Installation

Spl-IsoQuant requires a 64-bit Linux system or Mac OS and Python (3.8 and higher) to be pre-installed on it. Note that Spl-IsoQuant 3.11.x and earlier versions are not well compatible with Python 3.14. No special hardware is required.

Installing via pip or conda

Spl-IsoQuant is not distributed via PyPI or bioconda and will not be published there. To install Spl-IsoQuant, use GitHub.

The original IsoQuant provides the same functionality and is available from both resources:

pip install isoquant

conda create -c conda-forge -c bioconda -n isoquant python=3.12 isoquant

Note that these install the isoquant executable, not splisoquant. If you install this way, use isoquant in place of splisoquant in all commands throughout this documentation.

Verifying your installation

To verify Spl-IsoQuant installation run

splisoquant --test

to run on toy dataset. This should typically take less than 1 minute.

If the installation is successful, you will find the following information at the end of the log:

=== Spl-IsoQuant pipeline finished ===
=== TEST PASSED CORRECTLY ===

Installing from GitHub

To get Spl-IsoQuant from GitHub, you can clone the repository:

git clone https://github.com/algbio/spl-IsoQuant.git 
cd spl-IsoQuant
git checkout latest

Or download the latest release here.

Spl-IsoQuant can then be installed using pip:

pip install -e .

Alternatively, you can install the requirements manually:

pip install -r requirements.txt

Add samtools and minimap2 to the $PATH variable and run Spl-IsoQuant without installing it.

Typically, the whole installation takes a few minutes regardless of the method.

Libraries and software required by Spl-IsoQuant

• gffutils
• pysam
• pyfaidx
• ssw-py
• editdistance
• biopython
• numba
• mappy
• intervaltree
• xgboost
• scikit-learn
• pyyaml
• pandas
• numpy
• scipy
• matplotlib
• seaborn
• minimap2
• samtools
• STAR (optional)

The full requirements list can be found in requirements.txt.