Compiling and Installing CNVnator

Procedure

1. Use PuTTY to log in to the server as the root user.
2. Run the following commands to go to the CNVnator installation directory and create the dependency link:

   cd /path/to/CNVNATOR
   unzip CNVnator_v0.4.1.zip
   cd CNVnator_v0.4.1/src
   ln -s /path/to/SAMTOOLS/samtools-1.10 samtools
   ln -s /path/to/SOURCE/root_build root_build

3. Run the following command to modify the Makefile file:
   1. Open Makefile.

      vi Makefile

   2. Press i to enter the insert mode and add the following content to the beginning of line 4 in the Makefile file:

      ROOTSYS=root_build

   3. Press Esc, type :wq!, and press Enter to save the file and exit.
4. Run the following command to perform compilation:

   make LIBS="-lcrypto"

5. Run the following commands to load environment variables:

   export PATH=/path/to/CNVNATOR/CNVnator_v0.4.1/src:$PATH