Installing BWA

Prerequisites

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

Procedure

1. Use PuTTY to log in to the server as the root user.
2. Run the following command to decompress the BWA installation package:

   tar -xvf bwa-0.7.17.tar.bz2

3. Run the following command to switch to the directory generated after decompression:

   cd bwa-0.7.17

4. Run the following command to modify the Makefile file:
   1. Open Makefile.

      vi Makefile

   2. Press i to enter the insert mode and modify lines 1 and 14 of the file.

      CC=               /path/to/GNU/bin/gcc
      INCLUDES=       -I/path/to/GNU/gcc/include

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

      vi ksw.c

   2. Press i to enter the insert mode and modify lines 29 and 30 of the file.

      /*#include <emmintrin.h>*/
       #include <sse2neon.h>

   3. Press Esc, type :wq!, and press Enter to save the file and exit.
6. Run the following command to copy the Neon instruction conversion code to a specific directory of the compiler:

   cp sse2neon.h /path/to/GNU/gcc/include

7. Run the following command to perform the compilation:

   make

8. Run the following command to set the BWA environment variables:

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

9. Run the following command to check whether the installation is successful:

   bwa

   If information similar to the following is displayed, the installation is successful:

   bwa <command> [options]