Compilation and Installation

Procedure

Use PuTTY to log in to the server as the root user.
Go to the location of the DBG2OLC source code and compile the source code.
```
cd DBG2OLC
clang++ -O3 -o DBG2OLC *.cpp
```
Go to the location of the Sparc source code and compile the source code.
```
cd Sparc
clang++ -O3 -o Sparc *.cpp
```

Go to the location of the AssemblyUtility source code and compile the source code.

cd AssemblyUtility
clang++ -o AssemblyStatistics  -O3 AssemblyStatistics.cpp
clang++ -o SelectLongestReads  -O3 SelectLongestReads.cpp

Go to the location of the SparseAssembler source code and compile the source code.
```
cd SparseAssembler
clang++ -O3 -o SparseAssembler *.cpp
```
Go to the location of the blasr-master source code.
```
cd blasr-master
```
Install HDF5.
```
yum install -y hdf5 hdf5-devel
```
Modify the common.mk file.
1. Open common.mk.
```
vi common.mk
```
2. Press i to enter the insert mode, comment out line 19, and add line 20.
3. Press Esc, type :wq!, and press Enter to save the file and exit.
Modify the jabon/Makefile file.
1. Open jabon/Makefile.
```
vi jabon/Makefile
```
2. Press i to enter the insert mode, comment out line 5, and add line 6.
3. Press Esc, type :wq!, and press Enter to save the file and exit.
Perform the compilation.
```
make -j
```

In the DBG2OLC directory, copy the executable file to the specified path.

mkdir compiled
cp ../AssemblyUtility/AssemblyStatistics compiled
cp ../AssemblyUtility/SelectLongestReads compiled
cp ../Sparc/Sparc compiled
cp ../SparseAssembler/SparseAssembler compiled
cp ../blasr-master/alignment/bin/blasrmc compiled

Set the environment variables.

export PATH= /home/hpc/DBG2OLC/compiled:/home/hpc/DBG2OLC/utility:$PATH

Parent topic: DBG2OLC Porting Guide (openEuler 20.03)