Setup Clindet

2. Setup Clindet#

2.1. install conda, Docker and SingularityCE#

To build the complex Clindet analysis environment, you need to install Conda 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#

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, This script will download approximately ~170 GB of files. Please ensure you have sufficient available space.

2.2.3. Modify the config.yaml file#

Update the placeholder /AbsoPath/of/clindet/folder in clindet/workflow/config/config_local_test.yaml file to your actual Clindet directory path (e.g., /home/users/softwares/clindet) and then save the file as config.yaml.

2.2.3.1. generate a BED of gene exomes for WES analysis#

you can use the GTF to generate a BED file, contains four columns chr,start,end,gene_name (*optional), bellow is an example:

1       11858   12237   DDX11L1
1       12602   12731   DDX11L1
1       12964   13062   DDX11L1
1       13210   14511   DDX11L1;WASH7P

ClinDet provides a reference BED file for the b37 genome version (for Use Case I). You can modify this configuration according to your own requirements. Alternatively, you can use our provided script gtf2bed.R to convert gene annotation GTF files to the BED format.

You are now ready to start your analysis tasks!

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