Compiling and Installing VarScan

Procedure

1. Use PuTTY to log in to the server as the root user.
2. Install the dependencies.

   yum install ncurses-devel.aarch64 bzip2-devel.aarch64 xz-devel.aarch64 java-1.8.0-openjdk-devel.aarch64 -y

3. Go to the SAMTOOLS directory.

   cd /path/to/SAMTOOLS

4. Decompress the Samtools installation package.

   tar -xvf samtools-1.10.tar.gz

5. Go to the directory generated after the decompression.

   cd samtools-1.10

6. Perform the configuration.

   ./configure --prefix=/path/to/SAMTOOLS/samtools-1.10-build

7. Perform the compilation and installation.

   make -j16
   make install

8. Add the Samtools environment variable.

   export PATH=/path/to/SAMTOOLS/samtools-1.10-build/bin:$PATH

9. Go to the VarScan directory.

   cd /path/to/VARSCAN

10. Decompress varscan-2.4.2.tar.gz.

    tar -xvf varscan-2.4.2.tar.gz

11. Go to the directory generated after the decompression.

    cd varscan-2.4.2

12. Test the VarScan environment.

    java -jar VarScan.v2.4.2.jar

    If the following information is displayed, the environment is normal.