Installation

Welcome to the installation guide! Follow the steps below to set up ZipStrain on your system

Install using pip

To install ZipStrain using pip, follow these steps:

1- Make sure you have Python 3.12 or higher installed in your Python environment and activate it.

2- Open your terminal and run the following command to install ZipStrain:

pip install zipstrain

This will install all the necessary dependencies along with ZipStrain except samtools. Refer to samtools website for installation instructions: http://www.htslib.org/download/

3- Make sure the installation was successful by testing ZipStrain:

zipstrain test

Install using Conda

To install ZipStrain using Conda, run the following command in your conda environment with Python 3.12 or higher:

conda install -c conda-forge -c bioconda -c defaults zipstrain

This will install all the necessary dependencies along with ZipStrain including samtools.

Use Docker

To use ZipStrain with Docker, follow these steps:

1- Make sure you have Docker installed on your system.

2- Run ZipStrain using the Docker image:

docker run -it parsaghadermazi/zipstrain:latest zipstrain test

Note: Apptainer works in a very similar way to Docker:

apptainer run docker://parsaghadermazi/zipstrain:latest zipstrain test