Compiling and Installing BWA

Prerequisites

You have obtained SSE2NEON.h from https://github.com/jratcliff63367/sse2neon.

Procedure

1. Use PuTTY to log in to the server as the root user.
2. Go to the BWA installation package directory.

   cd /path/to/BWA

3. Decompress the BWA installation package.

   tar -xvf bwa-0.7.17.tar.bz2

4. Go to the directory generated after the decompression.

   cd bwa-0.7.17

5. Copy sse2neon.h to the compiler installation directory.

   cp SSE2NEON.h /path/to/GNU/lib/gcc/aarch64-unknown-linux-gnu/9.1.0/include

6. Modify the Makefile file.
   1. Open Makefile.

      vi Makefile

   2. Press i to enter the insert mode and modify line 14 of the file.

      INCLUDES= -I/path/to/GNU/lib/gcc/aarch64-unknown-linux-gnu/9.1.0/include

      

      Change the include directory to the include directory of the GNU compiler.

   3. Press Esc, type :wq!, and press Enter to save the file and exit.
7. Modify the ksw.c file.
   1. Open ksw.c.

      vi ksw.c

   2. Press i to enter the insert mode and modify line 29 of the file.

      include <SSE2NEON.h>

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

   make

9. Load the BWA environment.

   export PATH=/path/to/BWA/bwa-0.7.17:$PATH