the nanotimesort command.

In a conda environment

conda create -n nanotimesort python=3.12 pip
conda activate nanotimesort
pip install nanotimesort

For development

git clone https://github.com/duceppemo/nanoTimeSort.git
cd nanoTimeSort
pip install -e .[dev]   # adds pytest and ruff
pytest                  # run the test suite

Verify the installation

nanotimesort --version
# nanoTimeSort v1.0.0

Upgrading from v0.1 (nanopore_reads_binner.py)

The old script is deprecated but still works as a thin wrapper around the new CLI, with the same flags (-f, -o, -i, -p, -t). Just replace:

python nanopore_reads_binner.py -f fastq/ -o out/ -i 1h -p sample

with:

nanotimesort -f fastq/ -o out/ -i 1h -p sample

Output file naming is unchanged ({prefix}_0-{end}{unit}_{reads}reads_{bp}bp.fastq.gz). The numpy and python-dateutil dependencies of v0.1 are no longer needed.