Compilation and Installation

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. Obtain the SSE2NEON.h file.

   git clone https://github.com/jratcliff63367/sse2neon.git

6. Copy SSE2NEON.h to the installation directory of the compiler.

   cp SSE2NEON.h /opt/compiler/bisheng-compiler-1.3.3-aarch64-linux/lib/clang/10.0.1/include

   

   You need to change the compiler path based on the site requirements, and add or adjust paths strictly according to the ones described in this document. Otherwise, an error is reported.

7. Modify the Makefile file of BWA.
   1. Open the Makefile file.

      vi Makefile

   2. Press i to enter the edit mode and modify lines 1 and 14 in the Makefile file.

      CC=clang
      INCLUDES= -I/opt/compiler/bisheng-compiler-1.3.3-aarch64-linux/lib/clang/10.0.1/include

      

      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.
8. Modify the ksw.c file.
   1. Open the ksw.c file.

      vi ksw.c

   2. Press i to enter the edit mode, remove the comment of line 29 in the ksw.c file (using /* */), and edit the following content:

      #include <SSE2NEON.h>

      

      After performing 8.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.
9. Perform the compilation.

   make

10. Load the BWA environment.

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

11. Check whether the compilation is successful.

    bwa

    The compilation is successful if the following information is displayed:

    Usage:   bwa <command> [options]