Installation

Requirements

This package was tested for Python 3.10 - 3.12 on Linux (x64) and macOS (arm64) but not tested on Windows.

Note: Intel-based macOS (osx64) installation is ⚠️ DEPRECATED ⚠️

For stable installation, we recommend to first setup a conda environment.

Note: if your institution does not support anaconda, you can use miniforge instead to run the conda installations.

First create a conda environment:

conda create -n odt python=3.12
conda activate odt

To install the additional required tools via conda, please activate the bioconda and conda-forge channels in your conda environment and update conda and all packages in your environment:

conda config --add channels bioconda
conda config --add channels conda-forge
conda update --all

The additional tools need to be installed independently:

conda install "blast>=2.15.0"
conda install "bedtools>=2.30"
conda install "bowtie>=1.3.1"
conda install "bowtie2>=2.5"
conda install "bcftools>=1.22"
conda install "samtools>=1.22"

All other required packages are automatically installed if installation is done via pip (see below).

Install Options

The installation of the package is done via pip. Note: if you are using conda, first install pip with: conda install pip.

PyPI install:

pip install oligo-designer-toolsuite

Installation from source:

git clone https://github.com/HelmholtzAI-Consultants-Munich/oligo-designer-toolsuite.git
cd oligo-designer-toolsuite

Installation as python package (run inside directory):
```
          pip install .
```
Development installation as python package (run inside directory):
```
          pip install -e .[dev]
```