Running and Verification

Procedure

1. Use PuTTY to log in to the server as the root user.
2. Go to the test case directory.

   cd /path/to/BRAKER/BRAKER-2.1.6/example

3. Set the environment variable of each dependency.
   1. Add the environment variable AUGUSTUS to config in the installation directory.

      export AUGUSTUS_CONFIG_PATH=/path/to/augustus_config

   2. Add the environment variable AUGUSTUS to bin in the installation directory.

      export AUGUSTUS_BIN_PATH=/path/to/augustus_bin

   3. Add the environment variable AUGUSTUS to scripts in the installation directory.

      export AUGUSTUS_SCRIPTS_PATH=/path/to/augustus_scripts

   4. Add the environment variable DIAMOND to the directory of the executable file diamond.

      export DIAMOND_PATH=/path/to/diamond

   5. Add the environment variable GENEMARK to the directory of the executable file gmhmme3.

      export GENEMARK_PATH=/path/to/GENEMARK

   6. Add the environment variable BAMTOOLS to the directory of the executable file bamtools.

      export BAMTOOLS_PATH=/path/to/BAMTOOLS

   7. Add the environment variable CDBTOOLS to the directory of the executable file cdbfasta.

      export CDBTOOLS_PATH=/path/to/cdbfasta

   8. Add the environment variable SAMTOOLS to the directory of the executable file samtools.

      export SAMTOOLS_PATH=/path/to/samtools

4. Perform the verification.

   braker.pl --help