Compiling and Installing HISAT2

Prerequisites

You have downloaded the sse2neon.h file from https://github.com/DLTcollab/sse2neon/blob/master/sse2neon.h.

Procedure

Use PuTTY to log in to the server as the root user.
Copy the downloaded sse2neon.h file to the /path/to/GNU/lib/gcc/aarch64-unknown-linux-gnu/9.1.0/include directory.
Run the following commands to decompress the HISAT2 installation package:
```
cd /path/to/HISAT2
tar -xvf hisat2-2.1.0.tar.gz
cd hisat2-2.1.0
```
Run the following commands to set environment variables:
```
export NO_TBB=1
export POPCNT_CAPABILITY=0
```
Perform the following steps to modify the Makefile file:
1. Open Makefile.
```
vi Makefile
```
2. Press i to go to the insert mode, and modify the BITS=64 aarch64 branches of the file by inserting the following content in bold between line 140 and line 141:
  Currently, BITS=64 supports only x86 and does not support AArch64. The AArch64 branch needs to be added.
  Before the modification:
```
BITS=32
ifeq (x86_64,$(shell uname -m))
BITS=64
endif
```
  After the modification:
```
BITS=32
ifeq (x86_64,$(shell uname -m))
BITS=64
endif
ifeq (aarch64,$(shell uname -m))
BITS=64
endif
```
3. Press Esc, type :wq!, and press Enter to save the file and exit.
Perform the following steps to modify the Makefile file:
1. Open Makefile.
```
vi Makefile
```
2. Press i to go to the insert mode, and modify the -m64 and -msse2 AArch64 branches of the file by inserting the following content in bold between line 159 and line 160.
  The compilation options -m64 and -msse2 in Makefile support only x86 and does not support AArch64. The AArch64 branch needs to be added.
  Before the modification (line 149 to line 156 in the source file):
```
ifeq (32,$(BITS))
        BITS_FLAG = -m32
endif
 
ifeq (64,$(BITS))
        BITS_FLAG = -m64
endif
SSE_FLAG=-msse2
```
  After the modification:
```
ifeq (32,$(BITS))
        BITS_FLAG = -m32
endif
 
ifeq (64,$(BITS))
        BITS_FLAG = -m64
endif
SSE_FLAG=-msse2
 
ifeq (aarch64,$(shell uname -m))
        BITS_FLAG =
        SSE_FLAG =
endif
```
3. Press Esc, type :wq!, and press Enter to save the file and exit.

Perform the following steps to modify the Makefile file:

Open Makefile.
```
vi Makefile
```

Press i to go to the insert mode and modify the FLAGS parameters in the file.

Before the modification:

EXTRA_FLAGS += -DPOPCNT_CAPABILITY
DEBUG_FLAGS    = -O0 -g3 $(BIToS_FLAG) $(SSE_FLAG) 
DEBUG_DEFS     = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS)\""
RELEASE_FLAGS  = -O3 $(BITS_FLAG) $(SSE_FLAG) -funroll-loops -g3 
RELEASE_DEFS   = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(EXTRA_FLAGS)\""
NOASSERT_FLAGS = -DNDEBUG
FILE_FLAGS     = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE

After the modification:

EXTRA_FLAGS += 
DEBUG_FLAGS    = -O0 -g3 $(BIToS_FLAG) $(SSE_FLAG) -funroll-loops -std=c++98
DEBUG_DEFS     = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS)\""
RELEASE_FLAGS  = -O3 $(BITS_FLAG) $(SSE_FLAG) -funroll-loops -g3 -std=c++98 -Xlinker --allow-multiple-definition
RELEASE_DEFS   = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(EXTRA_FLAGS)\""
NOASSERT_FLAGS = -DNDEBUG
FILE_FLAGS     = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE

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

Perform the following steps to modify the aligner_sw.h and sse_util.h header files:
1. Upload the sse2neon.h file to the third_party directory.
2. Open aligner_sw.h.
```
vi aligner_sw.h
```
3. Press i to go to the insert mode. Replace #include <emmintrin.h> with #include <sse2neon.h>.
  Before the modification:
```
#include <emmintrin.h>
```
  After the modification:
```
#include <sse2neon.h>
```
4. Press Esc, type :wq!, and press Enter to save the file and exit.
5. Modify the sse_util.h file. For details, see 8.b to 8.d.
Run the following command to compile and install HISAT2:
```
make
```

Parent topic: HISAT2 2.1.0 Porting Guide (CentOS 7.6)