Compilation and Installation

Procedure

Use PuTTY to log in to the server as the root user.

Go to the installation directory and decompress the installation package.

cd /path/to/PLATANUS && tar -zxf Platanus_v1.2.4.tar.gz && cd Platanus_v1.2.4

Modify the Makefile file.
1. Open Makefile.
```
vi Makefile
```
2. Press i to enter the insert mode and edit lines 1 and 2.
  Before the modification:
```
1 CXX = g++
2 CXXFLAGS = -std=c++0x -O3 -funroll-loops -Wall -fopenmp -finline-limit-50000 -lm -Dnullptr=0
```
  After the modification:
```
1 CXX = clang++
2 CXXFLAGS = -std=c++0x -O3 -funroll-loops -Wall -fopenmp -lm -Dnullptr=0
```
  After performing 3.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.

Modify the counter.h file.

Open counter.h.
```
vi counter.h
```

Press i to enter the insert mode and modify lines 426, 455, and 684.

Before the modification:

426             countKmerOrWriteTemporary(loopFlag, key, tmpOccurrenceTable, unmappedFP, lock, kmer);
455 inline void Counter<KMER>::countKmerOrWriteTemporary(bool &loopFlag, const typename KMER::keyType &key, DoubleHash<typename KMER::keyType, unsigned short> tmpOccurrenceTable[], FILE *unmappedFP, omp_lock_t lock[], const KMER &kmer, const unsigned iterateTimes=32)
684 inline void Counter<KMER>::countKmerOrWriteTemporary(bool &loopFlag, const typename KMER::keyType &key, FILE *unmappedFP, omp_lock_t lock[], const KMER &kmer, const unsigned iterateTimes=32)

After the modification:

426             countKmerOrWriteTemporary(loopFlag, key, tmpOccurrenceTable, unmappedFP, lock, kmer, 32);
455 inline void Counter<KMER>::countKmerOrWriteTemporary(bool &loopFlag, const typename KMER::keyType &key, DoubleHash<typename KMER::keyType, unsigned short> tmpOccurrenceTable[], FILE *unmappedFP, omp_lock_t lock[], const KMER &kmer, const unsigned iterateTimes)
684 inline void Counter<KMER>::countKmerOrWriteTemporary(bool &loopFlag, const typename KMER::keyType &key, FILE *unmappedFP, omp_lock_t lock[], const KMER &kmer, const unsigned iterateTimes)

After performing 4.a, press Esc, type :set nu, and press Enter to display the line number.

Press Esc, type :wq!, and press Enter to save the file and exit.

Modify the graph.h file.
1. Open graph.h.
```
vi graph.h
```
2. Press i to enter the insert mode and modify line 1764.
  Before the modification:
```
1764 void BruijnGraph<KMER>::cutBranchIterative(const unsigned long long numThread=1)
```
  After the modification:
```
1764 void BruijnGraph<KMER>::cutBranchIterative(const unsigned long long numThread)
```
  After performing 5.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.
Modify the scaffoldGraph.cpp file.
1. Open scaffoldGraph.cpp.
```
vi scaffoldGraph.cpp
```
2. Press i to enter the insert mode and modify line 2280.
  Before the modification:
```
2280             if (abs(insertLength - averageInsSize) > tolerence) continue;
```
  After the modification:
```
2280             if (std::fabs(insertLength - averageInsSize) > tolerence) continue;
```
  After performing 6.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.
Modify the baseCommand.cpp file.
1. Open baseCommand.cpp.
```
vi baseCommand.cpp
```
2. Press i to enter the insert mode and modify line 175.
  Before the modification:
```
175     for (;moveArgs != '\0'; ++moveArgs) {
```
  After the modification:
```
175     for (;*moveArgs != '\0'; ++moveArgs) {
```
  After performing 7.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.
Compile and install Platanus.
```
make
```

Parent topic: Platanus 1.2.4 Porting Guide (openEuler 20.03)