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