Installation

FinaleToolkit needs Python 3.10 or newer. The filter-file command also needs samtools, bedtools, bgzip, and tabix on your PATH (conda install -c bioconda samtools bedtools htslib).

Install into a clean environment:

$ conda create -n finaletoolkit python=3.11 -y
$ conda activate finaletoolkit
$ pip install finaletoolkit

$ python3 -m venv .venv
$ source .venv/bin/activate
$ pip install finaletoolkit

$ git clone https://github.com/epifluidlab/finaletoolkit.git
$ cd finaletoolkit
$ pip install -e .

Then verify it:

$ finaletoolkit --version

Troubleshooting

  • ImportError on macOS: install a current curl (brew install curl).

  • NumPy ``_ARRAY_API not found``: a package in ~/.local was built against an incompatible NumPy. Run with PYTHONNOUSERSITE=1 or remove it.

  • Anything else: open an issue on the tracker with a reproducible example, the error output, and your finaletoolkit --version.