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INSTALL.md

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VCF2Dis: an ultra-fast and efficient tool to calculate pairwise genetic distance and construct population phylogeny from VCF files

INSTALL

We provide three alternative options to install VCF2Dis

Option 1 : Local compilation

Just sh make.sh to compile VCF2Dis. The executable VCF2Dis can be found in the folder of bin/VCF2Dis
For Linux /Unix and macOS

        tar -zxvf  VCF2DisXXX.tar.gz            # if Link do not work ,Try re-install [zlib]library
        cd VCF2DisXXX;                          # [zlib] and copy them to the library Dir
        sh make.sh;                             # VCF2Dis-xx/src/include/zlib
        ./bin/VCF2Dis

Note: If fail to link,try to re-install the libraries zlib
Note:: R with ape, dplyr and ggtree packages are recommended

Option 2: Docker container

You can use Docker to install and run VCF2Dis, following the steps listed below:

  1. Install Docker: Ensure Docker is installed on your system. If not, please install it by following the Docker Official Documentation.
  2. Pull the Docker Image: Use the following command to pull the VCF2Dis Docker image from the Alibaba Cloud Container Registry: 
    docker pull registry.cn-shenzhen.aliyuncs.com/knight134/vcf2dis:v1.53e    ##  Docker image from the Alibaba Cloud Container Registry
docker run -it --rm vcf2dis:v1.53e VCF2Dis                                ## After pulling the image, you can run the containe

Option 3: Singularity container

  1. Install Singularity: Ensure Singularity is installed on your system. If not, you can install it by following the Singularity Official Documentation.
  2. Build the SIF File: Use the following command to build a Singularity image file (SIF) from the Docker image: 
    singularity build vcf2dis_1.53e.sif docker://registry.cn-shenzhen.aliyuncs.com/knight134/vcf2dis:v1.53e   # you can download follows 
singularity exec  vcf2dis_1.53e.sif  VCF2Dis
  3. Download the SIF File:Alternatively, you can download the SIF file directly from the github: vcf2dis_1.53e.sif. Once downloaded, you can run it using Singularity.

Contact

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