Installing ProtHint

Procedure

Use PuTTY to log in to the server as the root user.
Go to the /path/to/BRAKER directory.
```
cd /path/to/BRAKER
```

Download and decompress the ProtHint installation package.

wget https://github.com/gatech-genemark/ProtHint/archive/refs/tags/v2.6.0.tar.gz
tar xvf v2.6.0.tar.gz

Go to the directory generated after the decompression.
```
cd ProHint-2.6.0
```

Download the dependency package.

wget https://github.com/ogotoh/spaln/archive/refs/tags/veer.2.4.9b.tar.gz

Decompress the dependency package.
```
tar xvf veer.2.4.9b.tar.gz
```
Go to the directory generated after the decompression.
```
cd spaln-veer.2.4.9b/src
```
Perform the configuration.
```
CXX=g++ ./configure
```
Modify the codepot.h file.
1. Open codepot.h.
```
vi codepot.h
```
2. Press i to enter the insert mode and modify line 37.
  Before the modification:
  
  After the modification:
  
  After performing 9.a, press Esc, type :set nu, and press Enter to display the line number.
3. Press Esc, type :wq!, and press Enter to save the file and exit.
Perform the compilation and installation.
```
make
make install
```

Load the environment variable.

export PATH=/path/to/BRAKER/ProHint-2.6.0/spaln-veer.2.4.9b/bin:$PATH

Go to the ProHint-2.6.0 directory.
```
cd /path/to/BRAKER/ProHint-2.6.0
```

Download spaln-boundary-scorer.git.

git clone https://github.com/gatech-genemark/spaln-boundary-scorer.git

Decompress the installation package.
```
tar xvf spaln-boundary-scorer.git
```
Go to the directory generated after the decompression.
```
cd spaln-boundary-scorer
```
Modify the Makefile file.
1. Open Makefile.
```
vi Makefile
```
2. Press i to enter the insert mode and change the content in the first line to CC=clang++.
3. Press Esc, type :wq!, and press Enter to save the file and exit.
Perform the compilation.
```
make
```

Set the environment variable.

export PATH=/path/to/BRAKER/ProHint-2.6.0/spaln-boundary-scorer:$PATH

Replace the dependencies.

cd /path/to/BRAKER/ProHint-2.6.0/dependencies
rm -rf spaln_table spaln spaln-boundary-scorer diamond
cp -r /path/to/BRAKER/ProHint-2.6.0/spaln-veer.2.4.9b/table spaln_table
cp /path/to/BRAKER/ProHint-2.6.0/spaln-veer.2.4.9b/bin/spaln .
cp /path/to/BRAKER/ProHint-2.6.0/spaln-boundary-scorer/spaln-boundary-scorer .

Copy the executable file diamond (generated after DIAMOND is installed in Table 1) to the current directory.

Parent topic: Configuring the Compilation Environment