2. Setup Clindet

2.1. install conda, Docker and SingularityCE

To build the complex Clindet analysis environment, you need to install Conda, Docker, and SingularityCE.

2.2. Install Clindet

2.2.1. clone clindet from github

git clone https://github.com/zyllifeworld/clindet.git
cd clindet

2.2.2. Run build_conda_env.sh to

Clindet provides a bash script to set up the computational environment required for running the software, as well as to download configuration files needed for various tools that use the human b37 reference genome (e.g., VCF, BED files). Run the script build_conda_env.sh to complete this setup.

2.2.3. Modify the config.yaml file

Replace the placeholder ‘/AbsoPath/of/clindet/folder’ in the clindet/workflow/config/config_local_test.yaml file located in the Clindet software directory with the absolute path to your Clindet folder, for example: /home/users/softwares/clindet. save the modified file as config.yaml.

You are now ready to start your analysis tasks!